update sambamba to 0.6.9

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

src/docker_modules/sambamba/0.6.9/Dockerfile

+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*

src/docker_modules/sambamba/0.6.9/docker_init.sh

+#!/bin/sh
+docker build src/docker_modules/sambamba/0.6.9 -t 'sambamba:0.6.9'

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"

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"

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"

psmn_modules @ 8a86db97

-Subproject commit 7941cf21b2ec744bb8d2eae0a623305c4ee23ced
+Subproject commit 8a86db97eb89833a88b1ee876880cb1c07ce8565

src/singularity_modules/sambamba/0.6.9/build.sh

+#/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

src/singularity_modules/sambamba/0.6.9/sambamba

+#/bin/bash
+singularity exec /sps/lbmc/common/singularity/sambamba:0.6.7.img sambamba $@

src/singularity_modules/sambamba/0.6.9/sambamba.def

+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 "$@"