bballew/NGS_singularity_recipes:samtools_1-9_bwa_0-7-17_picard_2-18-15
$ singularity pull shub://bballew/NGS_singularity_recipes:samtools_1-9_bwa_0-7-17_picard_2-18-15
Singularity Recipe
BootStrap: yum
OSVersion: 7
MirrorURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/os/$basearch/
Include: yum
%labels
AUTHOR BBallew
%setup
mkdir -p ${SINGULARITY_ROOTFS}/input
mkdir -p ${SINGULARITY_ROOTFS}/output
mkdir -p ${SINGULARITY_ROOTFS}/ref
mkdir -p ${SINGULARITY_ROOTFS}/scratch
%post
yum -y groupinstall "Development Tools"
yum -y install sudo autoconf automake make gcc wget perl-Data-Dumper zlib-devel bzip2 bzip2-devel xz-devel curl-devel openssl-devel ncurses-devel
# install bwa
wget https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2
tar xvjf bwa-0.7.17.tar.bz2
cd bwa-0.7.17/
make
cp bwa /usr/local/bin
cd -
# install samtools
wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
tar xvjf samtools-1.9.tar.bz2
cd samtools-1.9
./configure
make
make install
cd -
# install java
yum -y install java-1.8.0-openjdk-devel
# install picard
wget https://github.com/broadinstitute/picard/releases/download/2.18.15/picard.jar
mv picard.jar /bin
Collection
- Name: bballew/NGS_singularity_recipes
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/bballew-NGS_singularity_recipes-samtools_1-9_bwa_0-7-17_picard_2-18-15 |
collection name | bballew/NGS_singularity_recipes |
branch | master |
tag | samtools_1-9_bwa_0-7-17_picard_2-18-15 |
commit | 261b0ba21401aa85360fa54efa5ba7f093fdc71a |
version (container hash) | f9139b9587c1ae2975c59102c2d41a38 |
build date | 2019-04-02T14:29:35.970Z |
size (MB) | 1265 |
size (bytes) | 422830111 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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