From 4a1b22a8f0e098d1752c50cf322f45f8c241eaf6 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 4 Mar 2019 16:59:54 +0100
Subject: [PATCH] samtools: add singularity files
---
.../music/6613c53/build.sh | 3 ++
.../music/6613c53/music.def | 45 +++++++++++++++++++
src/singularity_modules/samtools/1.7/build.sh | 3 ++
.../samtools/1.7/samtools.def | 35 +++++++++++++++
4 files changed, 86 insertions(+)
create mode 100755 src/singularity_modules/music/6613c53/build.sh
create mode 100644 src/singularity_modules/music/6613c53/music.def
create mode 100755 src/singularity_modules/samtools/1.7/build.sh
create mode 100644 src/singularity_modules/samtools/1.7/samtools.def
diff --git a/src/singularity_modules/music/6613c53/build.sh b/src/singularity_modules/music/6613c53/build.sh
new file mode 100755
index 0000000..12d1b96
--- /dev/null
+++ b/src/singularity_modules/music/6613c53/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/music:6613c53.sif src/singularity_modules/music/6613c53/music.def
+singularity sign bin/music:6613c53.sif
diff --git a/src/singularity_modules/music/6613c53/music.def b/src/singularity_modules/music/6613c53/music.def
new file mode 100644
index 0000000..fe9b6b1
--- /dev/null
+++ b/src/singularity_modules/music/6613c53/music.def
@@ -0,0 +1,45 @@
+Bootstrap: docker
+From: alpine:3.8
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+MUSIC_VERSION=6613c53
+SAMTOOLS_VERSION=1.7
+PACKAGES="git \
+ make \
+ gcc \
+ musl-dev \
+ zlib-dev \
+ ncurses-dev \
+ bzip2-dev \
+ xz-dev \
+ ca-certificates \
+ bash"
+
+apk update && \
+apk add ${PACKAGES}
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+git clone https://github.com/gersteinlab/MUSIC.git && \
+cd MUSIC && \
+git checkout ${MUSIC_VERSION} && \
+make clean && \
+make && \
+cd .. && \
+mv MUSIC/bin/MUSIC /usr/bin/ && \
+mv MUSIC/bin/generate_multimappability_signal.csh /usr/bin/ && \
+mv MUSIC/bin/run_MUSIC.csh /usr/bin/ && \
+rm -Rf MUSIC
+
+chmod +x /usr/bin/*
+
+%environment
+export MUSIC_VERSION=6613c53
+
+%runscript
+exec /bin/bash "$@"
diff --git a/src/singularity_modules/samtools/1.7/build.sh b/src/singularity_modules/samtools/1.7/build.sh
new file mode 100755
index 0000000..695f99c
--- /dev/null
+++ b/src/singularity_modules/samtools/1.7/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/samtools:1.7.sif src/singularity_modules/samtools/1.7/samtools.def
+singularity sign bin/samtools:1.7.sif
diff --git a/src/singularity_modules/samtools/1.7/samtools.def b/src/singularity_modules/samtools/1.7/samtools.def
new file mode 100644
index 0000000..c73f4e8
--- /dev/null
+++ b/src/singularity_modules/samtools/1.7/samtools.def
@@ -0,0 +1,35 @@
+Bootstrap: docker
+From: alpine:3.8
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+SAMTOOLS_VERSION=1.7
+PACKAGES="git \
+ make \
+ gcc \
+ musl-dev \
+ zlib-dev \
+ ncurses-dev \
+ bzip2-dev \
+ xz-dev \
+ bash"
+apk update && \
+apk add ${PACKAGES}
+
+git clone https://github.com/samtools/htslib.git && \
+cd htslib && \
+git checkout ${SAMTOOLS_VERSION} && \
+cd .. && \
+git clone https://github.com/samtools/samtools.git && \
+cd samtools && \
+git checkout ${SAMTOOLS_VERSION} && \
+make && \
+cp samtools /usr/bin/
+
+%environment
+export SAMTOOLS_VERSION=1.7
+
+%runscript
+exec /bin/bash "$@"
--
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