[codex] Add ForestMamba Galaxy wrapper - #5
Draft
kgerb wants to merge 20 commits into
Draft
Conversation
Add 3Dtrees forest segmentation tool based on RayCloudTools
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Remove links assuming that those tools are installed in other Galaxy instances.
kgerb
force-pushed
the
codex/forestmamba-galaxy-wrapper
branch
from
June 22, 2026 20:06
aff3458 to
79b7518
Compare
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Adds a Galaxy wrapper for ForestMamba under
tools/3dtrees_forestmamba.forestmamba.xmlmodeled after the existing 3Dtrees SegmentAnyTree wrapper1.0.0+galaxy0forestmamba-3dtrees-runtime-readable:latestfor now/workspace/src/run.pywith parameters from the Galaxy XMLCUDA_VISIBLE_DEVICES; GPU allocation is left to the Galaxy/runtime schedulermikro.lazas test data and a deterministic missing-checkpoint failure testVisible Parameters
0runs normal one-pass inference;2enables the dense-forest bluepoint flow.instance_pred == -1required before the second bluepoint pass runs. Default0.01means more than 1%.WANDB_MODE=disabledis set internally to prevent upstream Weights & Biases experiment logging during Galaxy jobs.Related PRs
Validation
xml.etree.ElementTreeplanemo lint tools/3dtrees_forestmamba/forestmamba.xmlpassedRuntime Note
A GPU0 Docker run against
mikro.lazwas attempted withforestmamba-3dtrees-runtime-readable:latest, but Docker startup/exec hung before the wrapper command produced output. The GPU test still needs to be rerun once the local Docker runtime is responsive.