skptic/dpa-analysis:latest
$ singularity pull shub://skptic/dpa-analysis:latest
Singularity Recipe
Bootstrap:docker
From:debian:jessie
%labels
MAINTAINER Evan Floden
%environment
CACHE_4_TCOFFEE='${TMPDIR:-/tmp}/.tcoffee/cache'
LOCKDIR_4_TCOFFEE='${TMPDIR:-/tmp}/.tcoffee/lock'
TMP_4_TCOFFEE='${TMPDIR:-/tmp}/.tcoffee/tmp'
PYTHONPATH=$PYTHONPATH:/home/lib/python2.7/site-packages/
%post
apt-get update
apt-get install -y --no-install-recommends ed less vim-tiny wget git
apt-get install -y --no-install-recommends python build-essential cmake curl libargtable2-0
apt-get install -y --no-install-recommends python-biopython python-numpy ruby python-setuptools
apt-get install -y --no-install-recommends default-jdk libpng-dev
##
# install argtable
##
wget http://prdownloads.sourceforge.net/argtable/argtable2-13.tar.gz
tar -zxf argtable2-13.tar.gz
cd argtable2-13
./configure
make
make install
rm /argtable2-13.tar.gz
cd /
##
# install clustal omega
##
wget http://www.clustal.org/omega/clustal-omega-1.2.4.tar.gz
tar -zxf clustal-omega-1.2.4.tar.gz
cd clustal-omega-1.2.4
./configure
make
make install
rm /clustal-omega-1.2.4.tar.gz
cd /
##
# install mafft
##
wget https://mafft.cbrc.jp/alignment/software/mafft-7.397-with-extensions-src.tgz
tar xfvz mafft-7.397-with-extensions-src.tgz
cd mafft-7.397-with-extensions/core/
sed -i "s/PREFIX = \/usr\/local/PREFIX = \/mafft/g" Makefile
sed -i "s/BINDIR = \$(PREFIX)\/bin/BINDIR = \/mafft\/bin/g" Makefile
make clean
make
make install
wget http://mafft.cbrc.jp/alignment/software/newick2mafft.rb
chmod +x newick2mafft.rb
export "PATH=$PATH:/mafft/bin"
export MAFFT_BINARIES=""
cp /mafft/bin/* /bin/.
mv /mafft-7.397-with-extensions /mafft
rm /mafft-7.397-with-extensions-src.tgz
cd /
##
# install probcons
##
apt-get install -y --no-install-recommends probcons
##
# install msaprobs
##
wget "https://downloads.sourceforge.net/project/msaprobs/MSAProbs-0.9.7.tar.gz" -O msaprobs.tar.gz
tar zxf msaprobs.tar.gz
cd MSAProbs-0.9.7/MSAProbs
make
cp msaprobs /usr/bin
rm /msaprobs.tar.gz
cd /
##
# install UPP
##
git clone http://github.com/smirarab/sepp.git
cd sepp
mkdir -p /home/lib/python2.7/site-packages/
export PYTHONPATH=$PYTHONPATH:/home/lib/python2.7/site-packages/
python setup.py config -c
echo "/home/" > /sepp/home.path
sed -i "s/root/home/g" /sepp/.sepp/main.config
python setup.py install --prefix=/home/
python setup.py develop
mkdir /pasta-code
cd /pasta-code
git clone https://github.com/smirarab/pasta.git
git clone https://github.com/smirarab/sate-tools-linux.git
cd pasta
python setup.py develop -user
export PATH=$PATH:/pasta-code/pasta:/sepp
cd /sepp
python setup.py upp -c
sed -i "s/root/home/g" /sepp/.sepp/upp.config
cd /pasta-code/pasta
python setup.py develop
cd /
##
# install msa
##
wget ftp://ftp.ncbi.nih.gov/pub/msa/msa.tar.Z
tar xfvz msa.tar.Z
cd msa
make clean
make msa
rm /msa.tar.Z
chmod +x /msa/msa
cp /msa/msa /bin/.
cd /
##
# install tcoffee
##
git clone https://github.com/cbcrg/tcoffee.git tcoffee
cd tcoffee
git checkout 3c3d66e9797f32beaff56cf3d06522b8dd65460f
cd compile
make t_coffee
cp t_coffee /bin/.
cd /
##
# retrieve some test data
##
mkdir /test_data
cd test_data
wget https://raw.githubusercontent.com/skptic/dpa-analysis/master/tutorial/seqs/rnasemam.fa
wget https://raw.githubusercontent.com/skptic/dpa-analysis/master/tutorial/seqs/seatoxin.fa
wget https://raw.githubusercontent.com/skptic/dpa-analysis/master/tutorial/refs/rnasemam.ref
wget https://raw.githubusercontent.com/skptic/dpa-analysis/master/tutorial/refs/seatoxin.ref
wget https://raw.githubusercontent.com/skptic/dpa-analysis/master/tutorial/trees/rnasemam.dnd
wget https://raw.githubusercontent.com/skptic/dpa-analysis/master/tutorial/trees/seatoxin.dnd
Collection
- Name: skptic/dpa-analysis
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/skptic-dpa-analysis-latest |
collection name | skptic/dpa-analysis |
branch | master |
tag | latest |
commit | c9e853bfb72247e4d3976b4beb44981d981794a1 |
version (container hash) | c50f752b11009793d994940a340d80b8 |
build date | 2018-05-29T12:58:44.799Z |
size (MB) | 1448 |
size (bytes) | 686800927 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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