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Adding fix for LD_LIBRARY_PATH in singularity mode #4347

Merged
merged 10 commits into from
Nov 16, 2023
Merged

Adding fix for LD_LIBRARY_PATH in singularity mode #4347

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a1fb85b
Adding fix for LD_LIBRARY_PATH in singularity mode
asp8200 Nov 16, 2023
3c9c09b
Update modules/nf-core/sentieon/bwamem/main.nf
asp8200 Nov 16, 2023
2e584bd
Only modify LD_LIBRARY_PATH when in singularity mode
asp8200 Nov 16, 2023
6800586
Update modules/nf-core/sentieon/bwamem/main.nf
asp8200 Nov 16, 2023
5b4a59a
Merge branch 'master' into bioconda_sentieon
maxulysse Nov 16, 2023
16045d4
Removing redundant empty line
asp8200 Nov 16, 2023
24a006a
Merge branch 'bioconda_sentieon' of https://github.com/nf-core/module…
asp8200 Nov 16, 2023
a1c8c60
Update modules/nf-core/sentieon/bwamem/main.nf
asp8200 Nov 16, 2023
434c6f9
Adding dependencies in environment.ym
asp8200 Nov 16, 2023
28b77e4
Adding comment about fix_ld_library_path
asp8200 Nov 16, 2023
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18 changes: 13 additions & 5 deletions modules/nf-core/sentieon/bwamem/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,11 @@ process SENTIEON_BWAMEM {

secret 'SENTIEON_LICENSE_BASE64'

container 'nf-core/sentieon:202308'
conda "bioconda::sentieon=202308"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/sentieon:202308--h43eeafb_0' :
'biocontainers/sentieon:202308--h43eeafb_0' }"


input:
tuple val(meta), path(reads)
Expand All @@ -21,15 +25,17 @@ process SENTIEON_BWAMEM {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
def sentieon_auth_data_base64 = task.ext.sentieon_auth_data_base64 ?: ''

if (workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container) {
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fix_ld_library_path = 'LD_LIBRARY_PATH=/usr/local/lib/:\$LD_LIBRARY_PATH;export LD_LIBRARY_PATH'
} else {
fix_ld_library_path = ''
}

"""
if [ "\${#SENTIEON_LICENSE_BASE64}" -lt "1500" ]; then # If the string SENTIEON_LICENSE_BASE64 is short, then it is an encrypted url.
export SENTIEON_LICENSE=\$(echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d)
Expand All @@ -47,6 +53,8 @@ process SENTIEON_BWAMEM {
echo "Decoded and exported Sentieon test-license system environment variables"
fi

$fix_ld_library_path

INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`

sentieon bwa mem \\
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