added script to build a nightly build from git repo

scripts/ost-nightly-build.sh

+#!/bin/bash
+
+## Script to compile a nightly build of OpenStructure from the git repo
+##
+## This script requires that you can clone the OST repo and it uses the sciCORE 
+## software stack for dependencies so it will only work in the sciCORE login nodes
+##
+## Author: Pablo Escobar <pablo.escobarlopez@unibas.ch>
+
+
+# print help if no arguments supplied or -h or --help
+if [[ $# -eq 0 ]] || [ "$1" == "-h" ] || [ "$1" == "--help" ]; then
+	echo "Usage: $0 branch_to_clone"
+	exit 1
+fi	
+
+function main {
+
+CURRENT_DATE=$(date +"%Y%m%dT%H%M%SZ")
+GIT_BRANCH=$1
+
+# create a temporary directory to download the sources and do the build
+TEMP_DIR="/scratch/${USER}/ost-builds/$CURRENT_DATE"
+echo -e "\ncreating temporary dir to clone and build in $TEMP_DIR\n"
+mkdir -p $TEMP_DIR
+
+# clone the development branch of OST to $TEMP_DIR
+git_cmd="git clone -b $GIT_BRANCH ssh://git@git.scicore.unibas.ch:2222/schwede/openstructure.git $TEMP_DIR/openstructure"
+echo "cloning the OST code: $GIT_BRANCH branch"
+echo -e "running $git_cmd"
+$git_cmd
+
+# fetch the latest git commit ID. We will use this in the module name together with the branch name
+cd $TEMP_DIR/openstructure
+LATEST_COMMIT=`git rev-parse HEAD | cut -c1-8`
+
+# create a tarball with the sources. We will pass this to easybuild
+TARBALL_NAME="OpenStructure-nightly-${CURRENT_DATE}_${GIT_BRANCH}_commit${LATEST_COMMIT}.tar.bz2"
+echo -e "\nCreating a tarball with the source code to feed EasyBuild"
+echo -e "running tar -cjf $TARBALL_NAME openstructure"
+cd $TEMP_DIR
+tar -cjf $TARBALL_NAME openstructure
+
+# create the installation directory if it doesn't exists
+# by default $INSTALL_DIR is in the cluster shared scratch so the module
+# can be used from any compute node
+INSTALL_DIR="/scicore/scratch/$USER/ost-nightly-builds"
+echo -e "\nCreating install dir $INSTALL_DIR if it doesn't exists"
+if [ ! -d "$INSTALL_DIR" ]; then
+	mkdir -p $INSTALL_DIR
+fi
+
+# create a easyconfig to build OST
+echo -e "\nCreating an easyconfig in $TEMP_DIR/ost-easyconfig.eb based on the provided template"
+generate_easyconfig_template  # this function is defined at the bottom of the script to improve readability
+
+echo -e "\nSetting up the modules environment by executing 'source /etc/profile.d/lmod.sh'"
+source /etc/profile.d/lmod.sh
+
+echo -e "\nLoading the Easybuild module executing 'module load EasyBuild'"
+module load EasyBuild
+
+echo -e "\nRunning EasyBuild"
+eb_command="eb --optarch=GENERIC --sourcepath=$TEMP_DIR --buildpath=$TEMP_DIR/easybuild_build_dir --installpath=$INSTALL_DIR $TEMP_DIR/ost-easyconfig.eb"
+echo $eb_command
+$eb_command
+
+if [[ $? != 0 ]]; then
+	echo -e "\nBuild failed. Not deleting temp dir $TEMP_DIR"
+else
+        echo -e "\nBuild completed succesfully. Deleting temp dir $TEMP_DIR"
+	rm -fr $TEMP_DIR
+	echo -e "\nrun 'module use $INSTALL_DIR/modules/all/' to add the new modules to your \$MODULEPATH"
+	echo -e "If you don't see the new module try deleting your Lmod's cache doing 'rm ~/.lmod.d/.cache/*'\n"
+
+fi
+
+} # end of main function
+
+function generate_easyconfig_template {
+
+cat > $TEMP_DIR/ost-easyconfig.eb << EOF
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics
+
+easyblock = "CMakeMake"
+
+name = 'OpenStructure-nightly'
+version = '${CURRENT_DATE}'
+versionsuffix = '_${GIT_BRANCH}_commit${LATEST_COMMIT}'
+
+homepage = 'http://www.openstructure.org'
+description = "Open-Source Computational Structural Biology Framework"
+
+toolchain = {'name': 'goolf', 'version': '1.4.10'}
+
+sources = ['$TARBALL_NAME']
+
+builddependencies = [('CMake', '2.8.12')]
+
+pythonversion = "2.7.5"
+pythonshortversion = ".".join(pythonversion.split(".")[:-1])
+
+dependencies = [
+    ('Python', pythonversion),
+    ('Boost', '1.53.0', '-Python-%s' % (pythonversion)),
+    ('numpy', '1.9.1', '-Python-%s' % (pythonversion)),
+    ('Qt', '4.8.4'),
+    ('Eigen', '3.2.1'),
+#   ('FFTW', '3.3.3'),  # this dependency is already included with toolchain goolf-1.4.10
+    ('zlib', '1.2.8'),
+    ('bzip2', '1.0.6'),
+    ('libpng', '1.6.17'), 
+    ('LibTIFF', '4.0.3'), 
+    ('libjpeg-turbo', '1.4.0'), 
+    ('OpenMM', '6.1-Linux64', '', True), 
+    ('FFTW', '3.3.3', '-dynamic', ('gompi', '1.4.10')), 
+]
+
+configopts = " -DOPTIMIZE=1 -DCOMPILE_TMTOOLS=1 -DENABLE_GFX=OFF -DENABLE_GUI=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS_RELEASE='-O3 -DNDEBUG -Wno-unused-local-typedefs' -DUSE_NUMPY=1 -DUSE_RPATH=1"
+
+configopts += " -DCOMPOUND_LIB=/scicore/home/schwede/GROUP/OpenStructure/ChemLib/1.4/compounds.chemlib"
+
+configopts += " -DPYTHON_ROOT=\$EBROOTPYTHON -DEIGEN3_INCLUDE_DIR=\$EBROOTEIGEN -DFFTW_LIBRARY=\$EBROOTFFTW/lib/libfftw3f.a -DFFTW_INCLUDE_DIR=\$EBROOTFFTW/include -DBOOST_ROOT=\$EBROOTBOOST -DQT_QMAKE_EXECUTABLE=\$EBROOTQT/bin/qmake -DBoost_USE_MULTITHREADED=OFF"
+
+configopts += " -DENABLE_MM=1 -DOPEN_MM_LIBRARY=\$EBROOTOPENMM/lib/libOpenMM.so -DOPEN_MM_PLUGIN_DIR=\$EBROOTOPENMM/lib/plugins -DOPEN_MM_INCLUDE_DIR=\$EBROOTOPENMM/include"
+
+runtest = 'check'
+
+sanity_check_paths = { 
+    'files': ["bin/ost", "bin/chemdict_tool"],
+    'dirs': ["include/ost"],
+}
+
+# add \$INSTALLDIR/lib64/python2.7/site-packages to PYTHONPATH
+modextrapaths = {
+    'PYTHONPATH': 'lib64/python%s/site-packages' % (pythonshortversion)
+}
+
+# OST_ROOT env var points to install directory
+modextravars = {
+    'OST_ROOT': '%(installdir)s'
+}
+
+postinstallcmds = ["rm -fr %(installdir)s/share/openstructure/compounds.chemlib",
+                   "cd %(installdir)s/share/openstructure/ && ln -s /scicore/home/schwede/GROUP/OpenStructure/ChemLib/1.6/compounds.chemlib compounds.chemlib",]
+
+moduleclass = 'bio'
+EOF
+
+}
+
+main "$@"

[Pablo Escobar]

you are right, I will apply the suggested change

[Pablo Escobar]

I agree

[Pablo Escobar]

no, it's not a good idea to add the commit ID to the app name. It's better to keep the commit ID in the module suffix.

If the application has different names (different commit IDs in the name) then Lmod would think that they are different apps. It's better to keep the name fixed and only update the module name suffix so Lmod knows that they are different versions of the same app. This will also help so the most recently installed module is the default in Lmod (I took care of using the right date format in the module version so this is the case)

[Bienchen]

OK.

[Pablo Escobar]

I updated the script to use 1.6