mafreitas/singularity-openms:latest
$ singularity pull shub://mafreitas/singularity-openms:latest
Singularity Recipe
BootStrap: shub
From: mafreitas/singularity-openms:contrib
%environment
export PATH=/usr/local/openms_thirdparty/All/:$PATH
export PATH=/usr/local/openms_thirdparty/All/LuciPHOr2:$PATH
export PATH=/usr/local/openms_thirdparty/All/MSGFPlus:$PATH
export PATH=/usr/local/openms_thirdparty/All/Sirius:$PATH
export PATH=/usr/local/openms_thirdparty/Linux/64bit/:$PATH
export PATH=/usr/local/openms_thirdparty/Linux/64bit/Comet:$PATH
export PATH=/usr/local/openms_thirdparty/Linux/64bit/Fido:$PATH
export PATH=/usr/local/openms_thirdparty/Linux/64bit/MyriMatch:$PATH
export PATH=/usr/local/openms_thirdparty/Linux/64bit/OMSSA:$PATH
export PATH=/usr/local/openms_thirdparty/Linux/64bit/Percolator:$PATH
export PATH=/usr/local/openms_thirdparty/Linux/64bit/Sirius:$PATH
export PATH=/usr/local/openms_thirdparty/Linux/64bit/SpectraST:$PATH
export PATH=/usr/local/openms_thirdparty/Linux/64bit/XTandem:$PATH
export PATH=/usr/local/bin/:$PATH
export OPENMS_DATA_PATH=/usr/local/share/OpenMS
export JAVA_HOME=/usr/lib/jvm/java-8-oracle
%post
cd $HOME
git clone https://github.com/OpenMS/OpenMS.git
cd OpenMS
git checkout tags/Release2.3.0
hash=`git log | head -n 1 | cut -f 2 -d ' '`
sed -i "s/OPENMS_GIT_SHA1/\"$hash\"/" src/openms/source/CONCEPT/VersionInfo.cpp
rm -rf .git/ share/OpenMS/examples/
cd /usr/local/
git clone https://github.com/OpenMS/THIRDPARTY.git openms_thirdparty
cd openms_thirdparty
rm -rf .git Windows MacOS Linux/32bit
cd $HOME
mkdir openms-build
cd openms-build
cmake -DCMAKE_PREFIX_PATH="$HOME/contrib-build/;/usr/;/usr/local" \
-DCMAKE_INSTALL_PREFIX=/usr/local/ \
-DBOOST_USE_STATIC=OFF \
-DHAS_XSERVER=Off ../OpenMS
make TOPP -j6
make UTILS -j6
make install -j6
rm -rf src doc CMakeFiles
cd $HOME
rm -rf contrib contrib-build openms-build
Collection
- Name: mafreitas/singularity-openms
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/mafreitas-singularity-openms-latest |
collection name | mafreitas/singularity-openms |
branch | master |
tag | latest |
commit | 0b7a38d1ade9d7df20170778987f9f75ed21764c |
version (container hash) | 82a5fb1630e2bc3e0d22b294c0ba9ecb |
build date | 2020-07-11T09:15:36.194Z |
size (MB) | 2049 |
size (bytes) | 862617631 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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