Unverified Commit 32312418 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

add .signularity_in2p3 folder to fix lock problem in nf

parent 3192a86d
......@@ -5,11 +5,12 @@ fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|container = "|container =
fd ".*config" -E "nf_modules" src/ -x perl -pe 's|container = "lbmc/file://bin/(.*).img"|container = "lbmc/\1"|g' -i {}
# update singularity config
fd ".*config" -E "nf_modules" src/ -x perl -0776pe 's|\n\s*singularity {\n\s*singularity.enabled = true|\n singularity {\n singularity.enabled = true\n singularity.cacheDir = "./bin/"|mg' -i {}
fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|\n\s*singularity {\n\s*singularity.enabled = true|\n singularity {\n singularity.enabled = true\n singularity.cacheDir = "./bin/"|mg' -i {}
# update in2p3 config
fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|\n\s*ccin2p3 {\n\s*singularity.enabled = true|\n ccin2p3 {\n singularity.enabled = true\n singularity.cacheDir = "/sps/lbmc/common/singularity/"|mg' -i {}
fd ".*config" src/ -x perl -pe 's|container = "lbmc//sps/lbmc/common/singularity/(.*).img"|container = "lbmc/\1"|g' -i {}
fd ".*config" src/ -x perl -0777pe 's|singularity.cacheDir = "/sps/lbmc/common/singularity/"|singularity.cacheDir = "\$baseDir/.src/singularity_in2p3/"|mg' -i {}
# we remove the ccin2p3_conda section
fd ".*config" -E "nf_modules" src/ -x perl -0777pe "s|\s*ccin2p3_conda {.*ccin2p3 {\n|\n ccin2p3 {\n|msg" -i {}
......
......@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fasta_from_bed {
......
......@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
......
......@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
......
......@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
......
......@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
......
......@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
......
......@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
......
......@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
......
......@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: mapping_fastq {
......
......@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: adaptor_removal {
......
......@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: adaptor_removal {
......
......@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: trimming {
......
......@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: trimming {
......
......@@ -55,7 +55,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_bam {
......
......@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: compute_matrix {
......
......@@ -36,7 +36,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: plot_profile {
......
......@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastp_fastq {
......
......@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastp_fastq {
......
......@@ -35,7 +35,7 @@ profiles {
}
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
singularity.cacheDir = "$baseDir/.src/singularity_in2p3/"
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: fastqc_fastq {
......
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