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/kallisto/0.44.0/kallisto.def
+++ b/src/singularity_modules/kallisto/0.44.0/kallisto.def
@@ -4,7 +4,9 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
+
 KALLISTO_VERSION=0.44.0
 PACKAGES="curl \
 ca-certificates"
@@ -18,6 +20,7 @@ tar xzf kallisto_linux-v${KALLISTO_VERSION}.tar.gz && \
 cp kallisto_linux-v${KALLISTO_VERSION}/kallisto /usr/bin && \
 rm -Rf kallisto_linux-v${KALLISTO_VERSION}*

+
 %environment
 export KALLISTO_VERSION=0.44.0


--- a/src/singularity_modules/macs2/2.1.2/macs2.def
+++ b/src/singularity_modules/macs2/2.1.2/macs2.def
@@ -2,7 +2,8 @@ Bootstrap: docker
 From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo
-%post
+%pos
+mkdir -p /sps /pbs /scratch

 MACS_VERSION=2.1.2
 PACKAGES="git \

--- a/src/singularity_modules/multiqc/1.0/multiqc.def
+++ b/src/singularity_modules/multiqc/1.0/multiqc.def
@@ -4,7 +4,8 @@ From: debian:stretch
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 MULTIQC_VERSION=1.0
 PACKAGES="build-essential \
             python3-pip \

--- a/src/singularity_modules/multiqc/1.7/multiqc.def
+++ b/src/singularity_modules/multiqc/1.7/multiqc.def
@@ -4,7 +4,8 @@ From: debian:stretch
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 MULTIQC_VERSION=1.7
 PACKAGES="build-essential \
             python3-pip \

--- a/src/singularity_modules/music/6613c53/music.def
+++ b/src/singularity_modules/music/6613c53/music.def
@@ -4,7 +4,8 @@ From: alpine:3.8
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 MUSIC_VERSION=6613c53
 SAMTOOLS_VERSION=1.7
 PACKAGES="git \

--- a/src/singularity_modules/picard/2.18.11/picard.def
+++ b/src/singularity_modules/picard/2.18.11/picard.def
@@ -7,7 +7,8 @@ src/singularity_modules/picard/2.18.11/PicardCommandLine /usr/bin/
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 PICARD_VERSION=2.18.11
 PACKAGES="default-jre \
 curl \

--- a/src/singularity_modules/pigz/2.4/pigz.def
+++ b/src/singularity_modules/pigz/2.4/pigz.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 PIGZ_VERSION=2.4
 PACKAGES=pigz=${PIGZ_VERSION}*


--- a/src/singularity_modules/rsem/1.3.0/rsem.def
+++ b/src/singularity_modules/rsem/1.3.0/rsem.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 RSEM_VERSION=1.3.0
 BOWTIE2_VERSION=2.3.4.1
 SAMTOOLS_VERSION=1.7

--- a/src/singularity_modules/salmon/0.8.2/salmon.def
+++ b/src/singularity_modules/salmon/0.8.2/salmon.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 SALMON_VERSION=0.8.2
 PACKAGES="curl \
 ca-certificates"

--- a/src/singularity_modules/sambamba/0.6.7/sambamba.def
+++ b/src/singularity_modules/sambamba/0.6.7/sambamba.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 SAMBAMBA_VERSION=0.6.7
 PACKAGES="curl=7.58.0* \
 ca-certificates=20180409 \

--- a/src/singularity_modules/sambamba/0.6.9/sambamba.def
+++ b/src/singularity_modules/sambamba/0.6.9/sambamba.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 SAMBAMBA_VERSION=0.6.9
 PACKAGES="curl=7.58.0* \
 ca-certificates=20180409 \

--- a/src/singularity_modules/samblaster/0.1.24/samblaster.def
+++ b/src/singularity_modules/samblaster/0.1.24/samblaster.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 SAMBLASTER_VERSION=0.1.24
 PACKAGES="curl \
 ca-certificates \

--- a/src/singularity_modules/samtools/1.7/samtools.def
+++ b/src/singularity_modules/samtools/1.7/samtools.def
@@ -4,7 +4,8 @@ From: alpine:3.8
 %labels
 MAINTAINER Laurent Modolo

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

--- a/src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def
+++ b/src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 SRATOOLKIT_VERSION=2.8.2
 PACKAGES=sra-toolkit=${SRATOOLKIT_VERSION}*


--- a/src/singularity_modules/tophat/2.1.1/tophat.def
+++ b/src/singularity_modules/tophat/2.1.1/tophat.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 TOPHAT_VERSION=2.1.1
 PACKAGES=tophat=${BOWTIE2_VERSION}*


--- a/src/singularity_modules/trimmomatic/0.36/trimmomatic.def
+++ b/src/singularity_modules/trimmomatic/0.36/trimmomatic.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 TRIMMOMATIC_VERSION=0.36
 PACKAGES=trimmomatic=${TRIMMOMATIC_VERSION}*


--- a/src/singularity_modules/ucsc/375/ucsc.def
+++ b/src/singularity_modules/ucsc/375/ucsc.def
@@ -4,7 +4,8 @@ From: debian:jessie
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 UCSC_VERSION=375
 PACKAGES="apt-utils \
             curl \

--- a/src/singularity_modules/umi_tools/1.0.0/umi_tools.def
+++ b/src/singularity_modules/umi_tools/1.0.0/umi_tools.def
@@ -4,7 +4,8 @@ From: debian:stretch
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 UMI_TOOLS_VERSION=1.0.0
 PACKAGES="bash \
             python3 \

--- a/src/singularity_modules/urqt/d62c1f8/urqt.def
+++ b/src/singularity_modules/urqt/d62c1f8/urqt.def
@@ -4,7 +4,8 @@ From: debian:9
 %labels
 MAINTAINER Laurent Modolo

-%post
+%pos
+mkdir -p /sps /pbs /scratch
 URQT_VERSION=d62c1f8
 PACKAGES="git \
 g++ \