diff options
Diffstat (limited to 'deploy/CWL/run-common-workflow-language.org')
| -rw-r--r-- | deploy/CWL/run-common-workflow-language.org | 62 |
1 files changed, 60 insertions, 2 deletions
diff --git a/deploy/CWL/run-common-workflow-language.org b/deploy/CWL/run-common-workflow-language.org index 7ce8ddc..9658879 100644 --- a/deploy/CWL/run-common-workflow-language.org +++ b/deploy/CWL/run-common-workflow-language.org @@ -55,13 +55,71 @@ local version to skip IPFS). Make sure your PATH points to all the tools and : cwltool --no-container Workflows/test-workflow.cwl Jobs/local-small.ERR034597.test-workflow.yml + +in the first run gives an error: ERROR 'fastqc' not found. We need to +add the tool to the environment. For this I created a file .guix-deploy +in the root of the repo: + +: cat .guix-deploy +: env GUIX_PACKAGE_PATH=.:~/iwrk/opensource/guix/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C guix --ad-hoc cwltool trimmomatic-jar bwa fastqc go-ipfs curl --network + +You can see it requires the guix-bioinformatics, so you may need to clone +that repo first. Next start the Guix container: + +: . ./guix-deploy +: cwltool --no-container Workflows/test-workflow.cwl Jobs/local-small.ERR034597.test-workflow.yml + +Now the workflow should run fastq. When it works it should say + : <lots of output> : INFO Final process status is success -Note that I hard coded two paths which you need to point to your Guix +The current workflow is only working partly. It now complains with + +ILLUMINACLIP:/gnu/store/v2jys382g6j5b7lsxzh8v4vfhd414nhz-profile/lib/share/jar/adapters/TruSeq2-PE.fa:2:40:15. +Error: Unable to access jarfile /gnu/store/v2jys382g6j5b7lsxzh8v4vfhd414nhz-profile/lib/share/jar/trimmomatic-0.38.jar + +This is because I hard coded two paths which you need to point to your Guix profile first: : Tools/trimmomaticPE.cwl: valueFrom: /gnu/store/v2jys382g6j5b7lsxzh8v4vfhd414nhz-profile/lib/share/jar/trimmomatic-0.38.jar : Tools/trimmomaticPE.cwl: valueFrom: 'ILLUMINACLIP:/gnu/store/v2jys382g6j5b7lsxzh8v4vfhd414nhz-profile/lib/share/jar/adapters/TruSeq2-PE.fa:2:40:15' -This is not typical and I should find a proper way to do this ;) +In the container the Guix profile can be found with + +: echo $GUIX_ENVIRONMENT + +Plug it into above values. This is not typical and I should find a +proper way to do this. cwltool has a switch `--preserve-environment +ENVVAR'. After modifying the source by splitting in the GUIX_ENVIROMENT +it worked. + +#+begin_src diff +diff --git a/Tools/trimmomaticPE.cwl b/Tools/trimmomaticPE.cwl +index ed57eb5..aedd23a 100644 +--- a/Tools/trimmomaticPE.cwl ++++ b/Tools/trimmomaticPE.cwl +@@ -55,7 +55,7 @@ outputs: + + arguments: + - position: 1 +- valueFrom: /gnu/store/v2jys382g6j5b7lsxzh8v4vfhd414nhz-profile/lib/share/jar/trimmomatic-0.38.jar ++ valueFrom: /gnu/store/j1ljhxzaxmcqy8v6d4v1y37p48c68f5q-profile/lib/share/jar/trimmomatic-0.38.jar + - position: 2 + valueFrom: PE + - position: 5 +@@ -67,4 +67,4 @@ arguments: + - position: 8 + valueFrom: $(inputs.fq2.basename).trim.2U.fastq + - position: 9 +- valueFrom: 'ILLUMINACLIP:/gnu/store/v2jys382g6j5b7lsxzh8v4vfhd414nhz-profile/lib/share/jar/adapters/TruSeq2-PE.fa:2:40:15' ++ valueFrom: 'ILLUMINACLIP:/gnu/store/j1ljhxzaxmcqy8v6d4v1y37p48c68f5q-profile/lib/share/jar/adapters/TruSeq2-PE.fa:2:40:15' + +#+end_src + +Try + +: . ./guix-deploy +: cwltool --no-container --preserve-environment GUIX_ENVIRONMENT Workflows/test-workflow.cwl Jobs/local-small.ERR034597.test-workflow.yml +: (output) +: INFO Final process status is success |