From 420b7b9e59e3081ef2d775a320dc08986033c776 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 26 Mar 2019 17:24:56 +0100
Subject: [PATCH] multiqc: add v1.7
---
src/docker_modules/multiqc/1.7/Dockerfile | 25 ++++++++++++
src/docker_modules/multiqc/1.7/docker_init.sh | 2 +
src/nf_modules/multiqc/multiqc_paired.config | 10 ++---
src/nf_modules/multiqc/multiqc_single.config | 10 ++---
src/singularity_modules/multiqc/1.7/build.sh | 3 ++
.../multiqc/1.7/multiqc.def | 39 +++++++++++++++++++
6 files changed, 79 insertions(+), 10 deletions(-)
create mode 100644 src/docker_modules/multiqc/1.7/Dockerfile
create mode 100755 src/docker_modules/multiqc/1.7/docker_init.sh
create mode 100755 src/singularity_modules/multiqc/1.7/build.sh
create mode 100644 src/singularity_modules/multiqc/1.7/multiqc.def
diff --git a/src/docker_modules/multiqc/1.7/Dockerfile b/src/docker_modules/multiqc/1.7/Dockerfile
new file mode 100644
index 00000000..ea71b1ad
--- /dev/null
+++ b/src/docker_modules/multiqc/1.7/Dockerfile
@@ -0,0 +1,25 @@
+FROM debian:stretch
+MAINTAINER Laurent Modolo
+
+ENV MULTIQC_VERSION=1.7
+ENV PACKAGES build-essential \
+ python3-pip \
+ python3-setuptools \
+ python3-dev \
+ python3-wheel \
+ procps \
+ locales
+
+RUN apt-get update && \
+ apt-get install -y --no-install-recommends ${PACKAGES} && \
+ apt-get clean
+
+RUN locale-gen en_US.UTF-8
+ENV LC_ALL=en_US.utf-8
+ENV LANG=en_US.utf-8
+ENV LC_ALL=C.UTF-8
+ENV LANG=C.UTF-8
+
+
+RUN pip3 install multiqc==${MULTIQC_VERSION}
+
diff --git a/src/docker_modules/multiqc/1.7/docker_init.sh b/src/docker_modules/multiqc/1.7/docker_init.sh
new file mode 100755
index 00000000..67ff4536
--- /dev/null
+++ b/src/docker_modules/multiqc/1.7/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/multiqc/1.7 -t 'multiqc:1.7'
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 67e90317..aaa32da1 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -9,7 +9,7 @@ profiles {
cpus = 1
}
withName: multiqc {
- container = "multiqc:1.0"
+ container = "multiqc:1.7"
cpus = 1
}
}
@@ -22,7 +22,7 @@ profiles {
cpus = 1
}
withName: multiqc {
- container = "file://bin/multiqc:1.0.sif"
+ container = "file://bin/multiqc:1.7.sif"
cpus = 1
}
}
@@ -37,19 +37,19 @@ profiles {
cpus = 1
memory = "5GB"
time = "6h"
- queueSize = 1000
+ queueSize = 1.70
pollInterval = '60sec'
queue = 'monointeldeb128'
}
withName: multiqc {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "multiqc/1.0"
+ module = "multiqc/1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "5GB"
time = "6h"
- queueSize = 1000
+ queueSize = 1.70
pollInterval = '60sec'
queue = 'monointeldeb128'
}
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index cdab351f..bdf60504 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -8,7 +8,7 @@ profiles {
cpus = 1
}
withName: multiqc {
- container = "multiqc:1.0"
+ container = "multiqc:1.7"
cpus = 1
}
}
@@ -21,7 +21,7 @@ profiles {
cpus = 1
}
withName: multiqc {
- container = "file://bin/multiqc:1.0.sif"
+ container = "file://bin/multiqc:1.7.sif"
cpus = 1
}
}
@@ -36,19 +36,19 @@ profiles {
cpus = 1
memory = "5GB"
time = "6h"
- queueSize = 1000
+ queueSize = 1.70
pollInterval = '60sec'
queue = 'monointeldeb128'
}
withName: multiqc {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "multiqc/1.0"
+ module = "multiqc/1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
memory = "5GB"
time = "6h"
- queueSize = 1000
+ queueSize = 1.70
pollInterval = '60sec'
queue = 'monointeldeb128'
}
diff --git a/src/singularity_modules/multiqc/1.7/build.sh b/src/singularity_modules/multiqc/1.7/build.sh
new file mode 100755
index 00000000..7c2ae670
--- /dev/null
+++ b/src/singularity_modules/multiqc/1.7/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/multiqc:1.7.sif src/singularity_modules/multiqc/1.7/multiqc.def && \
+singularity sign bin/multiqc:1.7.sif
diff --git a/src/singularity_modules/multiqc/1.7/multiqc.def b/src/singularity_modules/multiqc/1.7/multiqc.def
new file mode 100644
index 00000000..db345390
--- /dev/null
+++ b/src/singularity_modules/multiqc/1.7/multiqc.def
@@ -0,0 +1,39 @@
+Bootstrap: docker
+From: debian:stretch
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+MULTIQC_VERSION=1.7
+PACKAGES="build-essential \
+ python3-pip \
+ python3-setuptools \
+ python3-dev \
+ python3-wheel \
+ procps \
+ locales"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+locale-gen en_US.UTF-8
+LC_ALL=en_US.utf-8
+LANG=en_US.utf-8
+LC_ALL=C.UTF-8
+LANG=C.UTF-8
+
+pip3 install multiqc==${MULTIQC_VERSION}
+
+%environment
+export KALLISTO_VERSION=0.44.0
+export locale-gen en_US.UTF-8
+export LC_ALL=en_US.utf-8
+export LANG=en_US.utf-8
+export LC_ALL=C.UTF-8
+export LANG=C.UTF-8
+
+%runscript
+exec /bin/bash "$@"
+
--
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