From 9737cccf1967a9a18c7bb8dce1f985b815109699 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 20 May 2019 16:12:59 +0200
Subject: [PATCH] singularity modules: add /sps /pbs and /scratch for ccin2p3
---
src/singularity_modules/bcftools/1.7/bcftools.def | 3 ++-
src/singularity_modules/bedtools/2.25.0/bedtools.def | 3 ++-
src/singularity_modules/bioawk/1.0/bioawk.def | 3 ++-
src/singularity_modules/bowtie/1.2.2/bowtie.def | 3 ++-
src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def | 3 ++-
src/singularity_modules/bwa/0.7.17/bwa.def | 3 ++-
src/singularity_modules/canu/1.6/canu.def | 3 ++-
src/singularity_modules/cutadapt/1.14/cutadapt.def | 3 ++-
src/singularity_modules/cutadapt/1.15/cutadapt.def | 3 ++-
src/singularity_modules/cutadapt/2.1/cutadapt.def | 3 ++-
src/singularity_modules/deeptools/3.0.2/deeptools.def | 3 ++-
src/singularity_modules/deeptools/3.1.1/deeptools.def | 3 ++-
src/singularity_modules/fastqc/0.11.5/fastqc.def | 3 ++-
src/singularity_modules/file_handle/0.1.1/file_handle.def | 3 ++-
src/singularity_modules/gatk/4.0.8.1/gatk.def | 3 ++-
src/singularity_modules/hisat2/2.0.0/hisat2.def | 3 ++-
src/singularity_modules/hisat2/2.1.0/hisat2.def | 3 ++-
src/singularity_modules/htseq/0.11.2/htseq.def | 3 ++-
src/singularity_modules/htseq/0.8.0/htseq.def | 3 ++-
src/singularity_modules/kallisto/0.43.1/kallisto.def | 3 ++-
src/singularity_modules/kallisto/0.44.0/kallisto.def | 5 ++++-
src/singularity_modules/macs2/2.1.2/macs2.def | 3 ++-
src/singularity_modules/multiqc/1.0/multiqc.def | 3 ++-
src/singularity_modules/multiqc/1.7/multiqc.def | 3 ++-
src/singularity_modules/music/6613c53/music.def | 3 ++-
src/singularity_modules/picard/2.18.11/picard.def | 3 ++-
src/singularity_modules/pigz/2.4/pigz.def | 3 ++-
src/singularity_modules/rsem/1.3.0/rsem.def | 3 ++-
src/singularity_modules/salmon/0.8.2/salmon.def | 3 ++-
src/singularity_modules/sambamba/0.6.7/sambamba.def | 3 ++-
src/singularity_modules/sambamba/0.6.9/sambamba.def | 3 ++-
src/singularity_modules/samblaster/0.1.24/samblaster.def | 3 ++-
src/singularity_modules/samtools/1.7/samtools.def | 3 ++-
src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def | 3 ++-
src/singularity_modules/tophat/2.1.1/tophat.def | 3 ++-
src/singularity_modules/trimmomatic/0.36/trimmomatic.def | 3 ++-
src/singularity_modules/ucsc/375/ucsc.def | 3 ++-
src/singularity_modules/umi_tools/1.0.0/umi_tools.def | 3 ++-
src/singularity_modules/urqt/d62c1f8/urqt.def | 3 ++-
39 files changed, 80 insertions(+), 39 deletions(-)
diff --git a/src/singularity_modules/bcftools/1.7/bcftools.def b/src/singularity_modules/bcftools/1.7/bcftools.def
index 1d353565..bf617260 100644
--- 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=${BCFTOOLS_VERSION}*
diff --git a/src/singularity_modules/bedtools/2.25.0/bedtools.def b/src/singularity_modules/bedtools/2.25.0/bedtools.def
index 0ca0f9ef..5bf1e2d9 100644
--- a/src/singularity_modules/bedtools/2.25.0/bedtools.def
+++ b/src/singularity_modules/bedtools/2.25.0/bedtools.def
@@ -4,7 +4,8 @@ From: ubuntu:16.04
%labels
MAINTAINER Laurent Modolo
-%post
+%pos
+mkdir -p /sps /pbs /scratch
BEDTOOLS_VERSION=2.25.0
PACKAGES=bedtools=${BEDTOOLS_VERSION}*
diff --git a/src/singularity_modules/bioawk/1.0/bioawk.def b/src/singularity_modules/bioawk/1.0/bioawk.def
index a5678b64..e2b5e766 100644
--- 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 \
diff --git a/src/singularity_modules/bowtie/1.2.2/bowtie.def b/src/singularity_modules/bowtie/1.2.2/bowtie.def
index 79da1161..047c3ceb 100644
--- 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=${BOWTIE_VERSION}* \
diff --git a/src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def b/src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def
index 73a177e4..294916ee 100644
--- a/src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def
+++ b/src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
%labels
MAINTAINER Laurent Modolo
-%post
+%pos
+mkdir -p /sps /pbs /scratch
BOWTIE2_VERSION=2.3.4.1
SAMTOOLS_VERSION=1.7
PACKAGES="bowtie2=${BOWTIE2_VERSION}* \
diff --git a/src/singularity_modules/bwa/0.7.17/bwa.def b/src/singularity_modules/bwa/0.7.17/bwa.def
index b2c8b22f..1071c4fc 100644
--- 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
diff --git a/src/singularity_modules/canu/1.6/canu.def b/src/singularity_modules/canu/1.6/canu.def
index c9d0a4ec..cd0636aa 100644
--- 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}*
diff --git a/src/singularity_modules/cutadapt/1.14/cutadapt.def b/src/singularity_modules/cutadapt/1.14/cutadapt.def
index 90cafb60..e04cc9a8 100644
--- 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 \
diff --git a/src/singularity_modules/cutadapt/1.15/cutadapt.def b/src/singularity_modules/cutadapt/1.15/cutadapt.def
index 041f3a18..113af205 100644
--- 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 \
diff --git a/src/singularity_modules/cutadapt/2.1/cutadapt.def b/src/singularity_modules/cutadapt/2.1/cutadapt.def
index 5236a508..7390051f 100644
--- 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 \
diff --git a/src/singularity_modules/deeptools/3.0.2/deeptools.def b/src/singularity_modules/deeptools/3.0.2/deeptools.def
index dc8fbdca..09be8f1d 100644
--- 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 \
diff --git a/src/singularity_modules/deeptools/3.1.1/deeptools.def b/src/singularity_modules/deeptools/3.1.1/deeptools.def
index 366b6218..1a903191 100644
--- 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 \
diff --git a/src/singularity_modules/fastqc/0.11.5/fastqc.def b/src/singularity_modules/fastqc/0.11.5/fastqc.def
index d2bc5389..3f414493 100644
--- 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*"
diff --git a/src/singularity_modules/file_handle/0.1.1/file_handle.def b/src/singularity_modules/file_handle/0.1.1/file_handle.def
index f80a9aee..0bcc238c 100644
--- 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 \
diff --git a/src/singularity_modules/gatk/4.0.8.1/gatk.def b/src/singularity_modules/gatk/4.0.8.1/gatk.def
index b13ef7ff..4d1111f5 100644
--- 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/
diff --git a/src/singularity_modules/hisat2/2.0.0/hisat2.def b/src/singularity_modules/hisat2/2.0.0/hisat2.def
index d9d77b68..85b5c64b 100644
--- 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 \
diff --git a/src/singularity_modules/hisat2/2.1.0/hisat2.def b/src/singularity_modules/hisat2/2.1.0/hisat2.def
index c6358b11..4f36b97d 100644
--- 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 \
diff --git a/src/singularity_modules/htseq/0.11.2/htseq.def b/src/singularity_modules/htseq/0.11.2/htseq.def
index ad74ee92..34f16ee5 100644
--- 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 \
diff --git a/src/singularity_modules/htseq/0.8.0/htseq.def b/src/singularity_modules/htseq/0.8.0/htseq.def
index d315b301..41f33ce4 100644
--- 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 \
diff --git a/src/singularity_modules/kallisto/0.43.1/kallisto.def b/src/singularity_modules/kallisto/0.43.1/kallisto.def
index 3b9899a0..4b3576bc 100644
--- 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"
diff --git a/src/singularity_modules/kallisto/0.44.0/kallisto.def b/src/singularity_modules/kallisto/0.44.0/kallisto.def
index 613218ac..b82ea3be 100644
--- 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
diff --git a/src/singularity_modules/macs2/2.1.2/macs2.def b/src/singularity_modules/macs2/2.1.2/macs2.def
index 0b56223a..5e31e46e 100644
--- 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 \
diff --git a/src/singularity_modules/multiqc/1.0/multiqc.def b/src/singularity_modules/multiqc/1.0/multiqc.def
index 195def47..4ca06cca 100644
--- 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 \
diff --git a/src/singularity_modules/multiqc/1.7/multiqc.def b/src/singularity_modules/multiqc/1.7/multiqc.def
index db345390..7ca4367e 100644
--- 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 \
diff --git a/src/singularity_modules/music/6613c53/music.def b/src/singularity_modules/music/6613c53/music.def
index 57a42904..49037523 100644
--- 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 \
diff --git a/src/singularity_modules/picard/2.18.11/picard.def b/src/singularity_modules/picard/2.18.11/picard.def
index 27a3e18a..caaa961c 100644
--- 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 \
diff --git a/src/singularity_modules/pigz/2.4/pigz.def b/src/singularity_modules/pigz/2.4/pigz.def
index 63e2d246..ec807108 100644
--- 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}*
diff --git a/src/singularity_modules/rsem/1.3.0/rsem.def b/src/singularity_modules/rsem/1.3.0/rsem.def
index 2e615b0d..fa8f79e9 100644
--- 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
diff --git a/src/singularity_modules/salmon/0.8.2/salmon.def b/src/singularity_modules/salmon/0.8.2/salmon.def
index d23673a4..94a9a83b 100644
--- 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"
diff --git a/src/singularity_modules/sambamba/0.6.7/sambamba.def b/src/singularity_modules/sambamba/0.6.7/sambamba.def
index f94a1b8b..c90c54a2 100644
--- 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 \
diff --git a/src/singularity_modules/sambamba/0.6.9/sambamba.def b/src/singularity_modules/sambamba/0.6.9/sambamba.def
index b5fbfec8..aa410dd0 100644
--- 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 \
diff --git a/src/singularity_modules/samblaster/0.1.24/samblaster.def b/src/singularity_modules/samblaster/0.1.24/samblaster.def
index d2abfd55..0141ec3d 100644
--- 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 \
diff --git a/src/singularity_modules/samtools/1.7/samtools.def b/src/singularity_modules/samtools/1.7/samtools.def
index c73f4e84..5ee2c8c0 100644
--- 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 \
diff --git a/src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def b/src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def
index 7fd70f27..0e780eac 100644
--- 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=${SRATOOLKIT_VERSION}*
diff --git a/src/singularity_modules/tophat/2.1.1/tophat.def b/src/singularity_modules/tophat/2.1.1/tophat.def
index c683ba38..1e3a751d 100644
--- a/src/singularity_modules/tophat/2.1.1/tophat.def
+++ b/src/singularity_modules/tophat/2.1.1/tophat.def
@@ -4,7 +4,8 @@ From: ubuntu:18.04
%labels
MAINTAINER Laurent Modolo
-%post
+%pos
+mkdir -p /sps /pbs /scratch
TOPHAT_VERSION=2.1.1
PACKAGES=tophat=${BOWTIE2_VERSION}*
diff --git a/src/singularity_modules/trimmomatic/0.36/trimmomatic.def b/src/singularity_modules/trimmomatic/0.36/trimmomatic.def
index 417e863d..c4c1ce20 100644
--- 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}*
diff --git a/src/singularity_modules/ucsc/375/ucsc.def b/src/singularity_modules/ucsc/375/ucsc.def
index a1d1a743..9c5220b4 100644
--- 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 \
diff --git a/src/singularity_modules/umi_tools/1.0.0/umi_tools.def b/src/singularity_modules/umi_tools/1.0.0/umi_tools.def
index c4beca1a..dc1c31cc 100644
--- 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 \
diff --git a/src/singularity_modules/urqt/d62c1f8/urqt.def b/src/singularity_modules/urqt/d62c1f8/urqt.def
index 21e78ce1..9b62e13f 100644
--- 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++ \
--
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