diff --git a/OConnor/resources/views/BloodCalendar.html b/OConnor/resources/views/BloodCalendar.html
index 2903e7e2..3d517e25 100644
--- a/OConnor/resources/views/BloodCalendar.html
+++ b/OConnor/resources/views/BloodCalendar.html
@@ -177,8 +177,13 @@
     				
     				
     				var content = document.createElement('span');
-    				content.innerHTML = '<a style= "font-size :14px" href="' + urls[i][t] + '">' + animal[i][t] + week[i][t] + '</a>';
-    				
+    				// Build the anchor with DOM APIs so list-derived values (URL, animal id, entry text) can't inject markup
+    				var anchor = document.createElement('a');
+    				anchor.setAttribute('style', 'font-size:14px');
+    				anchor.setAttribute('href', urls[i][t]);
+    				anchor.appendChild(document.createTextNode(animal[i][t] + week[i][t]));
+    				content.appendChild(anchor);
+
             		row.appendChild(content);
                 	column.appendChild(row);
  
diff --git a/OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsController.java b/OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsController.java
index fd6b148c..4361fe3f 100644
--- a/OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsController.java
+++ b/OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsController.java
@@ -16,49 +16,29 @@
 
 package org.labkey.oconnorexperiments;
 
-import org.apache.commons.io.FileUtils;
-import org.apache.logging.log4j.LogManager;
 import org.labkey.api.action.ApiResponse;
 import org.labkey.api.action.ApiSimpleResponse;
 import org.labkey.api.action.FormHandlerAction;
-import org.labkey.api.action.FormViewAction;
 import org.labkey.api.action.ReadOnlyApiAction;
-import org.labkey.api.action.ReturnUrlForm;
 import org.labkey.api.action.SimpleViewAction;
 import org.labkey.api.action.SpringActionController;
 import org.labkey.api.collections.CaseInsensitiveHashMap;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
-import org.labkey.api.data.CoreSchema;
-import org.labkey.api.data.DbSequenceManager;
-import org.labkey.api.data.SimpleFilter;
-import org.labkey.api.data.Sort;
-import org.labkey.api.data.SqlExecutor;
 import org.labkey.api.data.TableInfo;
-import org.labkey.api.data.TableSelector;
-import org.labkey.api.files.FileContentService;
 import org.labkey.api.portal.ProjectUrls;
 import org.labkey.api.query.BatchValidationException;
-import org.labkey.api.query.FieldKey;
-import org.labkey.api.query.QueryAction;
 import org.labkey.api.query.QueryService;
 import org.labkey.api.query.QueryUpdateService;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.security.RequiresLogin;
 import org.labkey.api.security.RequiresPermission;
-import org.labkey.api.security.User;
-import org.labkey.api.security.UserManager;
-import org.labkey.api.security.permissions.AdminPermission;
 import org.labkey.api.security.permissions.InsertPermission;
 import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.security.permissions.UpdatePermission;
-import org.labkey.api.services.ServiceRegistry;
 import org.labkey.api.util.DOM;
-import org.labkey.api.util.FileStream;
 import org.labkey.api.util.PageFlowUtil;
-import org.labkey.api.util.Path;
 import org.labkey.api.util.URLHelper;
-import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.HtmlView;
 import org.labkey.api.view.HttpView;
 import org.labkey.api.view.JspView;
@@ -66,18 +46,12 @@
 import org.labkey.api.view.NotFoundException;
 import org.labkey.api.view.RedirectException;
 import org.labkey.api.view.VBox;
-import org.labkey.api.webdav.WebdavResolver;
-import org.labkey.api.webdav.WebdavResource;
 import org.labkey.oconnorexperiments.query.OConnorExperimentsUserSchema;
 import org.springframework.validation.BindException;
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Collections;
-import java.util.Date;
 import java.util.List;
 import java.util.Map;
 
@@ -106,316 +80,6 @@ public void addNavTrail(NavTree root)
         }
     }
 
-    @RequiresPermission(AdminPermission.class)
-    public static class MigrateDataAction extends FormViewAction<UserForm>
-    {
-        @Override
-        public void validateCommand(UserForm target, Errors errors)
-        {
-        }
-
-        @Override
-        public ModelAndView getView(UserForm form, boolean reshow, BindException errors)
-        {
-            return new JspView<>("/org/labkey/oconnorexperiments/view/migrateData.jsp");
-        }
-
-        @Override
-        public boolean handlePost(UserForm form, BindException errors) throws Exception
-        {
-            if (form.isFinalMigration())
-            {
-                LogManager.getLogger(OConnorExperimentsController.class).info("Final migration to be performed - file move events will be performed (irreversible).");
-            }
-
-            // global containers
-            Container sourceContainer = ContainerManager.getForPath(form.getSourceProject());
-            Container targetContainer = getContainer();
-            FileContentService fileContentService = FileContentService.get();
-
-            // get table info for the source table
-            UserSchema sourceSchema = QueryService.get().getUserSchema(getUser(), sourceContainer, "oconnor");
-            TableInfo sourceTable = sourceSchema.getTable("simple_experiment");
-            TableSelector tableSelector = new TableSelector(sourceTable, null, new Sort("ExpNumber"));
-            Collection<Map<String, Object>> sourceCollection = tableSelector.getMapCollection();
-
-            // get table info for target table
-            UserSchema targetSchema = QueryService.get().getUserSchema(getUser(), getContainer(), OConnorExperimentsSchema.NAME);
-            TableInfo targetTable = targetSchema.getTable(OConnorExperimentsSchema.EXPERIMENTS);
-            QueryUpdateService queryUpdateService = targetTable.getUpdateService();
-            BatchValidationException batchErrors = new BatchValidationException();
-
-            TableInfo typeTable = targetSchema.getTable(OConnorExperimentsSchema.EXPERIMENT_TYPE);
-            QueryUpdateService typeUpdateService = typeTable.getUpdateService();
-
-            int maxExpNumber = 0;
-
-            // parse the sourceCollection into the target collection
-            for (Map<String, Object> databaseMap : sourceCollection)
-            {
-                Map<String, Object> map = new CaseInsensitiveHashMap<>();
-                map.put("ExperimentNumber", databaseMap.get("expnumber"));
-                int expNumber = (int) databaseMap.get("expnumber");
-                if (expNumber > form.getBeginRange() && expNumber < form.getEndRange())
-                {
-                    if (expNumber > maxExpNumber)
-                        maxExpNumber = expNumber;
-                    map.put("Name", databaseMap.get("expnumber"));
-                    map.put("Description", databaseMap.get("expDescription"));
-
-                    String currentType = (String) databaseMap.get("expType");
-                    Integer targetType = null;
-                    if (currentType != null)
-                    {
-                        TableSelector typeSelector = new TableSelector(typeTable, Collections.singleton("RowId"), new SimpleFilter(FieldKey.fromParts("Name"), currentType), null);
-                        targetType = typeSelector.getObject(Integer.class);
-                        if (targetType == null)
-                        {
-                            Map<String, Object> newType = new CaseInsensitiveHashMap<>();
-                            newType.put("Name", currentType);
-                            newType.put("Enabled", true);
-                            List<Map<String, Object>> newTypes = typeUpdateService.insertRows(getUser(), getContainer(), Collections.singletonList(newType), new BatchValidationException(), null, null);
-                            targetType = (Integer) newTypes.get(0).get("RowId");
-                        }
-                    }
-
-                    map.put("ExperimentTypeId", targetType);
-                    //map.put("Modified", databaseMap.get("created"));
-
-                    // get the user name
-                    User effectiveUser;
-                    if (databaseMap.get("initials") == null)
-                    {
-                        effectiveUser = getUser();
-                    }
-                    else
-                    {
-                        User user = UserManager.getUserByDisplayName((String) databaseMap.get("initials"));
-                        if (user == null)
-                        {
-                            LogManager.getLogger(OConnorExperimentsController.class).warn("User '" + databaseMap.get("initials") + "' not found for experiment " + databaseMap.get("expnumber"));
-                            effectiveUser = getUser();
-                        }
-                        else
-                        {
-                            effectiveUser = user;
-                        }
-                    }
-
-                    databaseMap.put("EffectiveUser", effectiveUser);
-                    LogManager.getLogger(OConnorExperimentsController.class).info("Insert on experiment " + databaseMap.get("expnumber"));
-                    List<Map<String, Object>> updateResult;
-                    try
-                    {
-                        updateResult = queryUpdateService.insertRows(getUser(), getContainer(), Collections.singletonList(map), batchErrors, null, null);
-                    }
-                    catch (Exception e)
-                    {
-                        // log the error to the logfile and continue
-                        LogManager.getLogger(OConnorExperimentsController.class).warn("Error inserting expNumber " + expNumber + " with exception " + e.getMessage());
-                        continue;
-                    }
-                    if (batchErrors.hasErrors())
-                    {
-                        // throw batchErrors.getLastRowError();
-                        LogManager.getLogger(OConnorExperimentsController.class).warn("Error inserting expNumber " + expNumber);
-                    }
-
-                    Container workbookContainer = ContainerManager.getForId((String)updateResult.get(0).get("EntityId"));
-                    databaseMap.put("ContainerObj", workbookContainer);
-                    databaseMap.put("ContainerStr", updateResult.get(0).get("EntityId"));
-
-                    // We don't want these fields to be spoofable through the QueryUpdateService (and hence the Client API),
-                    // so preserve the value from the source data manually
-                    Date created = (Date)databaseMap.get("created");
-                    new SqlExecutor(CoreSchema.getInstance().getSchema()).execute("UPDATE core.containers SET CreatedBy = ?, Created = ? WHERE RowId = ?", effectiveUser.getUserId(), created, workbookContainer.getRowId());
-
-                    // Move files
-                    File sourceFile = new File(fileContentService.getFileRoot(sourceContainer).getPath() + File.separator + "@files", databaseMap.get("expnumber").toString());
-                    File targetDir = new File(fileContentService.getFileRoot(targetContainer).getPath() + File.separator + databaseMap.get("expnumber").toString() + File.separator + "@files");
-                    LogManager.getLogger(OConnorExperimentsController.class).info("Copy from file '" + sourceFile + "' to directory '" + targetDir +"'" );
-                    if (sourceFile.exists())
-                    {
-                        FileUtils.copyDirectory(sourceFile, targetDir);
-                        // only fire the File Move Event if this is a final migration - it is difficult to reverse
-                        if (form.isFinalMigration())
-                        {
-                            fileContentService.fireFileMoveEvent(sourceFile, targetDir, effectiveUser, getContainer());
-                        }
-                    }
-                }
-            }
-
-            //
-            // 2nd pass - update all ParentExperiment fields
-            //
-            for (Map<String, Object> databaseMap : sourceCollection)
-            {
-                int expNumber = (int) databaseMap.get("expnumber");
-                if (expNumber > form.getBeginRange() && expNumber < form.getEndRange())
-                {
-                    Map<String, Object> map = new CaseInsensitiveHashMap<>();
-                    map.put("container", databaseMap.get("ContainerStr"));
-
-                    String[] parents;
-                    ArrayList<String> parentsEntityId = new ArrayList<>();
-                    if (databaseMap.get("expParent") != null)
-                    {
-                        String parentString = databaseMap.get("expParent").toString();
-                        parents = parentString.split("[\\s,;&]+");
-                        // get Container for SortOrder
-                        for ( int i =0; i< parents.length; i++)
-                        {
-                            if ( ! parents[i].equalsIgnoreCase("and"))
-                            {
-                                Container child = targetContainer.getChild(parents[i]);
-                                if (child != null)
-                                {
-                                    parentsEntityId.add( child.getEntityId().toString() );
-                                }
-                                else
-                                {
-                                    LogManager.getLogger(OConnorExperimentsController.class).warn("child container not found: " + parents[i] + " for experiment " + databaseMap.get("expnumber") + " with username " + databaseMap.get("initials"));
-                                }
-                            }
-                        }
-                        if (!parentsEntityId.isEmpty())
-                        {
-                            map.put("ParentExperiments", parentsEntityId.toArray(new String[0]));
-
-                            // workaround, pass user, container - databaseMap.get("Container"), singleton list
-                            LogManager.getLogger(OConnorExperimentsController.class).info("Update rows on experiment " + databaseMap.get("expnumber"));
-                            try
-                            {
-                                queryUpdateService.updateRows(getUser(), targetContainer, Collections.singletonList(map), null, null, null);
-                            }
-                            catch (Exception e)
-                            {
-                                // log the error to the logfile and continue
-                                LogManager.getLogger(OConnorExperimentsController.class).warn("Error updating parent experiments for experiment number " + expNumber + " with exception " + e.getMessage());
-                                continue;
-                            }
-
-                        }
-                    }
-                }
-            }
-
-            //
-            // 3rd pass update the wiki, done seperately so that the cache is not modified
-            //
-            for (Map<String, Object> databaseMap : sourceCollection)
-            {
-                int expNumber = (int) databaseMap.get("expnumber");
-                if (expNumber > form.getBeginRange() && expNumber < form.getEndRange())
-                {
-
-                    // Update the existing Wiki content with the value from the old table, if present
-                    String wikiText = (String)databaseMap.get("expcomments");
-                    if (wikiText != null)
-                    {
-                        User user = UserManager.getUserByDisplayName((String) databaseMap.get("initials"));
-                        User effectiveUser = user == null ? getUser() : user;
-                        Container workbookContainer = targetContainer.getChild(databaseMap.get("expnumber").toString());
-                        if (workbookContainer == null)
-                        {
-                            LogManager.getLogger(OConnorExperimentsController.class).warn("Updating wiki, container not found: " + databaseMap.get("expnumber"));
-                        }
-                        else
-                        {
-                            Path path = new Path("_webdav").append(workbookContainer.getParsedPath()).append("@wiki", "default", "default.html");
-                            WebdavResolver resolver = ServiceRegistry.get(WebdavResolver.class);
-                            WebdavResource resource = resolver.lookup(path);
-
-                            FileStream.StringFileStream in = new FileStream.StringFileStream(wikiText);
-                            try
-                            {
-                                resource.copyFrom(effectiveUser, in);
-                            }
-                            catch (Exception e)
-                            {
-                                // log the error to the logfile and continue
-                                LogManager.getLogger(OConnorExperimentsController.class).warn("Error wiki for experiment number " + expNumber + " with exception " + e.getMessage());
-                                continue;
-                            }
-                            finally
-                            {
-                                in.closeInputStream();
-                            }
-                            LogManager.getLogger(OConnorExperimentsController.class).info("Inserting wiki for experiment " + databaseMap.get("expnumber"));
-                        }
-                    }
-                }
-            }
-
-            // we need to leave the target location set up correctly so that the next experiment that's created gets the next value in the sequence
-            DbSequenceManager.get(targetContainer, ContainerManager.WORKBOOK_DBSEQUENCE_NAME).ensureMinimum(maxExpNumber);
-
-            return true;
-        }
-
-        @Override
-        public void addNavTrail(NavTree root)
-        {
-        }
-
-        @Override
-        public ActionURL getSuccessURL(UserForm form)
-        {
-            UserSchema targetSchema = QueryService.get().getUserSchema(getUser(), getContainer(), OConnorExperimentsSchema.NAME);
-            return targetSchema.getQueryDefForTable(OConnorExperimentsSchema.EXPERIMENTS).urlFor(QueryAction.executeQuery);
-        }
-    }
-
-    public static class UserForm extends ReturnUrlForm
-    {
-        private String _sourceProject;
-        private int _beginRange;
-        private int _endRange;
-        private boolean _finalMigration;
-
-        public String getSourceProject()
-        {
-            return _sourceProject;
-        }
-
-        public void setSourceProject(String sourceProject)
-        {
-            _sourceProject = sourceProject;
-        }
-
-        public int getBeginRange()
-        {
-            return _beginRange;
-        }
-
-        public void setBeginRange(int beginRange)
-        {
-            _beginRange = beginRange;
-        }
-
-        public int getEndRange()
-        {
-            return _endRange;
-        }
-
-        public void setEndRange(int endRange)
-        {
-            _endRange = endRange;
-        }
-
-        public boolean isFinalMigration()
-        {
-            return _finalMigration;
-        }
-
-        public void setFinalMigration(boolean finalMigration)
-        {
-            _finalMigration = finalMigration;
-        }
-    }
-
-
     /**
      * Use the QueryUpdateService to create a new experiment so the Experiment and Workbook defaults are used
      * then redirect to the newly created experiment begin page.
diff --git a/OConnorExperiments/src/org/labkey/oconnorexperiments/view/migrateData.jsp b/OConnorExperiments/src/org/labkey/oconnorexperiments/view/migrateData.jsp
deleted file mode 100644
index 9bacb186..00000000
--- a/OConnorExperiments/src/org/labkey/oconnorexperiments/view/migrateData.jsp
+++ /dev/null
@@ -1,41 +0,0 @@
-<%
-/*
- * Copyright (c) 2005-2014 Fred Hutchinson Cancer Research Center
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-%>
-<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
-<%@ page import="org.labkey.oconnorexperiments.OConnorExperimentsController"%>
-<%@ page extends="org.labkey.api.jsp.JspBase" %>
-
-<form <%=formAction(OConnorExperimentsController.MigrateDataAction.class, Method.Post)%>><labkey:csrf/>
-<h3>OConnor Experiments to Workbooks data migration</h3>
-<table><%=formatMissedErrorsInTable("form", 2)%>
-    <tr>
-        <td>Source Project Name:</td>
-        <td><input type="text" name="sourceProject" id="sourceProject" size="50" value=""></td>
-    </tr>
-    <tr>
-        <td>Experiment Number Range:</td>
-        <td><input type="text" name="beginRange" id="beginRange" size="10" value=""> - <input type="text" name="endRange" id="endRange" size="10" value=""></td>
-    </tr>
-    <tr>
-        <td>Final Migration:</td>
-        <td><input type="checkbox" name="finalMigration" id="finalMigration"></td>
-    </tr>
-    <tr>
-        <td colspan=2><%= button("Submit").submit(true) %></td>
-    </tr>
-</table>
-</form>
diff --git a/genotyping/src/org/labkey/genotyping/GenotypingController.java b/genotyping/src/org/labkey/genotyping/GenotypingController.java
index f215fab6..dfabbd10 100644
--- a/genotyping/src/org/labkey/genotyping/GenotypingController.java
+++ b/genotyping/src/org/labkey/genotyping/GenotypingController.java
@@ -25,7 +25,6 @@
 import org.labkey.api.action.FormHandlerAction;
 import org.labkey.api.action.FormViewAction;
 import org.labkey.api.action.HasViewContext;
-import org.labkey.api.action.MutatingApiAction;
 import org.labkey.api.action.QueryViewAction;
 import org.labkey.api.action.QueryViewAction.QueryExportForm;
 import org.labkey.api.action.ReturnUrlForm;
@@ -40,9 +39,11 @@
 import org.labkey.api.assay.actions.AssayRunsAction;
 import org.labkey.api.assay.actions.BaseAssayAction;
 import org.labkey.api.assay.actions.ProtocolIdForm;
+import org.labkey.api.audit.AuditLogService;
+import org.labkey.api.audit.AuditTypeEvent;
+import org.labkey.api.audit.provider.ContainerAuditProvider;
 import org.labkey.api.data.ActionButton;
 import org.labkey.api.data.ButtonBar;
-import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.DataRegion;
 import org.labkey.api.data.DataRegionSelection;
@@ -66,19 +67,14 @@
 import org.labkey.api.pipeline.PipelineValidationException;
 import org.labkey.api.pipeline.browse.PipelinePathForm;
 import org.labkey.api.portal.ProjectUrls;
-import org.labkey.api.query.CustomView;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.QueryService;
 import org.labkey.api.query.QuerySettings;
 import org.labkey.api.query.QueryView;
 import org.labkey.api.query.UserSchema;
-import org.labkey.api.security.CSRF;
 import org.labkey.api.security.IgnoresTermsOfUse;
-import org.labkey.api.security.RequiresNoPermission;
 import org.labkey.api.security.RequiresPermission;
 import org.labkey.api.security.User;
-import org.labkey.api.security.UserManager;
-import org.labkey.api.security.ValidEmail;
 import org.labkey.api.security.permissions.AdminPermission;
 import org.labkey.api.security.permissions.DeletePermission;
 import org.labkey.api.security.permissions.InsertPermission;
@@ -88,13 +84,11 @@
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.MinorConfigurationException;
 import org.labkey.api.util.PageFlowUtil;
-import org.labkey.api.util.Pair;
 import org.labkey.api.util.URLHelper;
 import org.labkey.api.util.logging.LogHelper;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.DataView;
 import org.labkey.api.view.DetailsView;
-import org.labkey.api.view.HttpView;
 import org.labkey.api.view.JspView;
 import org.labkey.api.view.NavTree;
 import org.labkey.api.view.NotFoundException;
@@ -105,9 +99,6 @@
 import org.labkey.api.view.template.PageConfig;
 import org.labkey.genotyping.GenotypingManager.SEQUENCE_PLATFORMS;
 import org.labkey.genotyping.GenotypingQuerySchema.TableType;
-import org.labkey.genotyping.galaxy.GalaxyFolderSettings;
-import org.labkey.genotyping.galaxy.GalaxyManager;
-import org.labkey.genotyping.galaxy.GalaxyUserSettings;
 import org.labkey.genotyping.sequences.FastqGenerator;
 import org.labkey.genotyping.sequences.FastqWriter;
 import org.labkey.genotyping.sequences.SequenceManager;
@@ -121,24 +112,18 @@
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.io.PrintWriter;
-import java.math.BigInteger;
-import java.net.MalformedURLException;
-import java.net.URL;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.Collection;
 import java.util.Collections;
-import java.util.Date;
 import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 import java.util.Properties;
 import java.util.Set;
-import java.util.SortedSet;
 import java.util.TreeMap;
 import java.util.TreeSet;
 
@@ -352,6 +337,13 @@ public boolean handlePost(MatchesForm form, BindException errors)
             try
             {
                 _count = GenotypingManager.get().deleteMatches(getContainer(), getUser(), form.getAnalysis(), matchIds);
+
+                if (_count > 0)
+                {
+                    AuditTypeEvent event = new AuditTypeEvent(ContainerAuditProvider.CONTAINER_AUDIT_EVENT, getContainer(),
+                            "Deleted " + _count + " genotyping match(es) from analysis " + form.getAnalysis() + ": " + matchIds);
+                    AuditLogService.get().addEvent(getUser(), event);
+                }
             }
             catch (IllegalStateException e)
             {
@@ -396,9 +388,8 @@ public URLHelper getSuccessURL(ReturnUrlForm form)
 
 
     // TODO: Annotate getters with @Nullable
-    public static class AdminForm extends ReturnUrlForm implements GenotypingFolderSettings, GalaxyFolderSettings, HasViewContext
+    public static class AdminForm extends ReturnUrlForm implements GenotypingFolderSettings, HasViewContext
     {
-        private String _galaxyURL;
         private String _sequencesQuery;
         private String _runsQuery;
         private String _samplesQuery;
@@ -415,9 +406,6 @@ public void setViewContext(ViewContext context)
             _runsQuery = genotypingSettings.getRunsQuery();
             _samplesQuery = genotypingSettings.getSamplesQuery();
             _haplotypesQuery = genotypingSettings.getHaplotypesQuery();
-
-            GalaxyFolderSettings galaxySettings = GalaxyManager.get().getSettings(c);
-            _galaxyURL = galaxySettings.getGalaxyURL();
         }
 
         @Override
@@ -426,18 +414,6 @@ public ViewContext getViewContext()
             throw new IllegalStateException();
         }
 
-        @Override
-        public @Nullable String getGalaxyURL()
-        {
-            return _galaxyURL;
-        }
-
-        @SuppressWarnings({"UnusedDeclaration"})
-        public void setGalaxyURL(@Nullable String galaxyURL)
-        {
-            _galaxyURL = galaxyURL;
-        }
-
         @Override
         public @Nullable String getSequencesQuery()
         {
@@ -521,20 +497,6 @@ public class AdminAction extends FormViewAction<AdminForm>
         @Override
         public void validateCommand(AdminForm form, Errors errors)
         {
-            String galaxyUrl = form.getGalaxyURL();
-
-            // Allow null, #11130
-            if (null != galaxyUrl)
-            {
-                try
-                {
-                    new URL(galaxyUrl);
-                }
-                catch (MalformedURLException e)
-                {
-                    errors.reject(ERROR_MSG, "Invalid Galaxy URL");
-                }
-            }
         }
 
         @Override
@@ -562,7 +524,6 @@ public boolean handlePost(AdminForm form, BindException errors)
         {
             // Save both the genotyping settings and Galaxy configuration settings
             GenotypingManager.get().saveSettings(getContainer(), form);
-            GalaxyManager.get().saveSettings(getContainer(), form);
             return true;
         }
 
@@ -656,124 +617,11 @@ public void setZipFileName(String zipFileName)
         }
     }
 
-    public static class MySettingsForm extends ReturnUrlForm implements GalaxyUserSettings, HasViewContext
-    {
-        private String _galaxyKey;
-
-        @Override
-        public void setViewContext(ViewContext context)
-        {
-            Container c = context.getContainer();
-            User user = context.getUser();
-            GalaxyUserSettings settings = GalaxyManager.get().getUserSettings(c, user);
-            _galaxyKey = settings.getGalaxyKey();
-        }
-
-        @Override
-        public ViewContext getViewContext()
-        {
-            throw new IllegalStateException();
-        }
-
-        @Override
-        public String getGalaxyKey()
-        {
-            return _galaxyKey;
-        }
-
-        @SuppressWarnings({"UnusedDeclaration"})
-        public void setGalaxyKey(String galaxyKey)
-        {
-            _galaxyKey = galaxyKey;
-        }
-    }
-
-
-    public static ActionURL getMySettingsURL(Container c, ActionURL returnUrl)
-    {
-        ActionURL url = new ActionURL(MySettingsAction.class, c);
-        url.addReturnUrl(returnUrl);
-        return url;
-    }
-
-
-    @RequiresPermission(ReadPermission.class)
-    public static class MySettingsAction extends FormViewAction<MySettingsForm>
-    {
-        @Override
-        public void validateCommand(MySettingsForm form, Errors errors)
-        {
-            String key = form.getGalaxyKey();
-
-            if (null == key)
-            {
-                errors.reject(ERROR_MSG, "Please provide a Galaxy web API key. To generate this, log into your Galaxy server and visit User -> Preferences -> Manage your information.");
-            }
-            else
-            {
-                key = key.trim();
-                String advice = " Please copy the web API key from your Galaxy server account (User -> Preferences -> Manage your information) and paste it below.";
-
-                if (key.length() != 32)
-                {
-                    errors.reject(ERROR_MSG, "Galaxy web API key is the wrong length." + advice);
-                }
-                else
-                {
-                    boolean success = false;
-
-                    try
-                    {
-                        BigInteger bi = new BigInteger(key, 16);
-                        String hex = bi.toString(16);
-
-                        if (hex.equalsIgnoreCase(key))
-                            success = true;
-                    }
-                    catch (NumberFormatException e)
-                    {
-                        // Error below
-                    }
-
-                    if (!success)
-                        errors.reject(ERROR_MSG, "Galaxy web API key is not valid hexadecimal." + advice);
-                }
-            }
-        }
-
-        @Override
-        public ModelAndView getView(MySettingsForm form, boolean reshow, BindException errors)
-        {
-            return new JspView<>("/org/labkey/genotyping/view/mySettings.jsp", form, errors);
-        }
-
-        @Override
-        public boolean handlePost(MySettingsForm form, BindException errors)
-        {
-            GalaxyManager.get().saveUserSettings(getContainer(), getUser(), form);
-            return true;
-        }
-
-        @Override
-        public URLHelper getSuccessURL(MySettingsForm form)
-        {
-            return form.getReturnUrlHelper();
-        }
-
-        @Override
-        public void addNavTrail(NavTree root)
-        {
-            root.addChild("My Galaxy Settings");
-        }
-    }
-
-
     public static class ImportReadsForm extends PipelinePathForm
     {
         private String _readsPath;
         private Integer _run;
         private Integer _metaDataRun = null;
-        private boolean _analyze = false;
         private boolean _pipeline = false;
         private String _platform;
         private String _prefix;
@@ -842,17 +690,6 @@ public void setMetaDataRun(Integer metaDataRun)
             _metaDataRun = metaDataRun;
         }
 
-        public boolean getAnalyze()
-        {
-            return _analyze;
-        }
-
-        @SuppressWarnings({"UnusedDeclaration"})
-        public void setAnalyze(boolean analyze)
-        {
-            _analyze = analyze;
-        }
-
         public boolean getPipeline()
         {
             return _pipeline;
@@ -995,9 +832,7 @@ public boolean handlePost(ImportReadsForm form, BindException errors) throws Exc
                 return true;
             }
 
-            // Successful submission via the UI... redirect either to the pipeline status grid or analyze action
-            ActionURL pipelineURL = PageFlowUtil.urlProvider(PipelineUrls.class).urlBegin(getContainer());
-            _successURL = form.getAnalyze() ? getAnalyzeURL(form.getRun(), pipelineURL) : pipelineURL;
+            _successURL = PageFlowUtil.urlProvider(PipelineUrls.class).urlBegin(getContainer());
 
             return true;
         }
@@ -1061,327 +896,6 @@ public void addNavTrail(NavTree root)
     }
 
 
-    public static class AnalyzeForm extends ReturnUrlForm
-    {
-        private int _run;
-        private String _sequencesView;
-        private String _description;
-        private String _samples;
-
-        public int getRun()
-        {
-            return _run;
-        }
-
-        @SuppressWarnings({"UnusedDeclaration"})
-        public void setRun(int run)
-        {
-            _run = run;
-        }
-
-        public String getSequencesView()
-        {
-            return _sequencesView;
-        }
-
-        @SuppressWarnings({"UnusedDeclaration"})
-        public void setSequencesView(String sequencesView)
-        {
-            _sequencesView = sequencesView;
-        }
-
-        public String getDescription()
-        {
-            return _description;
-        }
-
-        @SuppressWarnings({"UnusedDeclaration"})
-        public void setDescription(String description)
-        {
-            _description = description;
-        }
-
-        public String getSamples()
-        {
-            return _samples;
-        }
-
-        @SuppressWarnings({"UnusedDeclaration"})
-        public void setSamples(String samples)
-        {
-            _samples = samples;
-        }
-    }
-
-
-    private ActionURL getAnalyzeURL(int runId, ActionURL cancelURL)
-    {
-        ActionURL url = new ActionURL(AnalyzeAction.class, getContainer());
-        url.addParameter("run", runId);
-        url.addReturnUrl(cancelURL);
-        return url;
-    }
-
-
-    @RequiresPermission(InsertPermission.class)
-    public static class AnalyzeAction extends FormViewAction<AnalyzeForm>
-    {
-        @Override
-        public void validateCommand(AnalyzeForm target, Errors errors)
-        {
-        }
-
-        @Override
-        public ModelAndView getView(AnalyzeForm form, boolean reshow, BindException errors) throws Exception
-        {
-            GenotypingRun run = GenotypingManager.get().getRun(getContainer(), form.getRun());
-
-            // Verify that galaxy properties are set before submitting job.  This will throw NotFoundException if either URL or web API key isn't set.
-            // 12.1: relax this requirement... allow users to submit jobs without a galaxy server configured or available
-            //GalaxyUtils.get(getContainer(), getUser());
-
-            SortedSet<CustomView> views = new TreeSet<>((c1, c2) ->
-            {
-                String name1 = c1.getName();
-                String name2 = c2.getName();
-
-                return (null == name1 ? DEFAULT_VIEW_PLACEHOLDER : name1).compareTo((null == name2 ? DEFAULT_VIEW_PLACEHOLDER : name2));
-            });
-            GenotypingSchema gs = GenotypingSchema.get();
-            views.addAll(QueryService.get().getCustomViews(getUser(), getContainer(), getUser(), gs.getSchemaName(), gs.getSequencesTable().getName(), false));
-
-            Map<Integer, Pair<String, String>> sampleMap = new TreeMap<>();
-
-            try (Results results = SampleManager.get().selectSamples(getContainer(), getUser(), run, "library_sample_name, library_sample_species, key", "creating an analysis"))
-            {
-                Map<FieldKey, ColumnInfo> fieldMap = results.getFieldMap();
-                ColumnInfo sampleNameColumn = getColumnInfo(fieldMap, "library_sample_name");
-                ColumnInfo sampleSpeciesColumn = getColumnInfo(fieldMap, "library_sample_species");
-                ColumnInfo keyColumn = getColumnInfo(fieldMap, "key");
-
-                while (results.next())
-                {
-                    String sampleName = (String) sampleNameColumn.getValue(results);
-                    String species = (String) sampleSpeciesColumn.getValue(results);
-                    int sampleId = (Integer) keyColumn.getValue(results);
-                    sampleMap.put(sampleId, new Pair<>(sampleName, species));
-                }
-            }
-
-            return new JspView<>("/org/labkey/genotyping/view/analyze.jsp", new AnalyzeBean(views, sampleMap, form.getReturnActionURL()), errors);
-        }
-
-        // Throws NotFoundException if column doesn't exist
-        private ColumnInfo getColumnInfo(Map<FieldKey, ColumnInfo> fieldMap, String columnName)
-        {
-            ColumnInfo column = fieldMap.get(FieldKey.fromString(columnName));
-
-            if (null == column)
-                throw new NotFoundException("Expected to find a column named \"" + columnName + "\" in the samples query");
-
-            return column;
-        }
-
-        @Override
-        public boolean handlePost(AnalyzeForm form, BindException errors) throws Exception
-        {
-            GenotypingRun run = GenotypingManager.get().getRun(getContainer(), form.getRun());
-            if (run == null)
-            {
-                errors.rejectValue("run", ERROR_MSG, "No run found");
-                return false;
-            }
-
-            PipeRoot root = PipelineService.get().findPipelineRoot(getContainer());
-
-            FileLike readsFile = run.getWorkingDir().resolveChild(run.getFileName());
-            ViewBackgroundInfo vbi = new ViewBackgroundInfo(getContainer(), getUser(), getViewContext().getActionURL());
-
-            String sequencesViewName = form.getSequencesView();
-            String description = form.getDescription();
-            String sequencesView = DEFAULT_VIEW_PLACEHOLDER.equals(sequencesViewName) ? null : sequencesViewName;
-            String samples = form.getSamples();
-            if(samples == null)
-            {
-                errors.reject(ERROR_MSG, "Must provide a list of sample IDs");
-                return false;
-            }
-
-            Set<Integer> sampleKeys;
-            String[] keys = samples.split(",");
-            sampleKeys = new HashSet<>(keys.length);
-
-            for (String key : keys)
-                sampleKeys.add(Integer.parseInt(key));
-
-            GenotypingAnalysis analysis = GenotypingManager.get().createAnalysis(getContainer(), getUser(), run, description, sequencesView);
-            try
-            {
-                PipelineJob analysisJob = new SubmitAnalysisJob(vbi, root, readsFile, analysis, sampleKeys);
-                PipelineService.get().queueJob(analysisJob);
-            }
-            catch (MinorConfigurationException e)
-            {
-                errors.reject(ERROR_MSG, e.getMessage());
-                return false;
-            }
-
-            return true;
-        }
-
-        @Override
-        public URLHelper getSuccessURL(AnalyzeForm analyzeForm)
-        {
-            return PageFlowUtil.urlProvider(PipelineUrls.class).urlBegin(getContainer());
-        }
-
-        @Override
-        public void addNavTrail(NavTree root)
-        {
-            root.addChild("Submit Analysis");
-        }
-    }
-
-
-    public static class AnalyzeBean
-    {
-        private final SortedSet<CustomView> _sequencesViews;
-        private final Map<Integer, Pair<String, String>> _sampleMap;
-        private final ActionURL _returnUrl;
-
-        private AnalyzeBean(SortedSet<CustomView> sequenceViews, Map<Integer, Pair<String, String>> sampleMap, ActionURL returnUrl)
-        {
-            _sequencesViews = sequenceViews;
-            _sampleMap = sampleMap;
-            _returnUrl = returnUrl;
-        }
-
-        public SortedSet<CustomView> getSequencesViews()
-        {
-            return _sequencesViews;
-        }
-
-        public Map<Integer, Pair<String, String>> getSampleMap()
-        {
-            return _sampleMap;
-        }
-
-        public ActionURL getReturnUrl()
-        {
-            return _returnUrl;
-        }
-    }
-
-
-    public static ActionURL getWorkflowCompleteURL(Container c, GenotypingAnalysis analysis)
-    {
-        ActionURL url = new ActionURL(WorkflowCompleteAction.class, c);
-        url.addParameter("analysis", analysis.getRowId());
-        url.addParameter("path", analysis.getPath());
-        return url;
-    }
-
-
-    @RequiresNoPermission
-    @CSRF(CSRF.Method.NONE)
-    public class WorkflowCompleteAction extends MutatingApiAction<ImportAnalysisForm>
-    {
-        @Override
-        public void validateForm(ImportAnalysisForm form, Errors errors)
-        {
-            if (null == form.getAnalysis())
-                errors.reject(ERROR_MSG, "Must specify an analysis parameter");
-
-            if (null == form.getPath())
-                errors.reject(ERROR_MSG, "Must specify a path parameter");
-        }
-
-        @Override
-        public Object execute(ImportAnalysisForm form, BindException errors) throws Exception
-        {
-            LOG.info("Galaxy signaled the completion of analysis " + form.getAnalysis());
-            String message;
-
-            // Send any exceptions back to the Galaxy task so it can log it as well.
-            String FAILURE_PREFACE = "Failed to queue import analysis job: ";
-
-            try
-            {
-                FileLike analysisDir = FileSystemLike.getVerifiedFileLike(getContainer(), form.getPath());
-                int analysisId = form.getAnalysis();
-
-                User user = getUser();
-                if (user.isGuest())
-                {
-                    Properties props = GenotypingManager.get().readProperties(analysisDir);
-                    String email = (String)props.get("user");
-
-                    if (null != email)
-                    {
-                        // Possible that user doesn't exist or changed email (e.g., re-loading an old analysis)
-                        User test = UserManager.getUser(new ValidEmail(email));
-
-                        if (null != test)
-                            user = test;
-                    }
-                }
-
-                importAnalysis(analysisId, analysisDir, user);
-                message = "Import analysis job queued at " + new Date();
-            }
-            catch (FileNotFoundException fnf)
-            {
-                // Send back a vague, generic message in the case of all file-not-found-type problems, e.g., specified path is
-                // missing, isn't a directory, lacks a properties.xml file, or doesn't match the analysis table path. This
-                // prevents attackers from gaining any useful information about the file system.  Log the more detailed message.
-                message = FAILURE_PREFACE + "Analysis path doesn't match import path (see system log for more details)";
-
-                // But log more detail to the administrator so they're aware
-                LOG.error(FAILURE_PREFACE + fnf.getMessage());
-            }
-            catch (Exception e)
-            {
-                message = FAILURE_PREFACE + e.getMessage();
-                LOG.error(message);
-            }
-
-            // Plain text response back to Galaxy
-            sendPlainText(message);
-
-            return null;
-        }
-    }
-
-
-    public static class ImportAnalysisForm
-    {
-        private Integer _analysis = null;
-        private String _path = null;
-
-        public Integer getAnalysis()
-        {
-            return _analysis;
-        }
-
-        @SuppressWarnings({"UnusedDeclaration"})
-        public void setAnalysis(Integer analysis)
-        {
-            _analysis = analysis;
-        }
-
-        public String getPath()
-        {
-            return _path;
-        }
-
-        @SuppressWarnings({"UnusedDeclaration"})
-        public void setPath(String path)
-        {
-            _path = path;
-        }
-    }
-
-
     @RequiresPermission(InsertPermission.class)
     public class ImportAnalysisAction extends FormHandlerAction<PipelinePathForm>
     {
@@ -1838,47 +1352,22 @@ public ModelAndView getView(RunForm form, BindException errors) throws Exception
             if (null == _run)
                 throw new NotFoundException("Run not found");
 
-            final boolean allowAnalysis = GenotypingManager.SEQUENCE_PLATFORMS.LS454.toString().equals(_run.getPlatform());
-
-            ModelAndView readsView;
-            readsView = super.getView(form, errors);
+            ModelAndView readsView = super.getView(form, errors);
 
             // Just return the view in export case
             if (form.isExport())
                 return readsView;
 
             VBox vbox = new VBox();
-            final ActionButton submitAnalysis = new ActionButton("Add Analysis", getAnalyzeURL(_run.getRowId(), getViewContext().getActionURL()));
 
             if (GenotypingManager.get().hasAnalyses(_run))
             {
-                GenotypingAnalysesView analyses = new GenotypingAnalysesView(getViewContext(), null, "Analyses", new SimpleFilter(FieldKey.fromParts("Run"), _run.getRowId()), false) {
-                    @Override
-                    protected void populateButtonBar(DataView view, ButtonBar bar)
-                    {
-                        bar.add(submitAnalysis);
-                    }
-                };
+                GenotypingAnalysesView analyses = new GenotypingAnalysesView(getViewContext(), null, "Analyses", new SimpleFilter(FieldKey.fromParts("Run"), _run.getRowId()), false);
                 analyses.setButtonBarPosition(DataRegion.ButtonBarPosition.TOP);
                 analyses.setTitle("Analyses");
                 analyses.setTitleHref(getAnalysesURL(getContainer()));
                 vbox.addView(analyses);
             }
-            else
-            {
-                vbox.addView(new HttpView() {
-                    @Override
-                    protected void renderInternal(Object model, PrintWriter out) throws Exception
-                    {
-                        if(allowAnalysis)
-                        {
-                            submitAnalysis.render(new RenderContext(getViewContext()), out);
-                            out.println("<br><br>");
-                        }
-                    }
-                });
-            }
-
             vbox.addView(readsView);
 
             return vbox;
@@ -1924,6 +1413,13 @@ public boolean handlePost(Object o, BindException errors)
                 gm.deleteRun(run);
             }
 
+            if (!runs.isEmpty())
+            {
+                AuditTypeEvent event = new AuditTypeEvent(ContainerAuditProvider.CONTAINER_AUDIT_EVENT, getContainer(),
+                        "Deleted " + runs.size() + " genotyping run(s): " + runs);
+                AuditLogService.get().addEvent(getUser(), event);
+            }
+
             return true;
         }
 
@@ -1947,13 +1443,21 @@ public void validateCommand(Object target, Errors errors)
         public boolean handlePost(Object o, BindException errors) throws Exception
         {
             GenotypingManager gm = GenotypingManager.get();
+            Set<Integer> analysisIds = DataRegionSelection.getSelectedIntegers(getViewContext(), true);
 
-            for (Integer analysisId : DataRegionSelection.getSelectedIntegers(getViewContext(), true))
+            for (Integer analysisId : analysisIds)
             {
                 GenotypingAnalysis analysis = gm.getAnalysis(getContainer(), analysisId);
                 gm.deleteAnalysis(analysis);
             }
 
+            if (!analysisIds.isEmpty())
+            {
+                AuditTypeEvent event = new AuditTypeEvent(ContainerAuditProvider.CONTAINER_AUDIT_EVENT, getContainer(),
+                        "Deleted " + analysisIds.size() + " genotyping analysis/analyses: " + analysisIds);
+                AuditLogService.get().addEvent(getUser(), event);
+            }
+
             return true;
         }
 
diff --git a/genotyping/src/org/labkey/genotyping/SubmitAnalysisJob.java b/genotyping/src/org/labkey/genotyping/SubmitAnalysisJob.java
deleted file mode 100644
index f0102063..00000000
--- a/genotyping/src/org/labkey/genotyping/SubmitAnalysisJob.java
+++ /dev/null
@@ -1,333 +0,0 @@
-/*
- * Copyright (c) 2010-2018 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.labkey.genotyping;
-
-import com.fasterxml.jackson.annotation.JsonCreator;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import org.apache.commons.lang3.mutable.MutableInt;
-import org.jetbrains.annotations.NotNull;
-import org.jetbrains.annotations.Nullable;
-import org.labkey.api.data.SimpleFilter;
-import org.labkey.api.data.TSVWriter;
-import org.labkey.api.data.Table;
-import org.labkey.api.data.TableInfo;
-import org.labkey.api.data.TableSelector;
-import org.labkey.api.pipeline.PipeRoot;
-import org.labkey.api.pipeline.PipelineJob;
-import org.labkey.api.query.FieldKey;
-import org.labkey.api.settings.AppProps;
-import org.labkey.api.util.FileUtil;
-import org.labkey.api.util.MinorConfigurationException;
-import org.labkey.api.util.PageFlowUtil;
-import org.labkey.api.util.URLHelper;
-import org.labkey.api.view.NotFoundException;
-import org.labkey.api.view.ViewBackgroundInfo;
-import org.labkey.genotyping.galaxy.GalaxyServer;
-import org.labkey.genotyping.galaxy.GalaxyUtils;
-import org.labkey.genotyping.galaxy.WorkflowCompletionMonitor;
-import org.labkey.genotyping.sequences.SequenceManager;
-import org.labkey.vfs.FileLike;
-
-import java.io.File;
-import java.io.IOException;
-import java.net.URISyntaxException;
-import java.sql.SQLException;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Properties;
-import java.util.Set;
-
-/**
- * User: adam
- * Date: Sep 10, 2010
- * Time: 9:43:21 PM
- */
-public class SubmitAnalysisJob extends PipelineJob
-{
-    private final FileLike _dir;
-    private final GenotypingAnalysis _analysis;
-    private final FileLike _analysisDir;
-    private final Set<Integer> _sampleIds;
-
-    private URLHelper _galaxyURL = null;
-    private FileLike _completionFile = null;   // Used for dev mode only
-
-    // In dev mode only, we'll test the ability to connect to the Galaxy server once; if this connection fails, we'll
-    // skip trying to submit to Galaxy on subsequent attempts (until server restart).
-    private static Boolean _useGalaxy = null;
-
-    @JsonCreator
-    protected SubmitAnalysisJob(
-            @JsonProperty("_dir") FileLike dir,
-            @JsonProperty("_analysis") GenotypingAnalysis analysis,
-            @JsonProperty("_analysisDir") FileLike analysisDir,
-            @JsonProperty("_sampleIds") Set<Integer> sampleIds,
-            @JsonProperty("_galaxyURL") URLHelper galaxyURL,
-            @JsonProperty("_completionFile") FileLike completionFile,
-            @JsonProperty("_useGalaxy") Boolean useGalaxy
-    )
-    {
-        _dir = dir;
-        _analysis = analysis;
-        _analysisDir = analysisDir;
-        _sampleIds = sampleIds;
-        _galaxyURL = galaxyURL;
-        _completionFile = completionFile;
-        _useGalaxy = useGalaxy;
-    }
-    
-    public SubmitAnalysisJob(ViewBackgroundInfo info, PipeRoot root, FileLike reads, GenotypingAnalysis analysis, @NotNull Set<Integer> sampleIds)
-    {
-        super("Submit Analysis", info, root);      // No pipeline provider
-        _dir = reads.getParent();
-        _analysis = analysis;
-        _sampleIds = sampleIds;
-
-        _analysisDir = _dir.resolveChild("analysis_" + _analysis.getRowId());
-
-        if (_analysisDir.exists())
-            throw new MinorConfigurationException("Analysis directory already exists: " + _analysisDir.getPath());
-
-        try
-        {
-            _analysisDir.mkdir();
-        }
-        catch(IOException e)
-        {
-            throw new MinorConfigurationException("Can't create analysis directory: " + _analysisDir.getPath());
-        }
-
-        setLogFile(_analysisDir.resolveChild(FileUtil.makeFileNameWithTimestamp("submit_analysis", "log")).toNioPathForWrite());
-        info("Creating analysis directory: " + _analysisDir.getName());
-        _analysis.setPath(FileUtil.getAbsolutePath(_analysisDir.toNioPathForRead()));
-        _analysis.setFileName(_analysisDir.getName());
-        Table.update(getUser(), GenotypingSchema.get().getAnalysesTable(), PageFlowUtil.map("Path", _analysis.getPath(), "FileName", _analysis.getFileName()), _analysis.getRowId());
-    }
-
-
-    @Override
-    public URLHelper getStatusHref()
-    {
-        return _galaxyURL;
-    }
-
-
-    @Override
-    public String getDescription()
-    {
-        return "Submit genotyping analysis " + _analysis.getRowId();
-    }
-
-
-    @Override
-    public void run()
-    {
-        try
-        {
-            // Do this first to ensure that the Galaxy server is configured properly and the user has set a web API key
-            info("Verifying Galaxy configuration");
-            GalaxyServer server = null;
-
-            try
-            {
-                server = GalaxyUtils.get(getContainer(), getUser());
-            }
-            catch (NotFoundException e)
-            {
-                warn("Can't submit to Galaxy server: " + e.getMessage());
-            }
-
-            writeAnalysisSamples();
-            writeReads();
-            writeProperties(server);
-            writeFasta();
-            sendFilesToGalaxy(server);
-            monitorCompletion();
-            if (!GenotypingManager.get().updateAnalysisStatus(_analysis, getUser(), Status.NotSubmitted, Status.Submitted))
-                throw new IllegalStateException("Analysis status should be \"NotSubmitted\"");
-            info("Submitting genotyping analysis job complete");
-            setStatus(TaskStatus.complete);
-        }
-        catch (Exception e)
-        {
-            error("Submitting genotyping analysis failed", e);
-            setStatus(TaskStatus.error);
-        }
-    }
-
-
-    private void writeAnalysisSamples()
-    {
-        Map<String, Object> sampleMap = new HashMap<>();   // Map to reuse for each insertion to AnalysisSamples
-        sampleMap.put("analysis", _analysis.getRowId());
-
-        for (Integer sampleId : _sampleIds)
-        {
-            sampleMap.put("sampleId", sampleId);
-            Table.insert(getUser(), GenotypingSchema.get().getAnalysisSamplesTable(), sampleMap);
-        }
-    }
-
-
-    private void writeReads() throws IOException
-    {
-        info("Writing reads file");
-        setStatus("WRITING READS");
-
-        // Need a custom writer since TSVGridWriter does not work in background threads
-        try (TSVWriter writer = new TSVWriter() {
-            @Override
-            protected int write()
-            {
-                _pw.println("name\tsample\tsequence\tquality");
-
-                TableInfo ti = GenotypingSchema.get().getReadsTable();
-                SimpleFilter filter = new SimpleFilter(FieldKey.fromParts("run"), _analysis.getRun());
-                filter.addInClause(FieldKey.fromParts("SampleId"), _sampleIds);
-                MutableInt rows = new MutableInt();
-
-                new TableSelector(ti, ti.getColumns("name,sampleid,sequence,quality"), filter, null).forEach(rs -> {
-                    _pw.println(rs.getString(1) + "\t" + rs.getInt(2) + "\t" + rs.getString(3) + "\t" + rs.getString(4));
-                    rows.increment();
-                });
-
-                return rows.getValue();
-            }
-        })
-        {
-            writer.write(_analysisDir.resolveChild("reads.txt").toNioPathForWrite().toFile());
-        }
-    }
-
-
-    private void writeProperties(@Nullable GalaxyServer server) throws IOException
-    {
-        info("Writing properties file");
-        setStatus("WRITING PROPERTIES");
-        Properties props = new Properties();
-        props.put("url", GenotypingController.getWorkflowCompleteURL(getContainer(), _analysis).getURIString());
-        props.put("dir", _analysisDir.getName());
-        props.put("analysis", String.valueOf(_analysis.getRowId()));
-        props.put("user", getUser().getEmail());
-
-        // Tell Galaxy "workflow complete" task to write a file when the workflow is done.  In many dev mode configurations
-        // the Galaxy server can't communicate via HTTP with LabKey Server, so watch for this file as a backup plan.
-        if (AppProps.getInstance().isDevMode() || null == server)
-        {
-            _completionFile = _analysisDir.resolveChild("analysis_complete.txt");
-
-            if (_completionFile.exists())
-                throw new IllegalStateException("Completion file already exists: " + _completionFile.getPath());
-
-            props.put("completionFilename", _completionFile.getName());
-        }
-
-        GenotypingManager.get().writeProperties(props, _analysisDir);
-    }
-
-
-    private void writeFasta() throws IOException, SQLException
-    {
-        info("Writing FASTA file");
-        setStatus("WRITING FASTA");
-        File fastaFile = _analysisDir.resolveChild(GenotypingManager.SEQUENCES_FILE_NAME).toNioPathForWrite().toFile();
-        SequenceManager.get().writeFasta(getContainer(), getUser(), _analysis.getSequencesView(), fastaFile);
-    }
-
-
-    private void sendFilesToGalaxy(GalaxyServer server) throws IOException, URISyntaxException
-    {
-        if (!shouldUseGalaxy(server))
-            return;
-
-        info("Sending files to Galaxy");
-        setStatus("SENDING TO GALAXY");
-
-        try
-        {
-            GalaxyServer.DataLibrary library = server.createLibrary(_dir.getName() + "_" + _analysis.getRowId(), "MHC analysis " + _analysis.getRowId() + " for run " + _analysis.getRun(), "An MHC genotyping analysis");
-            GalaxyServer.Folder root = library.getRootFolder();
-            root.uploadFromImportDirectory(_dir.getName() + "/" + _analysisDir.getName(), "txt", null, true);
-
-            _galaxyURL = library.getURL();
-
-            // Hack for testing without invoking the entire galaxy workflow: if it exists, link the matches.txt file
-            // in /matches into the data library.
-            if (AppProps.getInstance().isDevMode())
-            {
-                FileLike matchesDir = _dir.resolveChild("matches");
-
-                if (matchesDir.exists())
-                {
-                    FileLike matchesFile = matchesDir.resolveChild(GenotypingManager.MATCHES_FILE_NAME);
-
-                    if (matchesFile.exists())
-                        root.uploadFromImportDirectory(_dir.getName() + "/matches", "txt", null, true);
-                }
-            }
-        }
-        catch (IOException e)
-        {
-            // Fail the job in production mode, but succeed in dev mode.  This allows us to test in an environment
-            // where Galaxy is not reachable.
-            if (!AppProps.getInstance().isDevMode())
-                throw e;
-
-            info("Could not connect to Galaxy server", e);
-        }
-    }
-
-
-    private synchronized boolean shouldUseGalaxy(@Nullable GalaxyServer server)
-    {
-        // First time through
-        if (null == _useGalaxy)
-        {
-            if (null == server)
-            {
-                // Galaxy is not configured, so don't use it
-                _useGalaxy = false;
-            }
-            else if (!AppProps.getInstance().isDevMode())
-            {
-                // With a Galaxy configuration in production mode, always try to connect to Galaxy server (even if failures occur)
-                _useGalaxy = true;
-            }
-            else
-            {
-                // In dev mode, attempt a connection now and if it fails skip subsequent connections
-                _useGalaxy = server.canConnect();
-
-                if (!_useGalaxy)
-                    warn("Test connect to Galaxy server failed");
-            }
-        }
-        else
-        {
-            if (!_useGalaxy && null != server)  // We already warned in the null case
-                warn("Skipping submit to Galaxy server due to previous connection failure");
-        }
-
-        return _useGalaxy;
-    }
-
-    // Wait until analysis is completely prepared and has been submitted to Galaxy before monitoring
-    private void monitorCompletion()
-    {
-        if (null != _completionFile)
-            WorkflowCompletionMonitor.get().monitor(_completionFile);
-    }
-}
diff --git a/genotyping/src/org/labkey/genotyping/galaxy/GalaxyFolderSettings.java b/genotyping/src/org/labkey/genotyping/galaxy/GalaxyFolderSettings.java
deleted file mode 100644
index a4a9ee30..00000000
--- a/genotyping/src/org/labkey/genotyping/galaxy/GalaxyFolderSettings.java
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * Copyright (c) 2010 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.labkey.genotyping.galaxy;
-
-/**
- * User: adam
- * Date: Sep 24, 2010
- * Time: 11:53:08 AM
- */
-public interface GalaxyFolderSettings
-{
-    String getGalaxyURL();
-}
diff --git a/genotyping/src/org/labkey/genotyping/galaxy/GalaxyManager.java b/genotyping/src/org/labkey/genotyping/galaxy/GalaxyManager.java
deleted file mode 100644
index 6936d006..00000000
--- a/genotyping/src/org/labkey/genotyping/galaxy/GalaxyManager.java
+++ /dev/null
@@ -1,94 +0,0 @@
-/*
- * Copyright (c) 2010-2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package org.labkey.genotyping.galaxy;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.labkey.api.data.Container;
-import org.labkey.api.data.PropertyManager;
-import org.labkey.api.data.PropertyManager.WritablePropertyMap;
-import org.labkey.api.security.User;
-
-import java.util.Map;
-
-/**
- * User: adam
- * Date: Sep 24, 2010
- * Time: 11:56:14 AM
- */
-
-public class GalaxyManager
-{
-    private static final Logger LOG = LogManager.getLogger(GalaxyManager.class);
-    private static final GalaxyManager _instance = new GalaxyManager();
-
-    private GalaxyManager()
-    {
-        // prevent external construction with a private default constructor
-    }
-
-    public static GalaxyManager get()
-    {
-        return _instance;
-    }
-
-    private static final String FOLDER_CATEGORY = "GalaxySettings";
-    private static final String GALAXY_URL = "GalaxyURL";
-
-    public void saveSettings(Container c, GalaxyFolderSettings settings)
-    {
-        WritablePropertyMap map = PropertyManager.getWritableProperties(c, FOLDER_CATEGORY, true);
-        map.put(GALAXY_URL, settings.getGalaxyURL());
-        map.save();
-    }
-
-    public GalaxyFolderSettings getSettings(final Container c)
-    {
-        return new GalaxyFolderSettings() {
-            private final Map<String, String> map = PropertyManager.getProperties(c, FOLDER_CATEGORY);
-
-            @Override
-            public String getGalaxyURL()
-            {
-                return map.get(GALAXY_URL);
-            }
-        };
-    }
-
-    private static final String USER_CATEGORY = "GalaxyUserSettings";
-    private static final String GALAXY_KEY = "GalaxyKey";
-
-    public void saveUserSettings(Container c, User user, GalaxyUserSettings userSettings)
-    {
-        WritablePropertyMap map = PropertyManager.getWritableProperties(user, c, USER_CATEGORY, true);
-        map.put(GALAXY_KEY, userSettings.getGalaxyKey());
-        map.save();
-    }
-
-    public GalaxyUserSettings getUserSettings(final Container c, final User user)
-    {
-        return new GalaxyUserSettings() {
-            private final Map<String, String> map = PropertyManager.getProperties(user, c, USER_CATEGORY);
-
-            @Override
-            public String getGalaxyKey()
-            {
-                return map.get(GALAXY_KEY);
-            }
-        };
-    }
-}
\ No newline at end of file
diff --git a/genotyping/src/org/labkey/genotyping/galaxy/GalaxyServer.java b/genotyping/src/org/labkey/genotyping/galaxy/GalaxyServer.java
deleted file mode 100644
index deac1c3f..00000000
--- a/genotyping/src/org/labkey/genotyping/galaxy/GalaxyServer.java
+++ /dev/null
@@ -1,342 +0,0 @@
-/*
- * Copyright (c) 2010-2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.labkey.genotyping.galaxy;
-
-import org.apache.hc.client5.http.classic.methods.HttpGet;
-import org.apache.hc.client5.http.classic.methods.HttpPost;
-import org.apache.hc.client5.http.classic.methods.HttpUriRequestBase;
-import org.apache.hc.client5.http.impl.classic.CloseableHttpClient;
-import org.apache.hc.client5.http.impl.classic.CloseableHttpResponse;
-import org.apache.hc.client5.http.impl.classic.HttpClientBuilder;
-import org.apache.hc.core5.http.ContentType;
-import org.apache.hc.core5.http.HttpEntity;
-import org.apache.hc.core5.http.HttpStatus;
-import org.apache.hc.core5.http.io.entity.StringEntity;
-import org.apache.logging.log4j.LogManager;
-import org.jetbrains.annotations.NotNull;
-import org.jetbrains.annotations.Nullable;
-import org.json.JSONArray;
-import org.json.JSONObject;
-import org.json.JSONStringer;
-import org.json.JSONWriter;
-import org.labkey.api.util.PageFlowUtil;
-import org.labkey.api.util.URLHelper;
-
-import java.io.IOException;
-import java.net.URISyntaxException;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-
-/**
- * User: adam
- * Date: Aug 25, 2010
- * Time: 3:36:36 PM
- */
-
-// Provides ability to query and modify a Galaxy Server via the HTTP Galaxy API.  All API calls require a Galaxy-generated
-// web API key (see User -> Preferences -> Manage your information).
-public class GalaxyServer
-{
-    private final String _serverUrl;
-    private final String _baseUrl;
-    private final String _key;
-    private final CloseableHttpClient _client;
-
-
-    public GalaxyServer(String serverUrl, String key)
-    {
-        _serverUrl = !serverUrl.endsWith("/") ? serverUrl : serverUrl.substring(0, serverUrl.length() - 1);
-        _baseUrl = _serverUrl + "/api/libraries";
-        _key = key;
-        _client = HttpClientBuilder.create().build();  // Note: not thread-safe; assumes GalaxyServer is used in a single thread
-    }
-
-
-    public String getServerUrl()
-    {
-        return _serverUrl;
-    }
-
-
-    public List<DataLibrary> getDataLibraries() throws IOException
-    {
-        return getDataLibraries(get(""));
-    }
-
-
-    // Parse one or more libraries from a JSON array
-    private List<DataLibrary> getDataLibraries(String body)
-    {
-        JSONArray array = new JSONArray(body);
-        List<DataLibrary> list = new LinkedList<>();
-
-        for (int i = 0; i < array.length(); i++)
-            list.add(new DataLibrary((JSONObject)array.get(i)));
-
-        return list;
-    }
-
-
-    private String get(String relativeUrl) throws IOException
-    {
-        return execute(new HttpGet(makeUrl(relativeUrl)));
-    }
-
-
-    private String execute(HttpUriRequestBase request) throws IOException
-    {
-        try (CloseableHttpResponse response = _client.execute(request))
-        {
-            HttpEntity entity = response.getEntity();
-            String contents = PageFlowUtil.getStreamContentsAsString(entity.getContent());
-
-            if (HttpStatus.SC_OK != response.getCode())
-                throw new IOException("HTTP " + request.getMethod() + " Failed: " + response);
-
-            return contents;
-        }
-    }
-
-
-    private String makeUrl(String relativeUrl)
-    {
-        return (relativeUrl.isEmpty() ? _baseUrl : _baseUrl + "/" + relativeUrl) + "?key=" + _key;
-    }
-
-
-    public boolean canConnect()
-    {
-        try
-        {
-            get("");
-            return true;
-        }
-        catch (IOException e)
-        {
-            LogManager.getLogger(GalaxyServer.class).info("Test connect to Galaxy server failed", e);
-            return false;
-        }
-    }
-
-
-    public DataLibrary createLibrary(String name, @Nullable String description, @Nullable String synopsis) throws IOException
-    {
-        JSONWriter writer = new JSONStringer();
-        writer.object();
-        writer.key("name").value(name);
-
-        if (null != description)
-            writer.key("description").value(description);
-
-        if (null != synopsis)
-            writer.key("synopsis").value(synopsis);
-
-        writer.endObject();
-
-        String response = post("", writer.toString());
-
-        List<DataLibrary> list = getDataLibraries(response);
-
-        assert 1 == list.size();
-
-        return list.get(0);
-    }
-
-
-    private String post(String relativeUrl, String body) throws IOException
-    {
-        HttpPost post = new HttpPost(makeUrl(relativeUrl));
-        post.setEntity(new StringEntity(body, ContentType.APPLICATION_JSON));
-        post.setHeader("Content-Type", "application/json");
-
-        return execute(post);
-    }
-
-
-    public static class Item
-    {
-        private final ItemType _type;
-        private final String _apiUrl;
-        private final String _name;
-        private final String _id;
-        private final @Nullable Item _parent;
-
-        private Item(@NotNull ItemType type, @Nullable Item parent, JSONObject json)
-        {
-            this(type, parent, json.getString("url"), json.getString("name"), json.getString("id"));
-        }
-
-        private Item(@NotNull ItemType type, @Nullable Item parent, String apiUrl, String name, String id)
-        {
-            _type = type;
-            _parent = parent;
-            _apiUrl = apiUrl;
-            _name = name;
-            _id = id;
-        }
-
-        public ItemType getType()
-        {
-            return _type;
-        }
-
-        public @Nullable Item getParent()
-        {
-            return _parent;
-        }
-
-        public String getApiUrl()
-        {
-            return _apiUrl;
-        }
-
-        public String getName()
-        {
-            return _name;
-        }
-
-        public String getId()
-        {
-            return _id;
-        }
-    }
-
-    public class DataLibrary extends Item
-    {
-        private DataLibrary(JSONObject library)
-        {
-            super(ItemType.DataLibrary, null, library);
-        }
-
-        public Folder getRootFolder() throws IOException
-        {
-            List<LibraryItem> children = getChildren();
-
-            for (LibraryItem child : children)
-            {
-                if (this.equals(child.getParent()) && "/".equals(child.getName()))
-                    return (Folder)child;
-            }
-
-            throw new IllegalStateException("No root folder found for data library " + getName());
-        }
-
-        public List<LibraryItem> getChildren() throws IOException
-        {
-            String body = get(getId() + "/contents");
-
-            JSONArray array = new JSONArray(body);
-            List<LibraryItem> list = new LinkedList<>();
-
-            for (int i = 0; i < array.length(); i++)
-                list.add(getLibraryItem(this, (JSONObject)array.get(i)));
-
-            return list;
-        }
-
-        public URLHelper getURL() throws URISyntaxException
-        {
-            return new URLHelper(getServerUrl() + "/library_common/browse_library?sort=name&f-description=All&f-name=All&cntrller=library&operation=browse").addParameter("id", getId());
-        }
-    }
-
-    public enum ItemType {DataLibrary, LibraryFolder, LibraryFile}
-
-    private LibraryItem getLibraryItem(Item parent, JSONObject json)
-    {
-        String type = json.getString("type");
-
-        if ("folder".equals(type))
-            return new Folder(parent, json);
-        else
-            return new File(parent, json);
-    }
-
-    public abstract class LibraryItem extends Item
-    {
-        private LibraryItem(@NotNull ItemType type, @Nullable Item parent, JSONObject json)
-        {
-            super(type, parent, json);
-        }
-
-        public Folder createFolder(String name, String description) throws IOException
-        {
-            JSONWriter writer = new JSONStringer();
-            writer.object();
-            writer.key("folder_id").value(getId());
-            writer.key("name").value(name);
-            writer.key("create_type").value("folder");
-
-            if (null != description)
-                writer.key("description").value(description);
-
-            writer.endObject();
-
-            String json = post(getId() + "/contents", writer.toString());
-            JSONArray array = new JSONArray(json);
-
-            return new Folder(this, (JSONObject)array.get(0));
-        }
-    }
-
-    public class Folder extends LibraryItem
-    {
-        private Folder(@Nullable Item parent, JSONObject json)
-        {
-            super(ItemType.LibraryFolder, parent, json);
-        }
-
-        public List<File> uploadFromImportDirectory(String serverPath, String fileType, @Nullable String dbKey, boolean linkData) throws IOException
-        {
-            JSONWriter writer = new JSONStringer();
-            writer.object();
-            writer.key("folder_id").value(getId());
-            writer.key("server_dir").value(serverPath);
-            writer.key("file_type").value(fileType);
-            writer.key("dbkey").value(null != dbKey ? dbKey : "?");
-            writer.key("upload_option").value("upload_directory");
-            writer.key("create_type").value("file");
-            writer.key("link_data_only").value(linkData ? "Yes" : "No");
-            writer.endObject();
-
-            String json = post(getId() + "/contents", writer.toString());
-
-            // Parse one or more folders from a JSON array
-            JSONArray array = new JSONArray(json);
-            List<File> list = new LinkedList<>();
-
-            for (int i = 0; i < array.length(); i++)
-                list.add(new File(this, (JSONObject)array.get(i)));
-
-            return list;
-        }
-    }
-
-    public class File extends LibraryItem
-    {
-        private File(@Nullable Item parent, JSONObject json)
-        {
-            super(ItemType.LibraryFile, parent, json);
-        }
-
-        public Map<String, Object> getProperties() throws IOException
-        {
-            String body = get(getParent().getId() + "/contents/" + getId());
-            return new JSONObject(body).toMap();
-        }
-    }
-}
diff --git a/genotyping/src/org/labkey/genotyping/galaxy/GalaxyUserSettings.java b/genotyping/src/org/labkey/genotyping/galaxy/GalaxyUserSettings.java
deleted file mode 100644
index d0911783..00000000
--- a/genotyping/src/org/labkey/genotyping/galaxy/GalaxyUserSettings.java
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * Copyright (c) 2010 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.labkey.genotyping.galaxy;
-
-/**
- * User: adam
- * Date: Sep 10, 2010
- * Time: 2:54:31 PM
- */
-public interface GalaxyUserSettings
-{
-    String getGalaxyKey();
-}
diff --git a/genotyping/src/org/labkey/genotyping/galaxy/GalaxyUtils.java b/genotyping/src/org/labkey/genotyping/galaxy/GalaxyUtils.java
deleted file mode 100644
index f9cdd41b..00000000
--- a/genotyping/src/org/labkey/genotyping/galaxy/GalaxyUtils.java
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * Copyright (c) 2010-2012 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.labkey.genotyping.galaxy;
-
-import org.labkey.api.data.Container;
-import org.labkey.api.security.User;
-import org.labkey.api.security.permissions.AdminPermission;
-import org.labkey.api.view.NotFoundException;
-
-/**
- * User: adam
- * Date: Oct 12, 2010
- * Time: 4:38:58 PM
- */
-
-// Provides a LabKey-specific way to create a GalaxyServer.  This keeps GalaxyServer very generic and easier to publish.
-public class GalaxyUtils
-{
-    // Throws NotFoundException if either galaxy URL (admin responsibility) or web API key (user responsibility) isn't configured.
-    public static GalaxyServer get(Container c, User user)
-    {
-        GalaxyFolderSettings settings = GalaxyManager.get().getSettings(c);
-
-        if (null == settings.getGalaxyURL())
-        {
-            String who = c.hasPermission(user, AdminPermission.class) ? "you" : "an administrator";
-            throw new NotFoundException("To submit data to Galaxy, " + who + " must configure a Galaxy server URL via the genotyping admin page.");
-        }
-
-        GalaxyUserSettings userSettings = GalaxyManager.get().getUserSettings(c, user);
-
-        if (null == userSettings.getGalaxyKey())
-            throw new NotFoundException("To submit data to Galaxy, you must first configure your Galaxy web API key using the \"my settings\" link");
-
-        return new GalaxyServer(settings.getGalaxyURL(), userSettings.getGalaxyKey());
-    }
-}
diff --git a/genotyping/src/org/labkey/genotyping/galaxy/WorkflowCompletionMonitor.java b/genotyping/src/org/labkey/genotyping/galaxy/WorkflowCompletionMonitor.java
deleted file mode 100644
index 0abbd0a3..00000000
--- a/genotyping/src/org/labkey/genotyping/galaxy/WorkflowCompletionMonitor.java
+++ /dev/null
@@ -1,157 +0,0 @@
-/*
- * Copyright (c) 2010-2016 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.labkey.genotyping.galaxy;
-
-import org.apache.logging.log4j.Logger;
-import org.labkey.api.util.ContextListener;
-import org.labkey.api.util.FileUtil;
-import org.labkey.api.util.ShutdownListener;
-import org.labkey.api.util.logging.LogHelper;
-import org.labkey.genotyping.GenotypingManager;
-import org.labkey.vfs.FileLike;
-
-import java.net.URI;
-import java.net.http.HttpClient;
-import java.net.http.HttpRequest;
-import java.net.http.HttpResponse;
-import java.net.http.HttpResponse.BodyHandler;
-import java.nio.charset.StandardCharsets;
-import java.util.List;
-import java.util.Properties;
-import java.util.concurrent.CopyOnWriteArrayList;
-import java.util.concurrent.Executors;
-import java.util.concurrent.ScheduledExecutorService;
-import java.util.concurrent.TimeUnit;
-
-/**
- * User: adam
- * Date: Sep 28, 2010
- * Time: 9:41:02 PM
- */
-public class WorkflowCompletionMonitor implements ShutdownListener
-{
-    private static final Logger LOG = LogHelper.getLogger(WorkflowCompletionMonitor.class, "Logger for Genotyping workflow completion monitor");
-    private static final WorkflowCompletionMonitor INSTANCE = new WorkflowCompletionMonitor();
-
-    private final ScheduledExecutorService _executor = Executors.newSingleThreadScheduledExecutor(r -> new Thread(r, "Genotyping Workflow Completion Monitor"));
-    private final List<FileLike> _pendingCompletionFiles = new CopyOnWriteArrayList<>();
-
-
-    static
-    {
-        ContextListener.addShutdownListener(INSTANCE);
-    }
-
-
-    /*
-        This gets used only if a genotyping analysis gets submitted to Galaxy while the server is in dev mode. Most
-        configurations don't support an external Galaxy server pinging back to a developer's LabKey Server, so we signal
-        workflow completion via a file in the analysis directory. Steps:
-
-        - SubmitAnalysisJob adds a "completeFilename" property to properties.xml
-        - SubmitAnalysisJob calls monitor() below cause WorkflowCompletionMonitor to watch for the specified file, checking
-          every 15 seconds for the existence of any pending files.
-        - When Galaxy workflow is complete, the workflow_complete task runs.  If "completeFilename" is set in properties.xml
-          the task creates the specified file.
-        - The CheckForWorkflowCompletionsRunnable detects the file and signals the LabKey Server by invoking the same URL
-          the Galaxy workflow_complete task would have pinged; this provides a good test of the HTTP signaling mechanism.
-    */
-
-    public static WorkflowCompletionMonitor get()
-    {
-        return INSTANCE;
-    }
-
-
-    private WorkflowCompletionMonitor()
-    {
-        // Check for workflow complete files every 15 seconds
-        _executor.scheduleWithFixedDelay(new WorkflowCompletionMonitor.CheckForWorkflowCompletionsRunnable(), 15, 15, TimeUnit.SECONDS);
-    }
-
-
-    public void monitor(FileLike completionFile)
-    {
-        _pendingCompletionFiles.add(completionFile);
-        LOG.info("Monitoring for {}", FileUtil.getAbsolutePath(completionFile.toNioPathForRead()));
-    }
-
-
-    @Override
-    public String getName()
-    {
-        return "Genotyping workflow completion monitor";
-    }
-
-    @Override
-    public void shutdownStarted()
-    {
-        _executor.shutdown();
-    }
-
-
-    private class CheckForWorkflowCompletionsRunnable implements Runnable
-    {
-        @Override
-        public void run()
-        {
-            int size = _pendingCompletionFiles.size();
-
-            if (size > 0)
-            {
-                LOG.info("Checking for completion of {} analys{}", size, 1 == size ? "is" : "es");
-
-                // TODO: with Java 21 this should be moved to an autoclosable
-                HttpClient client = HttpClient.newHttpClient();
-
-                for (FileLike file : _pendingCompletionFiles)
-                {
-                    if (file.exists())
-                    {
-                        try
-                        {
-                            // Load analysis properties
-                            Properties props = GenotypingManager.get().readProperties(file.getParent());
-
-                            // POST to the provided URL to signal LabKey Server that the workflow is complete
-                            String url = (String) props.get("url");
-                            String analysisId = (String) props.get("analysis");
-                            LOG.info("Detected completion file for analysis {}; attempting to signal LabKey Server at {}", analysisId, url);
-
-                            HttpRequest request = HttpRequest.newBuilder()
-                                    .uri(URI.create(url))
-                                    .POST(HttpRequest.BodyPublishers.noBody())
-                                    .build();
-                            BodyHandler<String> bodyHandler = HttpResponse.BodyHandlers.ofString(StandardCharsets.UTF_8);
-                            HttpResponse<String> response = client.send(request, bodyHandler);
-                            String message = response.body();
-
-                            LOG.info("LabKey response to analysis {} completion: \"{}\"", analysisId, message);
-                        }
-                        catch (Throwable t)
-                        {
-                            LOG.error("Exception while completing {}", file.toNioPathForRead().toAbsolutePath(), t);
-                        }
-                        finally
-                        {
-                            _pendingCompletionFiles.remove(file);
-                        }
-                    }
-                }
-            }
-        }
-    }
-}
diff --git a/genotyping/src/org/labkey/genotyping/view/analyze.jsp b/genotyping/src/org/labkey/genotyping/view/analyze.jsp
deleted file mode 100644
index 0bc9e449..00000000
--- a/genotyping/src/org/labkey/genotyping/view/analyze.jsp
+++ /dev/null
@@ -1,195 +0,0 @@
-<%
-/*
- * Copyright (c) 2010-2016 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-%>
-<%@ page import="org.labkey.api.query.CustomView" %>
-<%@ page import="org.labkey.api.util.Pair" %>
-<%@ page import="org.labkey.api.view.template.ClientDependencies" %>
-<%@ page import="org.labkey.genotyping.GenotypingController" %>
-<%@ page import="org.labkey.genotyping.GenotypingController.AnalyzeBean" %>
-<%@ page import="java.io.IOException" %>
-<%@ page import="java.util.Map" %>
-<%@ page import="java.util.SortedSet" %>
-<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
-<%@ page extends="org.labkey.api.jsp.JspBase" %>
-<%!
-    @Override
-    public void addClientDependencies(ClientDependencies dependencies)
-    {
-        dependencies.add("clientapi/ext3");
-    }
-%>
-<%
-    AnalyzeBean bean = (AnalyzeBean)getModelBean();
-
-// ext-all.css hard-codes a white background, we want transparent instead  %>
-<style type="text/css">
-    .x-panel-body{background-color: transparent;}
-</style>
-<labkey:errors/>
-<div id="form"></div>
-
-<script type="text/javascript" nonce="<%=getScriptNonce()%>">
-    var samples = [
-<%
-    String sep = "";
-
-    for (Map.Entry<Integer, Pair<String, String>> e : bean.getSampleMap().entrySet())
-    {
-        out.print(unsafe(sep));
-        out.print(unsafe("        ["));
-        out.print(q(String.valueOf(e.getKey())));
-        out.print(unsafe(", "));
-        out.print(q(e.getValue().getKey()));
-        out.print(unsafe(", "));
-        out.print(q(e.getValue().getValue()));
-        out.print(unsafe("]"));
-
-        sep = ",\n";
-    }
-%>
-    ];
-
-var sampleStore = new Ext.data.SimpleStore({
-    fields:['key', 'name', 'species'],
-    data:samples
-});
-
-var views = [
-<%
-    sep = "";
-
-    SortedSet<CustomView> views = bean.getSequencesViews();
-
-    // Add [default] view even if it hasn't been customized, #11110
-    if (views.isEmpty() || null != views.first().getName())
-        sep = addViewName(out, null, sep);
-
-    // Add all the defined custom views
-    for (CustomView view : bean.getSequencesViews())
-        sep = addViewName(out, view.getName(), sep);
-%><%!
-    private String addViewName(JspWriter out, String viewName, String sep) throws IOException
-    {
-        out.print(unsafe(sep));
-        viewName = (null == viewName ? GenotypingController.DEFAULT_VIEW_PLACEHOLDER : viewName);
-        out.print(unsafe("        [" + q(viewName) + "]"));
-        return ",\n";
-    }
-%>
-    ];
-
-var seqViews = new Ext.data.SimpleStore({
-    fields:['name'],
-    data:views
-});
-
-var sequencesViewCombo = new Ext.form.ComboBox({fieldLabel:'Reference Sequences', mode:'local', store:seqViews, valueField:'name', displayField:'name', allowBlank:false, hiddenName:'sequencesView', editable:false, triggerAction:'all'});
-var selectedSamples = new Ext.form.TextField({name:'samples', hidden:true});
-var description = new Ext.form.TextArea({name:'description', fieldLabel:'Description', width:600, height:200, resizable:true, autoCreate:{tag:"textarea", style:"font-family:'Courier'", autocomplete:"off", wrap:"off"}});
-
-var selModel = new Ext.grid.CheckboxSelectionModel();
-
-// create the table grid
-var samplesGrid = new Ext.grid.GridPanel({
-    fieldLabel:'Samples',
-    title:'&nbsp;',
-    store: sampleStore,
-    columns: [
-        selModel,
-        {id:'name', width: 160, sortable: false, dataIndex: 'name'},
-        {id:'species', width: 160, sortable: false, dataIndex: 'species'}
-    ],
-    stripeRows: true,
-    collapsed: true,
-    collapsible: true,
-    autoExpandColumn: 'name',
-    autoHeight: true,
-    width: 600,
-    selModel: selModel
-});
-
-var f = new LABKEY.ext.FormPanel({
-    width:955,
-    labelWidth:150,
-    border:false,
-    standardSubmit:true,
-    items:[
-        sequencesViewCombo,
-        samplesGrid,
-        description,
-        selectedSamples
-    ],
-    buttons:[{text:'Submit', type:'submit', handler:submit}, {text:'Cancel', handler:function() {document.location = <%=q(bean.getReturnUrl())%>;}}],
-    buttonAlign:'left'
-});
-
-Ext.onReady(function()
-{
-    samplesGrid.on('viewready', initializeSelection);
-    f.render('form');
-});
-
-function initializeSelection()
-{
-    samplesGrid.selModel.selectAll();
-    updateGridTitle();
-    samplesGrid.on('expand', updateGridTitle);
-    samplesGrid.on('collapse', updateGridTitle);
-    selModel.addListener('rowselect', updateGridTitle);
-    selModel.addListener('rowdeselect', updateGridTitle);
-}
-
-function submit()
-{
-    var value = '';
-    var sep = '';
-    samplesGrid.selModel.each(function(record) {
-            value = value + sep + record.get('key');
-            sep = ',';
-        });
-    selectedSamples.setValue(value);
-
-    f.getForm().submit();
-}
-
-function updateGridTitle()
-{
-    var title;
-    var selectedCount = samplesGrid.selModel.getCount();
-
-    if (selectedCount == sampleStore.getCount())
-    {
-        title = "All (" + selectedCount + ") samples";
-    }
-    else
-    {
-        if (0 == selectedCount)
-            title = "No samples";
-        else if (1 == selectedCount)
-            title = "1 sample";
-        else
-            title = selectedCount + " samples";
-    }
-
-    title += " will be analyzed";
-
-    if (samplesGrid.collapsed)
-        title += "; click + to change the samples to submit";
-
-    samplesGrid.setTitle(title);
-}
-</script>
diff --git a/genotyping/src/org/labkey/genotyping/view/configure.jsp b/genotyping/src/org/labkey/genotyping/view/configure.jsp
index 8b002b7c..8cffe2e2 100644
--- a/genotyping/src/org/labkey/genotyping/view/configure.jsp
+++ b/genotyping/src/org/labkey/genotyping/view/configure.jsp
@@ -116,9 +116,6 @@
         <tr><td colspan="3"><span style="color:green;"><%=h(form.getMessage())%></span></td></tr>
         <tr><td colspan=3>&nbsp;</td></tr>
         <%  } %>
-        <tr><td><b>Configure Galaxy</b></td></tr>
-        <tr><td>Galaxy server home page URL</td><td><input size="40" name="galaxyURL" value="<%=h(form.getGalaxyURL())%>"></td></tr>
-        <tr><td>&nbsp;</td></tr>
         <tr><td><b>Configure Genotyping Queries</b></td></tr>
         <tr>
             <td>External source of DNA reference sequences&nbsp;&nbsp;</td>
diff --git a/genotyping/src/org/labkey/genotyping/view/importReads.jsp b/genotyping/src/org/labkey/genotyping/view/importReads.jsp
index 66ec423d..9be3bdea 100644
--- a/genotyping/src/org/labkey/genotyping/view/importReads.jsp
+++ b/genotyping/src/org/labkey/genotyping/view/importReads.jsp
@@ -71,7 +71,6 @@
             <input type="hidden" name="platform" value="<%=bean.getPlatform()%>">
             <input type="hidden" name="pipeline" value="1">
             <input type="hidden" name="readsPath" value="<%=h(bean.getReadsPath())%>">
-            <input type="hidden" name="analyze" value="0">
         </td></tr>
         <tr><td><%= button("Import Reads").submit(true) %>
             <%=platform == SEQUENCE_PLATFORMS.LS454 ? button("Import Reads And Analyze").submit(true).onClick("document.importReads.analyze.value=1;") : HtmlString.EMPTY_STRING%>
diff --git a/genotyping/src/org/labkey/genotyping/view/mySettings.jsp b/genotyping/src/org/labkey/genotyping/view/mySettings.jsp
deleted file mode 100644
index c54465f9..00000000
--- a/genotyping/src/org/labkey/genotyping/view/mySettings.jsp
+++ /dev/null
@@ -1,53 +0,0 @@
-<%
-/*
- * Copyright (c) 2010-2014 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-%>
-<%@ page import="org.labkey.api.util.URLHelper"%>
-<%@ page import="org.labkey.genotyping.GenotypingController" %>
-<%@ page import="org.labkey.genotyping.GenotypingController.MySettingsAction" %>
-<%@ page import="org.labkey.genotyping.galaxy.GalaxyFolderSettings" %>
-<%@ page import="org.labkey.genotyping.galaxy.GalaxyManager" %>
-<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
-<%@ page extends="org.labkey.api.jsp.JspBase" %>
-<%
-    GenotypingController.MySettingsForm form = (GenotypingController.MySettingsForm)getModelBean();
-    GalaxyFolderSettings settings = GalaxyManager.get().getSettings(getContainer());
-    String serverURL = settings.getGalaxyURL();
-    String preferencesHTML = "the API Keys page";
-
-    // Make it a link if admin has set the Galaxy URL
-    if (null != serverURL)
-    {
-        URLHelper userURL = new URLHelper((serverURL.endsWith("/") ? serverURL : serverURL + "/") + "user/api_keys");
-        preferencesHTML = "<a href=\"" + h(userURL.getURIString()) + "\" target=\"pref\">" + preferencesHTML + "</a>";
-    }
-%>
-<labkey:form action="<%=urlFor(MySettingsAction.class)%>" method="post">
-    <table>
-        <%=formatMissedErrorsInTable("form", 2)%>
-        <tr>
-            <td colspan="2" width="600px">
-            You need to provide a Galaxy web API key to send data from LabKey to your Galaxy server. Galaxy generates a
-            unique web API key for each user and uses it to authorize every call to the Galaxy web API. You can find or
-            generate a key by logging into Galaxy and visiting <%=unsafe(preferencesHTML)%>. Copy the 32-character hexadecimal
-            string and paste it in the box below.
-            </td>
-        <tr><td>&nbsp;</td></tr>
-        <tr><td>Galaxy web API key</td><td><input size="40" name="galaxyKey" value="<%=h(form.getGalaxyKey())%>"></td></tr>
-        <tr><td>&nbsp;</td></tr>
-        <tr><td><%= button("Submit").submit(true) %> <%= button("Cancel").href(form.getReturnUrlHelper()) %><%=generateReturnUrlFormField(form)%></td></tr>
-    </table>
-</labkey:form>
diff --git a/genotyping/src/org/labkey/genotyping/view/overview.jsp b/genotyping/src/org/labkey/genotyping/view/overview.jsp
index d9fec53a..ec3c4fae 100644
--- a/genotyping/src/org/labkey/genotyping/view/overview.jsp
+++ b/genotyping/src/org/labkey/genotyping/view/overview.jsp
@@ -99,8 +99,7 @@
     </td></tr>
 
     <tr><td colspan="3" class="labkey-announcement-title"><span>Settings</span></td></tr>
-    <tr><td colspan="3" class="labkey-title-area-line"></td></tr>
-    <tr><td></td><td><%=link("My Settings", GenotypingController.getMySettingsURL(c, getActionURL()))%></td></tr><%
+    <tr><td colspan="3" class="labkey-title-area-line"></td></tr><%
     if (c.hasPermission(user, AdminPermission.class))
     {
     %>
diff --git a/genotyping/test/src/org/labkey/test/tests/GenotypingBaseTest.java b/genotyping/test/src/org/labkey/test/tests/GenotypingBaseTest.java
index 61e065b4..815f3c2f 100644
--- a/genotyping/test/src/org/labkey/test/tests/GenotypingBaseTest.java
+++ b/genotyping/test/src/org/labkey/test/tests/GenotypingBaseTest.java
@@ -90,17 +90,11 @@ protected void configureAdmin(boolean configureSequences)
                 _extHelper.waitForExt3MaskToDisappear(WAIT_FOR_JAVASCRIPT);
             }
         }
+        clickButton("Submit");
         if (configureSequences)
         {
-            setFormElement(Locator.name("galaxyURL"), "http://galaxy.labkey.org:8080");
-            clickButton("Submit");
             clickButton("Load Sequences");
-
-            log("Configure Galaxy Server Key");
-            clickAndWait(Locator.linkWithText("My Settings"));
-            setFormElement(Locator.name("galaxyKey"), "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa");
         }
-        clickButton("Submit");
     }
 
     @Override
diff --git a/genotyping/test/src/org/labkey/test/tests/GenotypingTest.java b/genotyping/test/src/org/labkey/test/tests/GenotypingTest.java
index 32d6c074..f7d3e09c 100644
--- a/genotyping/test/src/org/labkey/test/tests/GenotypingTest.java
+++ b/genotyping/test/src/org/labkey/test/tests/GenotypingTest.java
@@ -25,8 +25,6 @@
 import org.labkey.test.categories.OConnor;
 import org.openqa.selenium.NoSuchElementException;
 
-import java.io.File;
-
 @Category({CustomModules.class, OConnor.class})
 @BaseWebDriverTest.ClassTimeout(minutes = 9)
 public class GenotypingTest extends GenotypingBaseTest
@@ -34,8 +32,6 @@ public class GenotypingTest extends GenotypingBaseTest
     public static final String first454importNum = "207";
     public static final String second454importNum = "208";
 
-    protected int runNum = 0; //this is globally unique, so we need to retrieve it every time.
-
     @Override
     protected String getProjectName()
     {
@@ -65,9 +61,7 @@ public void testSteps()
     {
         //TODO: need to fix 454/genotyping tests
         importRunTest();
-        runAnalysisTest();
         importSecondRunTest();
-        verifyAnalysis();
     }
 
     private void importSecondRunTest()
@@ -95,65 +89,6 @@ private void importRunAgainTest()
         }
     }
 
-    private void runAnalysisTest()
-    {
-        sendDataToGalaxyServer();
-        receiveDataFromGalaxyServer();
-    }
-
-    private void verifyAnalysis()
-    {
-        goToProjectHome();
-
-        clickAndWait(Locator.linkWithText("View Analyses"));
-        clickAndWait(Locator.linkWithText("" + getRunNumber()));  // TODO: This is probably still too permissive... need a more specific way to get the run link
-
-        assertTextPresent("Reads", "Sample Id", "Percent", "TEST09");
-        assertElementPresent(Locator.paginationText(1, 100, 1410));
-    }
-
-    private void receiveDataFromGalaxyServer()
-    {
-        String[] filesToCopy = {"matches.txt", "analysis_complete.txt"};
-        String analysisFolder = "analysis_" + getRunNumber();
-        for (String file: filesToCopy)
-        {
-            copyFile(new File(getPipelineLoc(), file), new File(getPipelineLoc(), analysisFolder + "/" + file));
-        }
-        refresh();
-        waitForPipelineJobsToComplete(++pipelineJobCount, "Import genotyping analysis", false);
-    }
-
-    private int getRunNumber()
-    {
-        return runNum;
-    }
-
-    private void sendDataToGalaxyServer()
-    {
-        clickButton("Add Analysis");
-        _extHelper.selectComboBoxItem("Reference Sequences:", "[default]");                       //TODO:  this should be cyno
-        clickButton("Submit");
-        waitForPipelineJobsToComplete(++pipelineJobCount, "Submit genotyping analysis", false);
-        findAndSetAnalysisNumber();
-
-    }
-
-    private void findAndSetAnalysisNumber()
-    {
-        Locator l = Locator.tagContainingText("td", "Submit genotyping analysis");
-        isElementPresent(l);
-        getText(l);
-        String[] temp = getText(l).split(" ");
-        setAnalysisNumber(Integer.parseInt(temp[temp.length-1]));
-
-    }
-
-    private void setAnalysisNumber(int i)
-    {
-        runNum = i;
-    }
-
     private void importRunTest()
     {
         log("import genotyping run");
@@ -183,6 +118,5 @@ private void startImportRun(String file, String importAction, String associatedR
         _fileBrowserHelper.importFile(file, importAction);
         selectOptionByText(Locator.name("run"), associatedRun);
         clickButton("Import Reads");
-
     }
 }