From 870693e51d342456e0bb57d82d98a45fe50260ff Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 4 Mar 2019 14:58:40 +0100
Subject: [PATCH] cutadapt: add singularity files
---
.../2.25.0/{BEDtools.def => bedtools.def} | 0
.../bowtie/1.2.2/{Bowtie.def => bowtie.def} | 0
.../2.3.4.1/{Bowtie2.def => bowtie2.def} | 0
.../bwa/0.7.17/{BWA.def => bwa.def} | 0
.../cutadapt/1.14/build.sh | 3 ++
.../cutadapt/1.14/cutadapt.def | 27 ++++++++++++++++++
.../cutadapt/1.15/build.sh | 3 ++
.../cutadapt/1.15/cutadapt.def | 28 +++++++++++++++++++
.../urqt/d62c1f8/{UrQt.def => urqt.def} | 0
9 files changed, 61 insertions(+)
rename src/singularity_modules/bedtools/2.25.0/{BEDtools.def => bedtools.def} (100%)
rename src/singularity_modules/bowtie/1.2.2/{Bowtie.def => bowtie.def} (100%)
rename src/singularity_modules/bowtie2/2.3.4.1/{Bowtie2.def => bowtie2.def} (100%)
rename src/singularity_modules/bwa/0.7.17/{BWA.def => bwa.def} (100%)
create mode 100755 src/singularity_modules/cutadapt/1.14/build.sh
create mode 100644 src/singularity_modules/cutadapt/1.14/cutadapt.def
create mode 100755 src/singularity_modules/cutadapt/1.15/build.sh
create mode 100644 src/singularity_modules/cutadapt/1.15/cutadapt.def
rename src/singularity_modules/urqt/d62c1f8/{UrQt.def => urqt.def} (100%)
diff --git a/src/singularity_modules/bedtools/2.25.0/BEDtools.def b/src/singularity_modules/bedtools/2.25.0/bedtools.def
similarity index 100%
rename from src/singularity_modules/bedtools/2.25.0/BEDtools.def
rename to src/singularity_modules/bedtools/2.25.0/bedtools.def
diff --git a/src/singularity_modules/bowtie/1.2.2/Bowtie.def b/src/singularity_modules/bowtie/1.2.2/bowtie.def
similarity index 100%
rename from src/singularity_modules/bowtie/1.2.2/Bowtie.def
rename to src/singularity_modules/bowtie/1.2.2/bowtie.def
diff --git a/src/singularity_modules/bowtie2/2.3.4.1/Bowtie2.def b/src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def
similarity index 100%
rename from src/singularity_modules/bowtie2/2.3.4.1/Bowtie2.def
rename to src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def
diff --git a/src/singularity_modules/bwa/0.7.17/BWA.def b/src/singularity_modules/bwa/0.7.17/bwa.def
similarity index 100%
rename from src/singularity_modules/bwa/0.7.17/BWA.def
rename to src/singularity_modules/bwa/0.7.17/bwa.def
diff --git a/src/singularity_modules/cutadapt/1.14/build.sh b/src/singularity_modules/cutadapt/1.14/build.sh
new file mode 100755
index 0000000..d397310
--- /dev/null
+++ b/src/singularity_modules/cutadapt/1.14/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/cutadapt:1.14.sif src/singularity_modules/cutadapt/1.14/cutadapt.def
+singularity sign bin/cutadapt:1.14.sif
diff --git a/src/singularity_modules/cutadapt/1.14/cutadapt.def b/src/singularity_modules/cutadapt/1.14/cutadapt.def
new file mode 100644
index 0000000..90cafb6
--- /dev/null
+++ b/src/singularity_modules/cutadapt/1.14/cutadapt.def
@@ -0,0 +1,27 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+CUTADAPT_VERSION=1.14
+PACKAGES="bash \
+ python3 \
+ python3-dev \
+ musl-dev \
+ python3-pip \
+ gcc"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+pip3 install setuptools
+pip3 install cutadapt==${CUTADAPT_VERSION}
+
+%environment
+export CUTADAPT_VERSION=1.14
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/cutadapt/1.15/build.sh b/src/singularity_modules/cutadapt/1.15/build.sh
new file mode 100755
index 0000000..440d84a
--- /dev/null
+++ b/src/singularity_modules/cutadapt/1.15/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/cutadapt:1.15.sif src/singularity_modules/cutadapt/1.15/cutadapt.def
+singularity sign bin/cutadapt:1.15.sif
diff --git a/src/singularity_modules/cutadapt/1.15/cutadapt.def b/src/singularity_modules/cutadapt/1.15/cutadapt.def
new file mode 100644
index 0000000..041f3a1
--- /dev/null
+++ b/src/singularity_modules/cutadapt/1.15/cutadapt.def
@@ -0,0 +1,28 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+CUTADAPT_VERSION=1.15
+PACKAGES="bash \
+ python3 \
+ python3-dev \
+ musl-dev \
+ python3-pip \
+ gcc"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+pip3 install setuptools
+pip3 install cutadapt==${CUTADAPT_VERSION}
+
+%environment
+export CUTADAPT_VERSION=1.14
+
+%runscript
+exec /bin/bash "$@"
+xec /bin/bash "$@"
diff --git a/src/singularity_modules/urqt/d62c1f8/UrQt.def b/src/singularity_modules/urqt/d62c1f8/urqt.def
similarity index 100%
rename from src/singularity_modules/urqt/d62c1f8/UrQt.def
rename to src/singularity_modules/urqt/d62c1f8/urqt.def
--
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