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Add new SPRAS image and handle unpacked singularity images #145

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merged 30 commits into from
Jul 1, 2024
+444 −29
Merged

Add new SPRAS image and handle unpacked singularity images #145

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3e9800e
Add ability to unpack singularity images
jhiemstrawisc Feb 12, 2024
3dc73bc
Bump missed python versions
jhiemstrawisc Feb 12, 2024
21a8313
Bump more version
jhiemstrawisc Feb 12, 2024
b181448
Fix bad config parsing
jhiemstrawisc Feb 12, 2024
d3ee175
Make spras.sh run on as many cores as it can
jhiemstrawisc Feb 12, 2024
ddfa66c
Add check for already-unpacked sing images
jhiemstrawisc Feb 12, 2024
85d5e90
Update htcondor memory based on observed usage
jhiemstrawisc Feb 12, 2024
2a64269
Update testing documentation
jhiemstrawisc Feb 13, 2024
0f775e7
Update more 'zip' funcs to make linter happy
jhiemstrawisc Feb 13, 2024
a21cfab
Update package versions
jhiemstrawisc Feb 28, 2024
fee6b6c
Add __init__.py to test dirs
jhiemstrawisc Feb 28, 2024
3b17802
Add unpack sing test
jhiemstrawisc Feb 28, 2024
3061324
Update unpack test outfile to make unique
jhiemstrawisc Feb 28, 2024
67878d1
Add warning about cleaning up sing images to config.yaml
jhiemstrawisc Mar 15, 2024
10e2a5f
Update a few items based on review feedback
jhiemstrawisc Mar 18, 2024
d7c1536
Update SPRAS version to 0.1.0
jhiemstrawisc Mar 21, 2024
165710e
Update submit file and job wrapper
jhiemstrawisc Jun 28, 2024
4d2a1ca
Revert submit file container
jhiemstrawisc Jun 28, 2024
30c8d4a
Update Dockerfile and installation versions
jhiemstrawisc Jun 28, 2024
e3f981c
Update spras.sh to work with directories
jhiemstrawisc Jun 28, 2024
8265de2
Update SPRAS container README
jhiemstrawisc Jun 28, 2024
e017273
More SPRAS image README updates
jhiemstrawisc Jun 28, 2024
de8a8fc
Update spras.sub to include .sif replacement as comment
jhiemstrawisc Jun 28, 2024
b4c9748
Update SPRAS cont README with when to use .sif in submit file
jhiemstrawisc Jun 28, 2024
ef1e526
Update spras.sub to include snakemake job retries
jhiemstrawisc Jun 28, 2024
606de01
Fix typos and add clarity to READMEs based on feedback
jhiemstrawisc Jul 1, 2024
0184cea
Update spras.sub according to feedback
jhiemstrawisc Jul 1, 2024
dd444da
Revert Pandas version in pyproject.toml after finding NumPy version bug
jhiemstrawisc Jul 1, 2024
f78bf71
Update various zip functions' flag to True
jhiemstrawisc Jul 1, 2024
6cee79f
Add SPRAS docker build to CI workflows
jhiemstrawisc Jul 1, 2024
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Revert submit file container
@jhiemstrawisc
jhiemstrawisc committed Jul 1, 2024
commit 4d2a1ca39355a5d5d76d13343697600d2a3b15f5
3 changes: 1 addition & 2 deletions docker-wrappers/SPRAS/spras.sub
View file
Original file line number Diff line number Diff line change
@@ -16,8 +16,7 @@ NUM_PROCS = 4
# `unpack_singularity = true`. #
############################################################
universe = container
#container_image = docker://reedcompbio/spras:v0.1.0
container_image = docker://jhiemstra/spras:with-uid-v4
container_image = docker://reedcompbio/spras:v0.1.0

############################################################
# Specify names for log/stdout/stderr files generated by #