dp2ski/genome_software_aci:rec
$ singularity pull shub://dp2ski/genome_software_aci:rec
Singularity Recipe
Bootstrap: docker
From: centos:centos7
%runscript
%environment
export PATH=$PATH:/PBSuite_15.8.24/
export PYTHONPATH=$PYTHONPATH:/PBSuite_15.8.24/
%apprun fastQValidator
exec /fastQValidator/bin/fastQValidator "$@"
%apprun NxTrim
exec /NxTrim/nxtrim "$@"
%apprun RecoverY
exec python /RecoverY/recoverY.py "$@"
%apprun Trimmomatic
exec java -jar /Trimmomatic-0.38/trimmomatic-0.38.jar "$@"
%apprun PBJelly
exec /PBSuite_15.8.24/bin/Jelly.py "$@"
%post
# commands to be executed inside container during bootstrap
# add python and install some packages
# taken from one of will's singularity recipies
yum update -y
yum install -y epel-release
yum install -y terminator
yum install -y centos-release-scl
yum install -y vte-devel
yum install -y vte291-devel
yum install -y vte-profile
yum install -y devtoolset-7-gcc*
scl enable devtoolset-7 bash
yum -y groups install "Development Tools"
yum -y groups install "Base"
yum -y install git cmake gcc-c++ gcc binutils \
libX11-devel libXpm-devel libXft-devel libXext-devel
yum -y install gcc-gfortran openssl-devel pcre-devel \
mesa-libGL-devel mesa-libGLU-devel glew-devel ftgl-devel mysql-devel \
fftw-devel cfitsio-devel graphviz-devel \
avahi-compat-libdns_sd-devel libldap-dev python-devel \
libxml2-devel gsl-devel
yum -y install python-pip
pip install numpy
pip install biopython
pip install matplotlib
pip install seaborn
#ACI mappings
mkdir -p /storage/home
mkdir -p /storage/work
mkdir -p /gpfs/group
mkdir -p /gpfs/scratch
mkdir -p /var/spool/torque
git clone https://github.com/statgen/libStatGen
cd libStatGen
make all
cd ..
git clone https://github.com/statgen/fastQValidator
cd fastQValidator
make all
cd ..
git clone https://github.com/sequencing/NxTrim.git
cd NxTrim
make
cd ..
#this one is just a bunch of python scripts
git clone https://github.com/makovalab-psu/RecoverY
wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip
unzip Trimmomatic-0.38.zip
yum -y install java-1.8.0-openjdk
wget https://sourceforge.net/projects/pb-jelly/files/latest/download/PBSuite_15.8.24.tgz
tar -xzf PBSuite_15.8.24.tgz
pip install networkx==1.1
cd /PBSuite_15.8.24
sed -i 's\/stornext/snfs5/next-gen/scratch/english/Jelly/DevJelly/trunk\/PBSuite_15.8.24\g' setup.sh
source setup.sh
Collection
- Name: dp2ski/genome_software_aci
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/dp2ski-genome_software_aci-rec |
collection name | dp2ski/genome_software_aci |
branch | master |
tag | rec |
commit | a2acb6adaa565d93ba109cb20d1cb8c875e24b4a |
version (container hash) | 0458787dead64b2a2e1cc36a9aebd0f5 |
build date | 2019-02-05T16:48:48.026Z |
size (MB) | 2349 |
size (bytes) | 1072955423 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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