rampart ecoli_full_job.xml getting error with rampart 0.12.0

[jerowe]

Hello,

Here is the output:

[jillian@login-0-2 example_job_configs]$ rampart ecoli_full_job.xml
2015-10-11 10:39:02 INFO RampartCLI:227 - RAMPART Version: 0.12.0
2015-10-11 10:39:02 INFO RampartCLI:228 - Output dir: /scratch/jillian/source/rampart/rampart-0.12.0/etc/example_job_configs
2015-10-11 10:39:02 INFO RampartCLI:229 - Environment configuration file: /share/apps/NYUAD/rampart/gcc_4.9.1/0.12.0/etc/conan.properties
2015-10-11 10:39:02 INFO RampartCLI:230 - Logging properties file: /share/apps/NYUAD/rampart/gcc_4.9.1/0.12.0/etc/log4j.properties
2015-10-11 10:39:02 INFO RampartCLI:231 - Job Prefix: RAMPART20151011_103902
2015-10-11 10:39:02 INFO ConanProperties:145 - Loaded Conan properties from /share/apps/NYUAD/rampart/gcc_4.9.1/0.12.0/etc/conan.properties
2015-10-11 10:39:02 INFO RampartCLI:240 - Executing the following stages: MECQ,MECQ_ANALYSIS,KMER_CALC,MASS,MASS_ANALYSIS,MASS_SELECT,AMP,AMP_ANALYSIS,FINALISE,COLLECT
2015-10-11 10:39:02 INFO RampartCLI:243 - Parsing configuration file: /scratch/jillian/source/rampart/rampart-0.12.0/etc/example_job_configs/ecoli_full_job.xml
2015-10-11 10:39:02 INFO RampartConfig:134 - Found libraries element containing 1 libraries.
2015-10-11 10:39:02 INFO RampartConfig:135 - Running in single sample mode
Error validating XML Element: pipeline; Found unexpected child node: analyse_reads
uk.ac.tgac.conan.core.util.XmlHelper.validate(XmlHelper.java:170)
uk.ac.tgac.rampart.RampartPipeline$Args.(RampartPipeline.java:171)
uk.ac.tgac.rampart.RampartConfig.internalParseXml(RampartConfig.java:154)
uk.ac.tgac.conan.core.util.AbstractXmlJobConfiguration.parseXml(AbstractXmlJobConfiguration.java:103)
uk.ac.tgac.rampart.RampartCLI.initialise(RampartCLI.java:244)
uk.ac.tgac.rampart.RampartCLI.main(RampartCLI.java:452)

Best,
Jillian

[maplesond]

The problem is caused by out-of-date example configuration files. I've updated the interface since they were made. The head of the develop branch (commit: 15ebd4d) contains the latest configuration files.