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2.1
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2.1
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Bootstrap:docker
From:centos:7
Include: yum
%files
calcSAXS-bufSub.in /calcSAXS-bufSub.in
annoying-mars-cert.pem /etc/pki/ca-trust/source/anchors/mars-cert.pem
sadic-1.1b1.tar.gz /sadic-1.1b1.tar.gz
numarray-1.5.2.tar.gz /numarray-1.5.2.tar.gz
Python-2.4.6.tgz /Python-2.4.6.tgz
%environment
PATH=/opt/nmrPipe/bin:/opt/xplor-nih/bin:/opt/mars/bin:/opt/nmrPipe/talos/bin/:/opt/nmrPipe/spartaplus/bin:$PATH
export PATH:/opt/python2.4/bin
export MARSHOME=/opt/mars/bin
export SPARTAP_DIR=/opt/sparta
export SPARTA_DIR=/opt/sparta
%post
update-ca-trust
yum update -y
yum install -y epel-release
yum install -y git curl which vim wget tar bzip2 gzip gawk mesa-libGL mesa-libGLU tcsh xterm xterm.i686 libgcc.i686 glibc.i686 libX11.so.6 libX11.so.6.i686 libXext.so.6 libXext.so.6.i686 libstdc++.so.6 libstdc++.so.6.i686 xorg-x11-fonts-75dpi xorg-x11-fonts-ISO8859-1-75dpi xorg-x11-fonts-100dpi xorg-x11-fonts-ISO8859-1-100dpi xorg-x11-fonts-misc gcc gcc-c++ make
mkdir -p /opt/nmrPipe
mkdir -p /install
cd /opt/nmrPipe
curl -LO http://www.ibbr.umd.edu/nmrpipe/NMRPipeX.tZ
curl -LO http://www.ibbr.umd.edu/nmrpipe/s.tZ
curl -LO http://www.ibbr.umd.edu/nmrpipe/install.com
curl -LO http://www.ibbr.umd.edu/nmrpipe/binval.com
curl -LO http://www.ibbr.umd.edu/nmrpipe/dyn.tZ
curl -LO https://spin.niddk.nih.gov/bax/software/talos_nmrPipe.tZ
#NMRpipe and co install
chmod +x install.com
chmod +x binval.com
tcsh ./install.com +type linux212_64 +dest /opt/nmrPipe +nocshrc +nopost /opt/nmrPipe
cat << EOF > /etc/profile.d/nmrpipe.csh
#!/usr/bin/tcsh
if (-e /opt/nmrPipe/com/nmrInit.linux212_64.com) then
source /opt/nmrPipe/com/nmrInit.linux212_64.com
endif
if (-e /opt/nmrPipe/dynamo/com/dynInit.com) then
source /opt/nmrPipe/dynamo/com/dynInit.com
endif
EOF
cat << EOF > /etc/profile.d/singularity.csh
set prompt = 'nmrutils > '
EOF
ln -s /opt/nmrPipe/nmrbin.linux212_64 /opt/nmrPipe/bin
cd /install
curl -LO https://nmr.cit.nih.gov/xplor-nih/packages/xplor-nih-3.5-Linux_x86_64.tar.gz
curl -LO https://nmr.cit.nih.gov/xplor-nih/packages/xplor-nih-3.5-db.tar.gz
curl -LO https://www3.mpibpc.mpg.de/groups/zweckstetter/_software_files/_mars/mars-1.2_linux.tar.gz
#xplor install
tar -xzf xplor-nih-3.5-Linux_x86_64.tar.gz
tar -xzf xplor-nih-3.5-db.tar.gz
mv xplor-nih-3.5 /opt/xplor-nih
mv /calcSAXS-bufSub.in /opt/xplor-nih/bin/calcSAXS-bufSub.in
cd /opt/xplor-nih
./configure
cd bin
sed -i "s/#!\/usr\/bin\/env.*$/#!\/opt\/xplor-nih\/bin\/pyXplor/" *
cd /install
#mars
tar -xzf mars-1.2_linux.tar.gz
mv mars-1.2_linux /opt/mars
chmod -R o+rX /opt/mars
chmod o+rx /opt/mars/bin/*
#python for sadic
PYTHON_ROOT=/opt/python2.4
cd /
tar -xzf Python-2.4.6.tgz
cd Python-2.4.6
./configure --prefix=${PYTHON_ROOT}
make -j4
make install
rm -rf /Python-2.4.6
#sadic stuff
cd /
tar -xzf /numarray-1.5.2.tar.gz
cd numarray-1.5.2
${PYTHON_ROOT}/bin/python setup.py install
cd /
rm -rf /numarray-1.5.2*
tar -xzf /sadic-1.1b1.tar.gz
cp -r sadic-1.1b1 /opt/sadic
rm -rf /sadic-1.1b1
cd /opt/sadic
${PYTHON_ROOT}/bin/python setup.py install
#sparta+ included in nmrpipe supposedly
#talos+ also included in nmrpipe
#cleanup
yum clean all
rm -f calcSAXS-bufSub.in
rm -rf /var/cache/yum/*
rm -rf /install
rm -rf /opt/nmrPipe/{*.tZ,install.com,binval.com,nmrbin.mac11_64}
%runscript
exec "$@"