From 3cd89d35e01454ea19bab9f369a0332edd2e0d8d Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 10 May 2019 11:48:06 +0200
Subject: [PATCH] update sambamba to 0.6.9
---
src/conda_packages.sh | 1 -
src/docker_modules/sambamba/0.6.9/Dockerfile | 17 ++++++++++++
.../sambamba/0.6.9/docker_init.sh | 2 ++
src/nf_modules/sambamba/index_bams.config | 8 +++---
src/nf_modules/sambamba/sort_bams.config | 8 +++---
src/nf_modules/sambamba/split_bams.config | 8 +++---
src/psmn_modules | 2 +-
.../sambamba/0.6.9/build.sh | 3 +++
.../sambamba/0.6.9/sambamba | 2 ++
.../sambamba/0.6.9/sambamba.def | 27 +++++++++++++++++++
10 files changed, 64 insertions(+), 14 deletions(-)
create mode 100644 src/docker_modules/sambamba/0.6.9/Dockerfile
create mode 100755 src/docker_modules/sambamba/0.6.9/docker_init.sh
create mode 100755 src/singularity_modules/sambamba/0.6.9/build.sh
create mode 100644 src/singularity_modules/sambamba/0.6.9/sambamba
create mode 100644 src/singularity_modules/sambamba/0.6.9/sambamba.def
diff --git a/src/conda_packages.sh b/src/conda_packages.sh
index 1f54db0b..66a00c25 100644
--- a/src/conda_packages.sh
+++ b/src/conda_packages.sh
@@ -48,7 +48,6 @@ install_env deeptools 3.0.2 deeptools
install_env htseq 0.9.1 htseq
install_env htseq 0.11.2 htseq
install_env python 3.7 python
-install_env R 3.5.3 R
install_env R 3.4.3 R
install_env R 3.3.1 R
install_env file handle 0.1.1 file handle
diff --git a/src/docker_modules/sambamba/0.6.9/Dockerfile b/src/docker_modules/sambamba/0.6.9/Dockerfile
new file mode 100644
index 00000000..689d0265
--- /dev/null
+++ b/src/docker_modules/sambamba/0.6.9/Dockerfile
@@ -0,0 +1,17 @@
+FROM ubuntu:18.04
+MAINTAINER Laurent Modolo
+
+ENV SAMBAMBA_VERSION=0.6.9
+ENV PACKAGES curl=7.58.0* \
+ ca-certificates=20180409 \
+ build-essential=12.4* \
+ zlib1g-dev=1:1.2.11*
+
+RUN apt-get update && \
+ apt-get install -y --no-install-recommends ${PACKAGES} && \
+ apt-get clean
+
+RUN curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
+tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
+mv sambamba /usr/bin/ && \
+rm -R sambamba_v${SAMBAMBA_VERSION}_linux*
diff --git a/src/docker_modules/sambamba/0.6.9/docker_init.sh b/src/docker_modules/sambamba/0.6.9/docker_init.sh
new file mode 100755
index 00000000..f9a2f992
--- /dev/null
+++ b/src/docker_modules/sambamba/0.6.9/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/sambamba/0.6.9 -t 'sambamba:0.6.9'
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 335f0fa6..e8ab95ac 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: index_bam {
- container = "sambamba:0.6.7"
+ container = "sambamba:0.6.9"
cpus = 4
}
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: index_bam {
- container = "file://bin/sambamba:0.6.7.img"
+ container = "file://bin/sambamba:0.6.9.img"
cpus = 4
}
}
@@ -22,7 +22,7 @@ profiles {
process{
withName: index_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "sambamba/0.6.7"
+ module = "sambamba/0.6.9"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
@@ -37,7 +37,7 @@ profiles {
process{
withName: index_bam {
beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
- conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
+ conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 6865c9a3..a408436b 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: sort_bam {
- container = "sambamba:0.6.7"
+ container = "sambamba:0.6.9"
cpus = 4
}
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: sort_bam {
- container = "file://bin/sambamba:0.6.7.img"
+ container = "file://bin/sambamba:0.6.9.img"
cpus = 4
}
}
@@ -22,7 +22,7 @@ profiles {
process{
withName: sort_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "sambamba/0.6.7"
+ module = "sambamba/0.6.9"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 4
@@ -37,7 +37,7 @@ profiles {
process{
withName: sort_bam {
beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
- conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
+ conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 740c51e0..4bc3cda1 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: split_bam {
- container = "sambamba:0.6.7"
+ container = "sambamba:0.6.9"
cpus = 4
}
}
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: split_bam {
- container = "file://bin/sambamba:0.6.7.img"
+ container = "file://bin/sambamba:0.6.9.img"
cpus = 4
}
}
@@ -22,7 +22,7 @@ profiles {
process{
withName: split_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "sambamba/0.6.7"
+ module = "sambamba/0.6.9"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
@@ -37,7 +37,7 @@ profiles {
process{
withName: split_bam {
beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
- conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
+ conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/psmn_modules b/src/psmn_modules
index 7941cf21..8a86db97 160000
--- a/src/psmn_modules
+++ b/src/psmn_modules
@@ -1 +1 @@
-Subproject commit 7941cf21b2ec744bb8d2eae0a623305c4ee23ced
+Subproject commit 8a86db97eb89833a88b1ee876880cb1c07ce8565
diff --git a/src/singularity_modules/sambamba/0.6.9/build.sh b/src/singularity_modules/sambamba/0.6.9/build.sh
new file mode 100755
index 00000000..4976ecc2
--- /dev/null
+++ b/src/singularity_modules/sambamba/0.6.9/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/sambamba:0.6.9.img src/singularity_modules/sambamba/0.6.9/sambamba.def && \
+singularity sign bin/sambamba:0.6.9.img
diff --git a/src/singularity_modules/sambamba/0.6.9/sambamba b/src/singularity_modules/sambamba/0.6.9/sambamba
new file mode 100644
index 00000000..35b6aa72
--- /dev/null
+++ b/src/singularity_modules/sambamba/0.6.9/sambamba
@@ -0,0 +1,2 @@
+#/bin/bash
+singularity exec /sps/lbmc/common/singularity/sambamba:0.6.7.img sambamba $@
diff --git a/src/singularity_modules/sambamba/0.6.9/sambamba.def b/src/singularity_modules/sambamba/0.6.9/sambamba.def
new file mode 100644
index 00000000..b5fbfec8
--- /dev/null
+++ b/src/singularity_modules/sambamba/0.6.9/sambamba.def
@@ -0,0 +1,27 @@
+Bootstrap: docker
+From: ubuntu:18.04
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+SAMBAMBA_VERSION=0.6.9
+PACKAGES="curl=7.58.0* \
+ca-certificates=20180409 \
+build-essential=12.4* \
+zlib1g-dev=1:1.2.11*"
+
+apt-get update && \
+apt-get install -y --no-install-recommends ${PACKAGES} && \
+apt-get clean
+
+curl -k -L https://github.com/biod/sambamba/releases/download/v${SAMBAMBA_VERSION}/sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 -o sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
+tar xvjf sambamba_v${SAMBAMBA_VERSION}_linux.tar.bz2 && \
+mv sambamba /usr/bin/ && \
+rm -R sambamba_v${SAMBAMBA_VERSION}_linux*
+
+%environment
+export SAMBAMBA_VERSION=0.6.9
+
+%runscript
+exec /bin/bash "$@"
--
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