htseq: add v0.11.2

src/docker_modules/htseq/0.11.2/Dockerfile

+
+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}

src/docker_modules/htseq/0.11.2/docker_init.sh

+#!/bin/sh
+docker build src/docker_modules/htseq/0.11.2 -t 'htseq:0.11.2'

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

psmn_modules @ 5d8170aa

-Subproject commit d8bbe9f5b5fa9d4f42d073e87b2e237c1f140f88
+Subproject commit 5d8170aa039744a50c6cf967aabb3c2196efa7d9

src/singularity_modules/htseq/0.11.2/build.sh

+#/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

src/singularity_modules/htseq/0.11.2/htseq.def

+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 "$@"