jdwheaton/singularity-ngs:latest
$ singularity pull shub://jdwheaton/singularity-ngs:latest
Singularity Recipe
Bootstrap: docker
From: centos:7
%post
# Install required build tools
yum -y update
yum -y install git autoconf gcc make wget unzip bzip2
# Install htslib and samtools dependencies
yum -y install zlib-devel bzip2-devel xz-devel ncurses-devel
# Clone htslib and samtools from github
git clone https://github.com/samtools/htslib.git
git clone https://github.com/samtools/samtools.git
# Make and install htslib and samtools
cd htslib
autoheader
autoconf
./configure
make
make install
cd ../samtools
autoheader
autoconf
./configure
make
make install
# Download and compile bowtie2
cd /
wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.1/bowtie2-2.3.4.1-linux-x86_64.zip
unzip bowtie2-2.3.4.1-linux-x86_64.zip
rm bowtie2-2.3.4.1-linux-x86_64.zip
%environment
export PATH=$PATH:/bowtie2-2.3.4.1-linux-x86_64
%runscript
samtools --help
Collection
- Name: jdwheaton/singularity-ngs
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/jdwheaton-singularity-ngs-latest |
collection name | jdwheaton/singularity-ngs |
branch | master |
tag | latest |
commit | de66ff51bb6ba8d1fe31c08b581e21166c2901e4 |
version (container hash) | 9f12847c233853defff991c7ab30e39c |
build date | 2020-02-11T22:43:12.198Z |
size (MB) | 784 |
size (bytes) | 239636511 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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