From ad48514d8e3c2721b3f9eb9db87d5a64d6e5d1ca Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 28 Mar 2019 11:22:57 +0100
Subject: [PATCH] htseq: add v0.11.2
---
src/docker_modules/htseq/0.11.2/Dockerfile | 18 +++++++++++++
.../htseq/0.11.2/docker_init.sh | 2 ++
src/nf_modules/htseq/htseq.config | 6 ++---
src/psmn_modules | 2 +-
src/singularity_modules/htseq/0.11.2/build.sh | 3 +++
.../htseq/0.11.2/htseq.def | 27 +++++++++++++++++++
6 files changed, 54 insertions(+), 4 deletions(-)
create mode 100644 src/docker_modules/htseq/0.11.2/Dockerfile
create mode 100755 src/docker_modules/htseq/0.11.2/docker_init.sh
create mode 100755 src/singularity_modules/htseq/0.11.2/build.sh
create mode 100644 src/singularity_modules/htseq/0.11.2/htseq.def
diff --git a/src/docker_modules/htseq/0.11.2/Dockerfile b/src/docker_modules/htseq/0.11.2/Dockerfile
new file mode 100644
index 00000000..d9db9b15
--- /dev/null
+++ b/src/docker_modules/htseq/0.11.2/Dockerfile
@@ -0,0 +1,18 @@
+
+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV HTSEQ_VERSION=0.11.2
+ENV PACKAGES build-essential \
+ python3-pip \
+ python3-setuptools \
+ python3-dev \
+ python3-wheel
+
+RUN apt-get update && \
+ apt-get install -y --no-install-recommends ${PACKAGES} && \
+ apt-get clean
+
+RUN pip3 install numpy==1.14.3
+RUN pip3 install pysam==0.15.0
+RUN pip3 install HTSeq==${HTSEQ_VERSION}
diff --git a/src/docker_modules/htseq/0.11.2/docker_init.sh b/src/docker_modules/htseq/0.11.2/docker_init.sh
new file mode 100755
index 00000000..3d173e17
--- /dev/null
+++ b/src/docker_modules/htseq/0.11.2/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/htseq/0.11.2 -t 'htseq:0.11.2'
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 9e0a4e57..30646614 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -8,7 +8,7 @@ profiles {
cpus = 1
}
withName: counting {
- container = "htseq:0.8.0"
+ container = "htseq:0.11.2"
cpus = 1
}
}
@@ -17,7 +17,7 @@ profiles {
singularity.enabled = true
process {
withName: sort_bam {
- container = "file://bin/htseq:0.8.0.sif"
+ container = "file://bin/htseq:0.11.2.sif"
cpus = 1
}
}
@@ -36,7 +36,7 @@ profiles {
}
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "htseq/0.8.0"
+ module = "htseq/0.11.2"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/psmn_modules b/src/psmn_modules
index d8bbe9f5..5d8170aa 160000
--- a/src/psmn_modules
+++ b/src/psmn_modules
@@ -1 +1 @@
-Subproject commit d8bbe9f5b5fa9d4f42d073e87b2e237c1f140f88
+Subproject commit 5d8170aa039744a50c6cf967aabb3c2196efa7d9
diff --git a/src/singularity_modules/htseq/0.11.2/build.sh b/src/singularity_modules/htseq/0.11.2/build.sh
new file mode 100755
index 00000000..1c3c8170
--- /dev/null
+++ b/src/singularity_modules/htseq/0.11.2/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/htseq:0.11.2.sif src/singularity_modules/htseq/0.11.2/htseq.def && \
+singularity sign bin/htseq:0.11.2.sif
diff --git a/src/singularity_modules/htseq/0.11.2/htseq.def b/src/singularity_modules/htseq/0.11.2/htseq.def
new file mode 100644
index 00000000..ad74ee92
--- /dev/null
+++ b/src/singularity_modules/htseq/0.11.2/htseq.def
@@ -0,0 +1,27 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+HTSEQ_VERSION=0.11.2
+PACKAGES="build-essential \
+python3-pip \
+python3-setuptools \
+python3-dev \
+python3-wheel"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+pip3 install numpy==1.14.3
+pip3 install pysam==0.15.0
+pip3 install HTSeq==${HTSEQ_VERSION}
+
+%environment
+export HTSEQ_VERSION=0.11.2
+
+%runscript
+exec /bin/bash "$@"
--
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