From d280e93a248186e49120e608693a36c29da51f2f Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 9 Apr 2019 11:19:10 +0200
Subject: [PATCH] cutadapt: add v2.1
---
src/docker_modules/cutadapt/2.1/Dockerfile | 17 ++++++++++++
.../cutadapt/2.1/docker_init.sh | 2 ++
.../cutadapt/adaptor_removal_paired.config | 6 ++---
.../cutadapt/adaptor_removal_single.config | 6 ++---
.../cutadapt/trimming_paired.config | 6 ++---
.../cutadapt/trimming_single.config | 6 ++---
src/psmn_modules | 2 +-
src/singularity_modules/cutadapt/2.1/build.sh | 3 +++
.../cutadapt/2.1/cutadapt.def | 27 +++++++++++++++++++
9 files changed, 62 insertions(+), 13 deletions(-)
create mode 100644 src/docker_modules/cutadapt/2.1/Dockerfile
create mode 100755 src/docker_modules/cutadapt/2.1/docker_init.sh
create mode 100755 src/singularity_modules/cutadapt/2.1/build.sh
create mode 100644 src/singularity_modules/cutadapt/2.1/cutadapt.def
diff --git a/src/docker_modules/cutadapt/2.1/Dockerfile b/src/docker_modules/cutadapt/2.1/Dockerfile
new file mode 100644
index 00000000..cb394b2f
--- /dev/null
+++ b/src/docker_modules/cutadapt/2.1/Dockerfile
@@ -0,0 +1,17 @@
+FROM alpine:3.8
+MAINTAINER Laurent Modolo
+
+ENV CUTADAPT_VERSION=2.1
+ENV PACKAGES bash \
+ python3 \
+ python3-dev \
+ musl-dev \
+ gcc
+
+RUN apk update && \
+ apk add ${PACKAGES}
+
+RUN pip3 install --upgrade pip && \
+ pip3 install cutadapt==${CUTADAPT_VERSION}
+
+
diff --git a/src/docker_modules/cutadapt/2.1/docker_init.sh b/src/docker_modules/cutadapt/2.1/docker_init.sh
new file mode 100755
index 00000000..33192004
--- /dev/null
+++ b/src/docker_modules/cutadapt/2.1/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/cutadapt/2.1 -t 'cutadapt:2.1'
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 4f5b5b04..46e40043 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: adaptor_removal {
- container = "cutadapt:1.15"
+ container = "cutadapt:2.1"
cpus = 1
}
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: adaptor_removal {
- container = "file://bin/cutadapt:1.15.sif"
+ container = "file://bin/cutadapt:2.1.sif"
cpus = 1
}
}
@@ -22,7 +22,7 @@ profiles {
process{
withName: adaptor_removal {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "cutadapt/1.14"
+ module = "cutadapt/2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 4f5b5b04..46e40043 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: adaptor_removal {
- container = "cutadapt:1.15"
+ container = "cutadapt:2.1"
cpus = 1
}
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: adaptor_removal {
- container = "file://bin/cutadapt:1.15.sif"
+ container = "file://bin/cutadapt:2.1.sif"
cpus = 1
}
}
@@ -22,7 +22,7 @@ profiles {
process{
withName: adaptor_removal {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "cutadapt/1.14"
+ module = "cutadapt/2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 023d9758..b3c32aab 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: trimming {
- container = "cutadapt:1.15"
+ container = "cutadapt:2.1"
cpus = 1
}
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: trimming {
- container = "file://bin/cutadapt:1.15.sif"
+ container = "file://bin/cutadapt:2.1.sif"
cpus = 1
}
}
@@ -22,7 +22,7 @@ profiles {
process{
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "cutadapt/1.14"
+ module = "cutadapt/2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 023d9758..b3c32aab 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: trimming {
- container = "cutadapt:1.15"
+ container = "cutadapt:2.1"
cpus = 1
}
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: trimming {
- container = "file://bin/cutadapt:1.15.sif"
+ container = "file://bin/cutadapt:2.1.sif"
cpus = 1
}
}
@@ -22,7 +22,7 @@ profiles {
process{
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "cutadapt/1.14"
+ module = "cutadapt/2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/psmn_modules b/src/psmn_modules
index c27ac9cb..0c034f5b 160000
--- a/src/psmn_modules
+++ b/src/psmn_modules
@@ -1 +1 @@
-Subproject commit c27ac9cb52d47bb63f6b8a364e8398827682ed5a
+Subproject commit 0c034f5bbeb8e91cecc04466b74654503a94ac7c
diff --git a/src/singularity_modules/cutadapt/2.1/build.sh b/src/singularity_modules/cutadapt/2.1/build.sh
new file mode 100755
index 00000000..fdb8c4d0
--- /dev/null
+++ b/src/singularity_modules/cutadapt/2.1/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/cutadapt:2.1.sif src/singularity_modules/cutadapt/2.1/cutadapt.def && \
+singularity sign bin/cutadapt:2.1.sif
diff --git a/src/singularity_modules/cutadapt/2.1/cutadapt.def b/src/singularity_modules/cutadapt/2.1/cutadapt.def
new file mode 100644
index 00000000..5236a508
--- /dev/null
+++ b/src/singularity_modules/cutadapt/2.1/cutadapt.def
@@ -0,0 +1,27 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+CUTADAPT_VERSION=2.1
+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=2.1
+
+%runscript
+exec /bin/bash "$@"
--
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