85 lines
3.6 KiB
Bash
Executable file
85 lines
3.6 KiB
Bash
Executable file
#!/bin/bash
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# the job assumes that it is a good idea to run everything in PWD
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# the job manager should make sure that is true
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# fail whenever something is fishy, use -x to get verbose logfiles
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set -e -u -x
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dssource="$1"
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pushgitremote="$2"
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subd="$3"
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subid=$(basename $3)
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# get the analysis dataset, which includes the inputs as well
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# importantly, we do not clone from the lcoation that we want to push the
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# results too, in order to avoid too many jobs blocking access to
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# the same location and creating a throughput bottleneck
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datalad clone "${dssource}" ds
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# all following actions are performed in the context of the superdataset
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cd ds
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# in order to avoid accumulation temporary git-annex availability information
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# and to avoid a syncronization bottleneck by having to consolidate the
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# git-annex branch across jobs, we will only push the main tracking branch
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# back to the output store (plus the actual file content). Final availability
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# information can be establish via an eventual "git-annex fsck -f cat12.8.1_out-storage".
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# this remote is never fetched, it accumulates a larger number of branches
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# and we want to avoid progressive slowdown. Instead we only ever push
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# a unique branch per each job (subject AND process specific name)
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git remote add outputstore "$pushgitremote"
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# all results of this job will be put into a dedicated branch
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git checkout -b "job-${JOBID}"
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# we pull down the input subject manually in order to discover relevant
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# files. We do this outside the recorded call, because on a potential
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# re-run we want to be able to do fine-grained recomputing of individual
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# outputs. The recorded calls will have specific paths that will enable
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# recomputation outside the scope of the original Condor setup
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datalad get -n "inputs/ABIDE2/${subd}"
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# the meat of the matter
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# look for T1w files in the input data for the given participant
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# it is critical for reproducibility that the command given to
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# "containers-run" does not rely on any property of the immediate
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# computational environment (env vars, services, etc)
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find \
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inputs/ABIDE2/${subd} \
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-name "${subid}*T1w.nii.gz" \
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-exec sh -c '
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odir=$(echo {} | cut -d / -f3-5);
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datalad containers-run \
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-m "Compute $odir" \
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-n cat12-8-1\
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--explicit \
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-o $odir \
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-i {} \
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sh -e -u -x -c "
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rm -rf {outputs[0]} ;
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mkdir -p {outputs[0]} \
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&& cp {inputs[0]} {outputs[0]} \
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&& /singularity -b code/cat_standalone_segment_enigma_subdir_rp_MSA.m {outputs[0]}/*.nii.gz \
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&& /singularity -b code/pipeline/batches/cat_standalone_batch-surfext.m {outputs[0]}/surf/lh.central.* \
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&& /singularity -b code/pipeline/batches/cat_standalone_batch-thick1.m {outputs[0]}/surf/lh.thickness.* \
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&& /singularity -b code/pipeline/batches/cat_standalone_batch-thick2.m {outputs[0]}/surf/lh.thickness.* \
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&& rm -f {outputs[0]}/*.nii* \
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&& gzip {outputs[0]}/*/*.nii \
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" \
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' \;
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# remove big files from results after hashing before pushing to ria
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datalad drop --what filecontent --reckless kill */sub-*/*/mri/iy* */sub-*/*/mri/y* */sub-*/*/mri/anon_m* */sub-*/*/*/*.pdf */sub-*/*/surf/*sphere*
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#### Maybe remove simlinks without data and commit ???
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# rm -f */sub-*/*/mri/iy* */sub-*/*/mri/y* # */sub-*/*/mri/anon_m* */sub-*/*/*/*.pdf # */sub-*/*/surf/*sphere*
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# datalad save -m "remove simlinks without data"
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# file content first -- does not need a lock, no interaction with Git
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datalad push --to cat12.8.1_out-storage
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# and the output branch
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flock --verbose $DSLOCKFILE git push outputstore
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echo SUCCESS
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# job handler should clean up workspace
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