cutadapt: add v2.1

src/docker_modules/cutadapt/2.1/Dockerfile

+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}
+
+

src/docker_modules/cutadapt/2.1/docker_init.sh

+#!/bin/sh
+docker build src/docker_modules/cutadapt/2.1 -t 'cutadapt:2.1'

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

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

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

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

psmn_modules @ 0c034f5b

-Subproject commit c27ac9cb52d47bb63f6b8a364e8398827682ed5a
+Subproject commit 0c034f5bbeb8e91cecc04466b74654503a94ac7c

src/singularity_modules/cutadapt/2.1/build.sh

+#/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

src/singularity_modules/cutadapt/2.1/cutadapt.def

+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 "$@"