ResearchIT/Scanfold:latest
$ singularity pull shub://ResearchIT/Scanfold:latest
Singularity Recipe
Bootstrap: docker
From: centos:7
%post
yum -y update
yum -y install epel-release wget git gcc-c++ zlib-devel make which
yum -y install python36 python36-devel
yum -y install python34-pip python34-devel
wget https://bootstrap.pypa.io/get-pip.py
python36 get-pip.py
python36 -m pip install biopython
python36 -m pip install numpy
python36 -m pip install pybigwig
python36 -m pip install requests
python3.4 -m pip install biopython numpy requests
# Install ViennaRNA & Python bindings
if [ ! -f /usr/bin/RNAfold ];
then
wget https://www.tbi.univie.ac.at/RNA/download/epel/epel_7/perl-rna-2.4.11-1.x86_64.rpm
wget https://www.tbi.univie.ac.at/RNA/download/epel/epel_7/viennarna-2.4.11-1.x86_64.rpm
wget https://www.tbi.univie.ac.at/RNA/download/epel/epel_7/python3-rna-2.4.11-1.x86_64.rpm
yum -y install viennarna-2.4.11-1.x86_64.rpm perl-rna-2.4.11-1.x86_64.rpm python3-rna-2.4.11-1.x86_64.rpm
fi
# Install RNAstructure
if [ ! -d /opt/rnastructure ];
then
mkdir -p /opt/rnastructure
wget http://rna.urmc.rochester.edu/Releases/current/RNAstructureSource.tgz
tar xzvf RNAstructureSource.tgz -C /opt/rnastructure
pushd /opt/rnastructure/RNAstructure
make ct2dot
popd
fi
# Install ScanFold
if [ ! -d /opt/scanfold ]
then
mkdir -p /opt/scanfold
git clone https://github.com/moss-lab/ScanFold.git /opt/scanfold
pushd /opt/scanfold
git checkout master
popd
else
pushd /opt/scanfold
git checkout master
git pull
popd
fi
%environment
export PATH=/opt/rnastructure/RNAstructure/exe:/opt/scanfold:$PATH
export DATAPATH=/opt/rnastructure/RNAstructure/data_tables
%runscript
exec python36 $@
%apprun scan
exec python3.4 /opt/scanfold/ScanFold-Scan_Webserver.py $@
%apprun fold
exec python36 /opt/scanfold/ScanFold-Fold_spinoff.py $@
%help
Run this container by specifying the scan or fold step:
e.g.
$ singularity run shub://ResearchIT/scanfold fold -i input.tsv ...
Collection
- Name: ResearchIT/Scanfold
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/ResearchIT-Scanfold-latest |
collection name | ResearchIT/Scanfold |
branch | master |
tag | latest |
commit | 2c0c9b480f42f29a907c0ae802bac1b987eb7c18 |
version (container hash) | 9b8d0b18bad4f87206c9e829500857c3 |
build date | 2019-05-02T19:59:05.855Z |
size (MB) | 996 |
size (bytes) | 345993247 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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