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Fix DeepARG depenency issue with singularity containers (#1397)

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* fix: remove left-over unnecessary code

* Adds --fakeroot option for singularity usage with DeepARG as workaround for broken conda dependency

* Update modules/deeparg/downloaddata/main.nf

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>

* Update modules/deeparg/predict/main.nf

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>

* Apply suggestions from code review

* Update main.nf

* Update main.nf

* Update main.nf

* Update main.nf

* Go back to original logic

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
This commit is contained in:
James A. Fellows Yates 2022-03-17 13:08:51 +01:00 committed by GitHub
parent df60a58426
commit f469045a95
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2 changed files with 11 additions and 0 deletions
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6
modules/deeparg/downloaddata/main.nf
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@ -7,6 +7,12 @@ process DEEPARG_DOWNLOADDATA {
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' : 'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' :
'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }" 'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }"
/*
We have to force singularity to run with --fakeroot to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
This flag may not be available on all systems and may be considered a security problem. so please document and /or warn for this in your pipeline!
*/
containerOptions { "${workflow.containerEngine}" == 'singularity' ? '--fakeroot' : '' }
input: input:

5
modules/deeparg/predict/main.nf
View file

@ -8,6 +8,11 @@ process DEEPARG_PREDICT {
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity//deeparg:1.0.2--pyhdfd78af_1' : 'https://depot.galaxyproject.org/singularity//deeparg:1.0.2--pyhdfd78af_1' :
'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }" 'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }"
/*
We have to force singularity to run with --fakeroot to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
This flag may not be available on all systems and may be considered a security problem. so please document and /or warn for this in your pipeline!
*/
containerOptions { "${workflow.containerEngine}" == 'singularity' ? '--fakeroot' : '' }
input: input:
tuple val(meta), path(fasta), val(model) tuple val(meta), path(fasta), val(model)