From 93f2be99262ada048ccb66569846840fc79b81ba Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 20 Feb 2019 13:53:53 +0100
Subject: [PATCH] cudatapt: add cutadapt v1.15 for docker and nf
---
src/docker_modules/cutadapt/1.15/Dockerfile | 14 ++++++++++++++
src/docker_modules/cutadapt/1.15/docker_init.sh | 2 ++
.../cutadapt/adaptor_removal_paired.config | 2 +-
.../cutadapt/adaptor_removal_single.config | 2 +-
src/nf_modules/cutadapt/trimming_paired.config | 2 +-
src/nf_modules/cutadapt/trimming_single.config | 2 +-
6 files changed, 20 insertions(+), 4 deletions(-)
create mode 100644 src/docker_modules/cutadapt/1.15/Dockerfile
create mode 100755 src/docker_modules/cutadapt/1.15/docker_init.sh
diff --git a/src/docker_modules/cutadapt/1.15/Dockerfile b/src/docker_modules/cutadapt/1.15/Dockerfile
new file mode 100644
index 00000000..96bbd20d
--- /dev/null
+++ b/src/docker_modules/cutadapt/1.15/Dockerfile
@@ -0,0 +1,14 @@
+FROM alpine:3.8
+MAINTAINER Laurent Modolo
+
+ENV CUTADAPT_VERSION=1.15
+ENV PACKAGES bash \
+ python3 \
+ python3-dev \
+ musl-dev \
+ gcc
+
+RUN apk update && \
+ apk add ${PACKAGES}
+
+RUN pip3 install cutadapt==${CUTADAPT_VERSION}
diff --git a/src/docker_modules/cutadapt/1.15/docker_init.sh b/src/docker_modules/cutadapt/1.15/docker_init.sh
new file mode 100755
index 00000000..b3cf5413
--- /dev/null
+++ b/src/docker_modules/cutadapt/1.15/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/cutadapt/1.15 -t 'cutadapt:1.15'
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 5f176c68..335a697e 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:1.14"
+ container = "cutadapt:1.15"
}
}
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 5f176c68..335a697e 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:1.14"
+ container = "cutadapt:1.15"
}
}
}
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 984e336a..c2f05ec2 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:1.14"
+ container = "cutadapt:1.15"
}
}
}
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 984e336a..c2f05ec2 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:1.14"
+ container = "cutadapt:1.15"
}
}
}
--
GitLab