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Deeparg singularity container fix 2 (#1406)

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* fix: remove left-over unnecessary code

* Switch to more portable solution for singularity container issue by using bind paths

* Fix input collision of dummy files

* Repalce dummy with which bash

* Remove dummy usage from tests

* Apply suggestions from code review

* Fix singularity typo
This commit is contained in:
James A. Fellows Yates 2022-03-18 16:21:55 +01:00 committed by GitHub
parent ea41a8a6f7
commit 15c7190e22
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5 changed files with 10 additions and 10 deletions
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6
modules/deeparg/downloaddata/main.nf
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@ -8,10 +8,10 @@ process DEEPARG_DOWNLOADDATA {
'https://depot.galaxyproject.org/singularity/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!
We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
Original report: https://github.com/nf-core/funcscan/issues/23
*/
containerOptions { "${workflow.containerEngine}" == 'singularity' ? '--fakeroot' : '' }
containerOptions { "${workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' }
input:

2
modules/deeparg/downloaddata/meta.yml
View file

@ -17,7 +17,7 @@ tools:
licence: ["MIT"]
input:
- none: There is no input. This module downloads a pre-built database for use with deepARG.
- none: No input required for download module.
output:
- versions:

8
modules/deeparg/predict/main.nf
View file

@ -6,13 +6,13 @@ process DEEPARG_PREDICT {
conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity//deeparg:1.0.2--pyhdfd78af_1' :
'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' :
'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }"
/*
We have to force singularity to run with --fakeroot to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
This flag may not be available on all systems and may be considered a security problem. so please document and /or warn for this in your pipeline!
We have to force singularity to run with -B to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
Original report: https://github.com/nf-core/funcscan/issues/23
*/
containerOptions { "${workflow.containerEngine}" == 'singularity' ? '--fakeroot' : '' }
containerOptions { "${workflow.containerEngine}" == 'singularity' ? '-B $(which bash):/usr/local/lib/python2.7/site-packages/Theano-0.8.2-py2.7.egg-info/PKG-INFO' : '' }
input:
tuple val(meta), path(fasta), val(model)