singularity modules: add /sps /pbs and /scratch for ccin2p3

9737cccf · Laurent Modolo · 09e2b2fc · 9737cccf · 9737cccf · 9737cccf
Verified Commit 9737cccf authored 5 years ago by Laurent Modolo
--- a/src/singularity_modules/bcftools/1.7/bcftools.def
+++ b/src/singularity_modules/bcftools/1.7/bcftools.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 BCFTOOLS_VERSION=1.7
 PACKAGES=bcftools=${BCFTOOLS_VERSION}*


--- a/src/singularity_modules/bedtools/2.25.0/bedtools.def
+++ b/src/singularity_modules/bedtools/2.25.0/bedtools.def
@@ -4,7 +4,8 @@ From: ubuntu:16.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 BEDTOOLS_VERSION=2.25.0
 PACKAGES=bedtools=${BEDTOOLS_VERSION}*


--- a/src/singularity_modules/bioawk/1.0/bioawk.def
+++ b/src/singularity_modules/bioawk/1.0/bioawk.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 BIOAWK_VERSION=1.0
 PACKAGES="git \
   build-essential \

--- a/src/singularity_modules/bowtie/1.2.2/bowtie.def
+++ b/src/singularity_modules/bowtie/1.2.2/bowtie.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 BOWTIE_VERSION=1.2.2
 SAMTOOLS_VERSION=1.7
 PACKAGES="bowtie=${BOWTIE_VERSION}* \

--- a/src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def
+++ b/src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 BOWTIE2_VERSION=2.3.4.1
 SAMTOOLS_VERSION=1.7
 PACKAGES="bowtie2=${BOWTIE2_VERSION}* \

--- a/src/singularity_modules/bwa/0.7.17/bwa.def
+++ b/src/singularity_modules/bwa/0.7.17/bwa.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 BWA_VERSION=0.7.17
 SAMBLASTER_VERSION=0.1.24


--- a/src/singularity_modules/canu/1.6/canu.def
+++ b/src/singularity_modules/canu/1.6/canu.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 CANU_VERSION=1.6
 PACKAGES=canu=${CANU_VERSION}*


--- a/src/singularity_modules/cutadapt/1.14/cutadapt.def
+++ b/src/singularity_modules/cutadapt/1.14/cutadapt.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 CUTADAPT_VERSION=1.14
 PACKAGES="bash \
             python3 \

--- a/src/singularity_modules/cutadapt/1.15/cutadapt.def
+++ b/src/singularity_modules/cutadapt/1.15/cutadapt.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 CUTADAPT_VERSION=1.15
 PACKAGES="bash \
             python3 \

--- a/src/singularity_modules/cutadapt/2.1/cutadapt.def
+++ b/src/singularity_modules/cutadapt/2.1/cutadapt.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 CUTADAPT_VERSION=2.1
 PACKAGES="bash \
             python3 \

--- a/src/singularity_modules/deeptools/3.0.2/deeptools.def
+++ b/src/singularity_modules/deeptools/3.0.2/deeptools.def
@@ -4,7 +4,8 @@ From: debian:stretch
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 DEEPTOOLS_VERSION=3.0.2
 PACKAGES="build-essential \
             python3-pip \

--- a/src/singularity_modules/deeptools/3.1.1/deeptools.def
+++ b/src/singularity_modules/deeptools/3.1.1/deeptools.def
@@ -4,7 +4,8 @@ From: debian:stretch
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 DEEPTOOLS_VERSION=3.1.1
 PACKAGES="build-essential \
             python3-pip \

--- a/src/singularity_modules/fastqc/0.11.5/fastqc.def
+++ b/src/singularity_modules/fastqc/0.11.5/fastqc.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 FASTQC_VERSION=0.11.5
 PACKAGES="fastqc=${FASTQC_VERSION}* \
 perl=5.26*"

--- a/src/singularity_modules/file_handle/0.1.1/file_handle.def
+++ b/src/singularity_modules/file_handle/0.1.1/file_handle.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch

 FILE_HANDLE_VERSION=0.1.1
 PACKAGES="git \

--- a/src/singularity_modules/gatk/4.0.8.1/gatk.def
+++ b/src/singularity_modules/gatk/4.0.8.1/gatk.def
@@ -4,7 +4,8 @@ From: broadinstitute/gatk:4.0.8.1
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch

 GATK_VERSION=4.0.8.1
 cp gatk/gatk /usr/bin/

--- a/src/singularity_modules/hisat2/2.0.0/hisat2.def
+++ b/src/singularity_modules/hisat2/2.0.0/hisat2.def
@@ -4,7 +4,8 @@ From: alpine:3.8
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 SAMTOOLS_VERSION=1.7
 HISAT2_VERSION=2.0.0
 PACKAGES="git \

--- a/src/singularity_modules/hisat2/2.1.0/hisat2.def
+++ b/src/singularity_modules/hisat2/2.1.0/hisat2.def
@@ -4,7 +4,8 @@ From: alpine:3.8
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 SAMTOOLS_VERSION=1.7
 HISAT2_VERSION=2.1.0
 PACKAGES="git \

--- a/src/singularity_modules/htseq/0.11.2/htseq.def
+++ b/src/singularity_modules/htseq/0.11.2/htseq.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 HTSEQ_VERSION=0.11.2
 PACKAGES="build-essential \
 python3-pip \

--- a/src/singularity_modules/htseq/0.8.0/htseq.def
+++ b/src/singularity_modules/htseq/0.8.0/htseq.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 HTSEQ_VERSION=0.8.0
 PACKAGES="build-essential \
 python3-pip \

--- a/src/singularity_modules/kallisto/0.43.1/kallisto.def
+++ b/src/singularity_modules/kallisto/0.43.1/kallisto.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 KALLISTO_VERSION=0.43.1
 PACKAGES="curl \
 ca-certificates"