shamanpi/dummy:latest
$ singularity pull shub://shamanpi/dummy:latest
Singularity Recipe
Bootstrap: yum
OSVersion: 7
MirrorURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/os/$basearch/
Include: yum
%runscript
echo "Angsd-Wrapper install test.\n"
declare -a args=("$@")
INPUTSOURCE="${args[0]}"
BASESOURCE="${args[1]}"
if [[ -d "${INPUTSOURCE}" ]]; then # Checks if cluster has enabled 'overlayfs'. Which allows for full filepath.
SOURCE="${INPUTSOURCE}"
else # If full file paths are not allow on your cluster than operate from users locale directory
SOURCE="${BASESOURCE}"
fi
cd ${SOURCE}
cd dependencies
ROOT=$(pwd)
wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
tar -jxvf samtools-1.9.tar.bz2
rm samtools-1.9.tar.bz2
cd samtools-1.9
samPath=$(pwd)
echo "export PATH=$(pwd)/bin:"'${PATH}' >> ~/.bash_profile # Add the path to bash_profile
HTSLIB_DIR=$(pwd -P)/htslib-1.9
cd "${HTSLIB_DIR}"
./configure --prefix=$(pwd)
make
make install
cd "${samPath}"
./configure --with-htslib=${HTSLIB_DIR} --prefix=$(pwd)
make
make install
cd "${ROOT}"
git clone https://github.com/fgvieira/ngsF.git
cd ngsF
git reset --hard d980b85c0746c297285e2e415193914aa0d0412a
make
cd "${ROOT}"
# wget http://popgen.dk/software/download/angsd/angsd0.928.tar.gz
# tar -xvf angsd0.928.tar.gz
# rm angsd0.928.tar.gz
git clone https://github.com/ANGSD/angsd
git clone https://github.com/samtools/htslib/
cd "${ROOT}"/htslib
make
cd "${ROOT}"/angsd
#make HTSSRC="${HTSLIB_DIR}"
make HTSSRC="${ROOT}"/htslib
cd "${ROOT}"
mkdir ngsAdmix
cd ngsAdmix
wget http://popgen.dk/software/download/NGSadmix/ngsadmix32.cpp
g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix
cd "${ROOT}"
git clone https://github.com/mfumagalli/ngsPopGen.git
cd ngsPopGen
git reset --hard 8ead2d469f42942f413f6c93664b568d2eb8a124
make
cd "${ROOT}"
echo alias "angsd-wrapper='${SOURCE}/angsd-wrapper'" >> ~/.bash_profile
echo "export PATH=${samPath}:"'${PATH}' >> ~/.bash_profile # Add the path to bash_profile
%post
yum group install -y "Development Tools"
yum -y install wget
yum install -y tar.x86_64
yum install -y git
yum install -y bzip2
yum install -y gcc
yum install -y ncurses-devel
yum install -y zlib-devel
yum install -y bzip2-devel
yum install -y xz-devel
#yum groupinstall -y "Development Tools"
yum install -y xz
yum install -y curl-devel
yum install -y openssl-devel
yum install -y epel-release
yum -y update
yum clean all
Collection
- Name: shamanpi/dummy
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/shamanpi-dummy-latest |
collection name | shamanpi/dummy |
branch | master |
tag | latest |
commit | e6ccb97bcedd72bad12450cf934a1a0cce0b4595 |
version (container hash) | d3b23148e9a1eba5058609052b0fcdca |
build date | 2020-07-14T15:21:30.569Z |
size (MB) | 796.0 |
size (bytes) | 251617311 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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