From b150232b706eef74f5be80b2f08ffb56385481d4 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 29 Mar 2019 15:12:25 +0100
Subject: [PATCH] hisat2: add v2.1.0
---
src/docker_modules/hisat2/2.1.0/Dockerfile | 20 ++++++++
.../hisat2/2.1.0/docker_init.sh | 2 +
src/nf_modules/hisat2/indexing.config | 6 +--
src/nf_modules/hisat2/mapping_paired.config | 6 +--
src/nf_modules/hisat2/mapping_single.config | 6 +--
src/psmn_modules | 2 +-
src/singularity_modules/hisat2/2.1.0/build.sh | 3 ++
.../hisat2/2.1.0/hisat2.def | 50 +++++++++++++++++++
8 files changed, 85 insertions(+), 10 deletions(-)
create mode 100644 src/docker_modules/hisat2/2.1.0/Dockerfile
create mode 100755 src/docker_modules/hisat2/2.1.0/docker_init.sh
create mode 100755 src/singularity_modules/hisat2/2.1.0/build.sh
create mode 100644 src/singularity_modules/hisat2/2.1.0/hisat2.def
diff --git a/src/docker_modules/hisat2/2.1.0/Dockerfile b/src/docker_modules/hisat2/2.1.0/Dockerfile
new file mode 100644
index 00000000..5f937ce5
--- /dev/null
+++ b/src/docker_modules/hisat2/2.1.0/Dockerfile
@@ -0,0 +1,20 @@
+FROM samtools:1.7
+MAINTAINER Nicolas Fontrodona
+
+ENV HISAT2_VERSION=2.1.0
+ENV PACKAGES curl \
+ zip \
+ g++ \
+ perl \
+ python
+
+RUN apk update && \
+ apk add ${PACKAGES}
+
+RUN curl -k -L http://ccb.jhu.edu/software/hisat2/dl/hisat2-${HISAT2_VERSION}-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip && \
+unzip hisat2_linux-v${HISAT2_VERSION}.zip && \
+cd hisat2-${HISAT2_VERSION} && \
+make && \
+cp hisat2 /usr/bin && \
+cp hisat2-* /usr/bin && \
+rm -Rf hisat2-${HISAT2_VERSION}
diff --git a/src/docker_modules/hisat2/2.1.0/docker_init.sh b/src/docker_modules/hisat2/2.1.0/docker_init.sh
new file mode 100755
index 00000000..3004f07a
--- /dev/null
+++ b/src/docker_modules/hisat2/2.1.0/docker_init.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+docker build src/docker_modules/hisat2/2.1.0 -t 'hisat2:2.1.0'
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index 47c14a57..b259633a 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: index_fasta {
- container = "hisat2:2.0.0"
+ container = "hisat2:2.1.0"
cpus = 4
}
}
@@ -14,7 +14,7 @@ profiles {
process {
withName: index_fasta {
cpus = 4
- container = "file://bin/hisat2:2.0.0.sif"
+ container = "file://bin/hisat2:2.1.0.sif"
}
}
}
@@ -22,7 +22,7 @@ profiles {
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "hisat2/2.0.0"
+ module = "hisat2/2.1.0"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index e23abd8a..02c92edf 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -5,7 +5,7 @@ profiles {
process {
withName: mapping_fastq {
cpus = 4
- container = "hisat2:2.0.0"
+ container = "hisat2:2.1.0"
}
}
}
@@ -14,7 +14,7 @@ profiles {
process {
withName: mapping_fastq {
cpus = 4
- container = "file://bin/hisat2:2.0.0.sif"
+ container = "file://bin/hisat2:2.1.0.sif"
}
}
}
@@ -22,7 +22,7 @@ profiles {
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "hisat2/2.0.0:samtools/1.7"
+ module = "hisat2/2.1.0:samtools/1.7"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index e23abd8a..02c92edf 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -5,7 +5,7 @@ profiles {
process {
withName: mapping_fastq {
cpus = 4
- container = "hisat2:2.0.0"
+ container = "hisat2:2.1.0"
}
}
}
@@ -14,7 +14,7 @@ profiles {
process {
withName: mapping_fastq {
cpus = 4
- container = "file://bin/hisat2:2.0.0.sif"
+ container = "file://bin/hisat2:2.1.0.sif"
}
}
}
@@ -22,7 +22,7 @@ profiles {
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
- module = "hisat2/2.0.0:samtools/1.7"
+ module = "hisat2/2.1.0:samtools/1.7"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
diff --git a/src/psmn_modules b/src/psmn_modules
index 9ae41bf7..746ce102 160000
--- a/src/psmn_modules
+++ b/src/psmn_modules
@@ -1 +1 @@
-Subproject commit 9ae41bf72d4f536d73a76dfd13e375bca7d4f48e
+Subproject commit 746ce10272091f40f3c98e6972dede47df4b0beb
diff --git a/src/singularity_modules/hisat2/2.1.0/build.sh b/src/singularity_modules/hisat2/2.1.0/build.sh
new file mode 100755
index 00000000..074f4ce6
--- /dev/null
+++ b/src/singularity_modules/hisat2/2.1.0/build.sh
@@ -0,0 +1,3 @@
+#/bin/sh
+sudo singularity build --force bin/hisat2:2.1.0.sif src/singularity_modules/hisat2/2.1.0/hisat2.def && \
+singularity sign bin/hisat2:2.1.0.sif
diff --git a/src/singularity_modules/hisat2/2.1.0/hisat2.def b/src/singularity_modules/hisat2/2.1.0/hisat2.def
new file mode 100644
index 00000000..c6358b11
--- /dev/null
+++ b/src/singularity_modules/hisat2/2.1.0/hisat2.def
@@ -0,0 +1,50 @@
+Bootstrap: docker
+From: alpine:3.8
+
+%labels
+MAINTAINER Laurent Modolo
+
+%post
+SAMTOOLS_VERSION=1.7
+HISAT2_VERSION=2.1.0
+PACKAGES="git \
+ make \
+ gcc \
+ musl-dev \
+ zlib-dev \
+ ncurses-dev \
+ bzip2-dev \
+ xz-dev \
+ bash \
+ curl \
+ zip \
+ g++ \
+ perl \
+ python"
+apk update && \
+apk add ${PACKAGES}
+
+git clone https://github.com/samtools/htslib.git && \
+cd htslib && \
+git checkout ${SAMTOOLS_VERSION} && \
+cd .. && \
+git clone https://github.com/samtools/samtools.git && \
+cd samtools && \
+git checkout ${SAMTOOLS_VERSION} && \
+make && \
+cp samtools /usr/bin/
+
+curl -k -L http://ccb.jhu.edu/software/hisat2/dl/hisat2-${HISAT2_VERSION}-source.zip -o hisat2_linux-v${HISAT2_VERSION}.zip && \
+unzip hisat2_linux-v${HISAT2_VERSION}.zip && \
+cd hisat2-${HISAT2_VERSION} && \
+make && \
+cp hisat2 /usr/bin && \
+cp hisat2-* /usr/bin && \
+rm -Rf hisat2-${HISAT2_VERSION}
+
+%environment
+export SAMTOOLS_VERSION=1.7
+export HISAT2_VERSION=2.1.0
+
+%runscript
+exec /bin/bash "$@"
--
GitLab