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install-devel.sh
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install-devel.sh
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#!/usr/bin/env bash
# Travis: repo is provided by travis.
# build conda environment
#
# Jenkins: repo is provided by jenkins
#
# Local: code can be downloaded (--clone-from-repo)
#
# References
# http://kvz.io/blog/2013/11/21/bash-best-practices/
# http://jvns.ca/blog/2017/03/26/bash-quirks/
# exit when a command fails
set -o errexit
# exit if any pipe commands fail
set -o pipefail
# exit when your script tries to use undeclared variables
#set -o nounset
# trace what gets executed
#set -o xtrace
#set -o errtrace
# Bash traps
# http://aplawrence.com/Basics/trapping_errors.html
# https://stelfox.net/blog/2013/11/fail-fast-in-bash-scripts/
SCRIPT_NAME="$0"
SCRIPT_PARAMS="$@"
error_handler() {
echo
echo " ########################################################## "
echo
echo " An error occurred in:"
echo
echo " - line number: ${1}"
shift
echo " - exit status: ${1}"
shift
echo " - command: ${@}"
echo
echo " The script will abort now. User input was: "
echo
echo " ${SCRIPT_NAME} ${SCRIPT_PARAMS}"
echo
echo " Please copy and paste this error and report it via Git Hub: "
echo " https://github.com/cgat-developers/cgat-flow/issues "
print_env_vars
echo " ########################################################## "
}
trap 'error_handler ${LINENO} $? ${BASH_COMMAND}' ERR INT TERM
# log installation information
log() {
echo "# install-devel.sh log | `hostname` | `date` | $1 "
}
# report error and exit
report_error() {
echo
echo $1
echo
echo "Aborting."
echo
exit 1
}
# detect CGAT installation
detect_cgat_installation() {
if [[ -z "$CGAT_HOME" ]] ; then
if [[ -d "$HOME/cgat-install/conda-install" ]] ; then
UNINSTALL_DIR="$HOME/cgat-install"
fi
else
if [[ -d "$CGAT_HOME/conda-install" ]] ; then
UNINSTALL_DIR="$CGAT_HOME"
fi
fi
} # detect_cgat_installation
# configure environment variables
# set: CGAT_HOME, CONDA_INSTALL_DIR, CONDA_INSTALL_TYPE_PIPELINES
get_cgat_env() {
if [[ -z $CGAT_HOME ]] ; then
CGAT_HOME=$HOME/cgat-install
fi
if [[ -z $CGATFLOW_REPO ]] ; then
CGATFLOW_REPO="$CGAT_HOME/cgat-flow"
fi
if [[ $INSTALL_DEVEL ]] || [[ $INSTALL_PIPELINE_DEPENDENCIES ]]; then
CONDA_INSTALL_TYPE_PIPELINES="cgat-flow.yml"
CONDA_INSTALL_TYPE_APPS="cgat-apps.yml"
CONDA_INSTALL_TYPE_CORE="cgat-core.yml"
elif [[ $RUN_TESTS ]] || [[ $INSTALL_UPDATE ]] ; then
if [[ -d $CGAT_HOME/conda-install ]] ; then
AUX=`find $CGAT_HOME/conda-install/envs/cgat-* -maxdepth 0`
CONDA_INSTALL_TYPE_PIPELINES=`basename $AUX`
else
echo " The location of the CGAT code was not found (function: get_cgat_env). "
echo " Please install it first or use --location option with full path to your installation. "
echo
exit 1
fi
else
echo
echo " Wrong installation type! "
echo " Installation aborted. "
echo
exit 1
fi # if install type
# set installation folder
CONDA_INSTALL_DIR=$CGAT_HOME/conda-install
# set conda environment name
[[ ${CONDA_INSTALL_ENV} ]] || CONDA_INSTALL_ENV="cgat-flow"
} # get_cgat_env
# check whether the 'cgat-flow' conda environment is enabled
# and try to enable it if not
is_env_enabled() {
# disable error checking
set +e
# is conda available?
CONDA_PATH=$(which conda)
if [[ $? -ne 0 ]] ; then
# conda is not available
get_cgat_env
source ${CONDA_INSTALL_DIR}/etc/profile.d/conda.sh
fi
# is conda available?
CONDA_PATH=$(which conda)
if [[ $? -eq 0 ]] ; then
# conda is available
# activate cgat-flow env
conda activate ${CONDA_INSTALL_ENV}
else
# conda is not available
report_error " Conda can't be found! "
fi
# enable error checking again
set -e
}
# setup environment variables
setup_env_vars() {
export CFLAGS=$CFLAGS" -I$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/include -L$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/lib"
export CPATH=$CPATH" -I$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/include -L$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/lib"
export C_INCLUDE_PATH=$C_INCLUDE_PATH:$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/include
export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/include
export LIBRARY_PATH=$LIBRARY_PATH:$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/lib
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/lib:$CONDA_INSTALL_DIR/envs/$CONDA_INSTALL_ENV/lib/R/lib
} # setup_env_vars
# print related environment variables
print_env_vars() {
echo
echo " Debugging: "
echo " CFLAGS: "$CFLAGS
echo " CPATH: "$CPATH
echo " C_INCLUDE_PATH: "$C_INCLUDE_PATH
echo " CPLUS_INCLUDE_PATH: "$CPLUS_INCLUDE_PATH
echo " LIBRARY_PATH: "$LIBRARY_PATH
echo " LD_LIBRARY_PATH: "$LD_LIBRARY_PATH
echo " CGAT_HOME: "$CGAT_HOME
echo " CGATFLOW_DIR: "$CGATFLOW_DIR
echo " CGATFLOW_REPO: "$CGATFLOW_REPO
echo " CONDA_INSTALL_DIR: "$CONDA_INSTALL_DIR
echo " CONDA_INSTALL_TYPE_CORE:"$CONDA_INSTALL_TYPE_CORE
echo " CONDA_INSTALL_TYPE_APPS: "$CONDA_INSTALL_TYPE_APPS
echo " CONDA_INSTALL_TYPE_PIPELINES: "$CONDA_INSTALL_TYPE_PIPELINES
echo " CONDA_INSTALL_ENV: "$CONDA_INSTALL_ENV
echo " PYTHONPATH: "$PYTHONPATH
[[ ! $RUN_TESTS ]] && echo " CGATFLOW_BRANCH: "$CGATFLOW_BRANCH
[[ ! $RUN_TESTS ]] && echo " CGATAPPS_BRANCH: "$CGATAPPS_BRANCH
[[ ! $RUN_TESTS ]] && echo " CGATCORE_BRANCH: "$CGATCORE_BRANCH
[[ ! $RUN_TESTS ]] && echo " RELEASE: "$RELEASE
echo " CODE_DOWNLOAD_TYPE: "$CODE_DOWNLOAD_TYPE
echo " CLUSTER: "$CLUSTER
echo
} # print_env_vars
# Travis installations are running out of RAM
# with large conda installations. Issue has been submitted here:
# https://github.com/conda/conda/issues/1197
# While we wait for a response, we'll try to clean up the conda
# installation folder as much as possible
conda_cleanup() {
conda clean --index-cache
conda clean --lock
conda clean --tarballs -y
conda clean --packages -y
}
# proceed with conda installation
conda_install() {
log "installing conda"
detect_cgat_installation
if [[ -n "$UNINSTALL_DIR" ]] ; then
echo
echo " An installation of the CGAT code was found in: $UNINSTALL_DIR"
echo " Please use --location to install CGAT code in a different location "
echo " or uninstall the current version before proceeding."
echo
echo " Installation is aborted."
echo
exit 1
fi
# get environment variables: CGAT_HOME, CONDA_INSTALL_DIR, CONDA_INSTALL_TYPE_PIPELINES
get_cgat_env
mkdir -p $CGAT_HOME
cd $CGAT_HOME
# select Miniconda bootstrap script depending on Operating System
MINICONDA=
if [[ `uname` == "Linux" ]] ; then
# Conda 4.4 breaks everything again!
# Conda 4.5 looks better
MINICONDA="Miniconda3-latest-Linux-x86_64.sh"
#MINICONDA="Miniconda3-4.3.31-Linux-x86_64.sh"
elif [[ `uname` == "Darwin" ]] ; then
# Conda 4.4 breaks everything again!
# Conda 4.5 looks better
MINICONDA="Miniconda3-latest-MacOSX-x86_64.sh"
#MINICONDA="Miniconda3-4.3.31-MacOSX-x86_64.sh"
else
echo
echo " Unsupported operating system detected. "
echo
echo " Aborting installation... "
echo
exit 1
fi
log "downloading miniconda"
# download and install conda
wget https://repo.continuum.io/miniconda/${MINICONDA} -O miniconda.sh;
log "installing miniconda"
bash miniconda.sh -b -p $CONDA_INSTALL_DIR
source ${CONDA_INSTALL_DIR}/bin/activate
hash -r
# install cgat environment
# Conda 4.4 breaks everything again!
# Conda 4.5 looks better
#conda install --quiet --yes 'conda=4.3.33'
conda update --all --yes
conda info -a
log "installing conda CGAT environment"
# Now using conda environment files:
# https://conda.io/docs/using/envs.html#use-environment-from-file
log "curl -o env-cgat-core.yml -O https://raw.githubusercontent.com/cgat-developers/cgat-core/${CGATCORE_BRANCH}/conda/environments/${CONDA_INSTALL_TYPE_CORE}"
curl -o env-cgat-core.yml -O https://raw.githubusercontent.com/cgat-developers/cgat-core/${CGATCORE_BRANCH}/conda/environments/${CONDA_INSTALL_TYPE_CORE}
log "curl -o env-cgat-apps.yml -O https://raw.githubusercontent.com/cgat-developers/cgat-apps/${CGATAPPS_BRANCH}/conda/environments/${CONDA_INSTALL_TYPE_APPS}"
curl -o env-cgat-apps.yml -O https://raw.githubusercontent.com/cgat-developers/cgat-apps/${CGATAPPS_BRANCH}/conda/environments/${CONDA_INSTALL_TYPE_APPS}
log "curl -o env-cgat-flow.yml -O https://raw.githubusercontent.com/cgat-developers/cgat-flow/${TRAVIS_BRANCH}/conda/environments/${CONDA_INSTALL_TYPE_PIPELINES}"
curl -o env-cgat-flow.yml -O https://raw.githubusercontent.com/cgat-developers/cgat-flow/${TRAVIS_BRANCH}/conda/environments/${CONDA_INSTALL_TYPE_PIPELINES}
[[ ${CLUSTER} -eq 0 ]] && sed -i'' -e '/drmaa/d' env-cgat-flow.yml
log "creating environment with cgat-core dependencies"
conda env create --name ${CONDA_INSTALL_ENV} --file env-cgat-core.yml
log "updating with cgat-apps dependencies"
conda env update --name ${CONDA_INSTALL_ENV} --file env-cgat-apps.yml
log "updating with cgat-flow dependencies"
conda env update --name ${CONDA_INSTALL_ENV} --file env-cgat-flow.yml
# activate cgat environment
conda activate ${CONDA_INSTALL_ENV}
# install extra deps
install_extra_deps
# install all other pipeline dependencies
# this step has to be done here, see:
# https://github.com/cgat-developers/cgat-flow/pull/119
if [[ $INSTALL_PIPELINE_DEPENDENCIES -eq 1 ]]; then
install_pipeline_deps
fi
# Set up other environment variables
#setup_env_vars
# install cgat-core
install_cgat_core
# install cgat-apps
install_cgat_apps
# install cgat-flow
install_cgat_flow
} # conda install
# install extra dependencies
install_extra_deps() {
log "install extra deps"
curl -O https://raw.githubusercontent.com/cgat-developers/cgat-flow/${TRAVIS_BRANCH}/conda/environments/pipelines-extra.yml
conda env update --name ${CONDA_INSTALL_ENV} --file pipelines-extra.yml
}
# install dependencies for running the pipelines
install_pipeline_deps() {
cd $CGAT_HOME
get_cgat_env
# activate cgat environment
is_env_enabled
log "install pipeline deps"
curl -O https://raw.githubusercontent.com/cgat-developers/cgat-flow/${TRAVIS_BRANCH}/conda/environments/cgat-flow-pipelines.yml
conda env update --name ${CONDA_INSTALL_ENV} --file cgat-flow-pipelines.yml
install_extra_envs
}
# install Python 2 dependencies in a different conda environment
install_extra_envs() {
log "install extra environments"
curl -O https://raw.githubusercontent.com/cgat-developers/cgat-flow/${TRAVIS_BRANCH}/conda/environments/pipelines-macs2.yml
conda env update --file pipelines-macs2.yml
curl -O https://raw.githubusercontent.com/cgat-developers/cgat-flow/${TRAVIS_BRANCH}/conda/environments/pipelines-tophat2.yml
conda env update --file pipelines-tophat2.yml
curl -O https://raw.githubusercontent.com/cgat-developers/cgat-flow/${TRAVIS_BRANCH}/conda/environments/pipeline-peakcalling-sicer.yml
conda env update --file pipeline-peakcalling-sicer.yml
curl -O https://raw.githubusercontent.com/cgat-developers/cgat-flow/${TRAVIS_BRANCH}/conda/environments/pipelines-splicing.yml
conda env update --file pipelines-splicing.yml
curl -O https://raw.githubusercontent.com/cgat-developers/cgat-flow/${TRAVIS_BRANCH}/conda/environments/pipelines-sailfish.yml
conda env update --file pipelines-sailfish.yml
curl -O https://raw.githubusercontent.com/cgat-developers/cgat-flow/${TRAVIS_BRANCH}/conda/environments/pipelines-salmon.yml
conda env update --file pipelines-salmon.yml
}
# helper function to install cgat-flow
install_cgat_flow() {
log "install cgat flow"
OLDWD=`pwd`
cd $CGAT_HOME
# download the code out of jenkins
if [[ ${CLONE_FROM_REPO} -eq 1 ]] ; then
if [[ $CODE_DOWNLOAD_TYPE -eq 0 ]] ; then
# get the latest version from Git Hub in zip format
curl -LOk https://github.com/cgat-developers/cgat-flow/archive/$CGATFLOW_BRANCH.zip
unzip $CGATFLOW_BRANCH.zip
rm $CGATFLOW_BRANCH.zip
if [[ ${RELEASE} ]] ; then
NEW_NAME=`echo $CGATFLOW_BRANCH | sed 's/^v//g'`
mv cgat-flow-$NEW_NAME/ $CGATFLOW_REPO
else
mv cgat-flow-$CGATFLOW_BRANCH/ $CGATFLOW_REPO
fi
elif [[ $CODE_DOWNLOAD_TYPE -eq 1 ]] ; then
# get latest version from Git Hub with git clone
git clone --branch=$CGATFLOW_BRANCH https://github.com/cgat-developers/cgat-flow.git $CGATFLOW_REPO
elif [[ $CODE_DOWNLOAD_TYPE -eq 2 ]] ; then
# get latest version from Git Hub with git clone
git clone --branch=$CGATFLOW_BRANCH [email protected]:cgat-developers/cgat-flow.git $CGATFLOW_REPO
else
report_error " Unknown download type for CGAT code... "
fi
# make sure you are in the CGAT_HOME/cgat-flow folder
cd $CGATFLOW_REPO
else
log "using existing cgat-flow repo in $CGATFLOW_REPO"
cd "$CGATFLOW_REPO"
fi
# Python preparation
log "linking cgat-flow code into conda environment"
sed -i'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py
sed -i'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py
python setup.py develop
if [[ $? -ne 0 ]] ; then
echo
echo " There was a problem doing: 'python setup.py develop' "
echo " Installation did not finish properly. "
echo
echo " Please submit this issue via Git Hub: "
echo " https://github.com/cgat-developers/cgat-flow/issues "
echo
print_env_vars
else
clear
echo
echo " The code successfully installed!"
echo
echo " To activate the CGAT environment type: "
echo " $ source $CONDA_INSTALL_DIR/etc/profile.d/conda.sh"
echo " $ conda activate base"
echo " $ conda activate $CONDA_INSTALL_ENV"
echo
echo " To deactivate the environment, use:"
echo " $ conda deactivate"
echo
fi # if-$?
# revert setup.py if downloaded with git
[[ $CODE_DOWNLOAD_TYPE -ge 1 ]] && git checkout -- setup.py
# environment pinning
# python scripts/conda.py
# go back to old working directory
cd $OLDWD
} # install_cgat_flow
# helper function to install cgat-apps
install_cgat_apps() {
log "install cgat apps"
OLDWD=`pwd`
cd $CGAT_HOME
if [[ $CODE_DOWNLOAD_TYPE -eq 0 ]] ; then
# get the latest version from Git Hub in zip format
curl -LOk https://github.com/cgat-developers/cgat-apps/archive/$CGATAPPS_BRANCH.zip
unzip $CGATAPPS_BRANCH.zip
rm $CGATAPPS_BRANCH.zip
if [[ ${RELEASE} ]] ; then
NEW_NAME=`echo $CGATAPPS_BRANCH | sed 's/^v//g'`
mv cgat-apps-$NEW_NAME/ cgat-apps/
else
mv cgat-apps-$CGATAPPS_BRANCH/ cgat-apps/
fi
elif [[ $CODE_DOWNLOAD_TYPE -eq 1 ]] ; then
# get latest version from Git Hub with git clone
git clone --branch=$CGATAPPS_BRANCH https://github.com/cgat-developers/cgat-apps.git
elif [[ $CODE_DOWNLOAD_TYPE -eq 2 ]] ; then
# get latest version from Git Hub with git clone
git clone --branch=$CGATAPPS_BRANCH [email protected]:cgat-developers/cgat-apps.git
else
report_error " Unknown download type for CGAT code... "
fi
cd cgat-apps/
# remove install_requires (no longer required with conda package)
sed -i'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py
sed -i'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py
python setup.py develop
if [[ $? -ne 0 ]] ; then
echo
echo " There was a problem doing: 'python setup.py develop' "
echo " Installation did not finish properly. "
echo
echo " Please submit this issue via Git Hub: "
echo " https://github.com/cgat-developers/cgat-flow/issues "
echo
print_env_vars
fi # if-$?
# revert setup.py if downloaded with git
[[ $CODE_DOWNLOAD_TYPE -ge 1 ]] && git checkout -- setup.py
# go back to old working directory
cd $OLDWD
} # install_cgat_apps
# helper function to install cgat-core
install_cgat_core() {
log "install cgat core"
OLDWD=`pwd`
cd $CGAT_HOME
if [[ $CODE_DOWNLOAD_TYPE -eq 0 ]] ; then
# get the latest version from Git Hub in zip format
curl -LOk https://github.com/cgat-developers/cgat-core/archive/$CGATCORE_BRANCH.zip
unzip $CGATCORE_BRANCH.zip
rm $CGATCORE_BRANCH.zip
if [[ ${RELEASE} ]] ; then
NEW_NAME=`echo $CGATCORE_BRANCH | sed 's/^v//g'`
mv cgat-core-$NEW_NAME/ cgat-core/
else
mv cgat-core-$CGATCORE_BRANCH/ cgat-core/
fi
elif [[ $CODE_DOWNLOAD_TYPE -eq 1 ]] ; then
# get latest version from Git Hub with git clone
git clone --branch=$CGATCORE_BRANCH https://github.com/cgat-developers/cgat-core.git
elif [[ $CODE_DOWNLOAD_TYPE -eq 2 ]] ; then
# get latest version from Git Hub with git clone
git clone --branch=$CGATCORE_BRANCH [email protected]:cgat-developers/cgat-core.git
else
report_error " Unknown download type for CGAT core... "
fi
cd cgat-core/
# remove install_requires (no longer required with conda package)
sed -i'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py
sed -i'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py
python setup.py develop
if [[ $? -ne 0 ]] ; then
echo
echo " There was a problem doing: 'python setup.py develop' "
echo " Installation did not finish properly. "
echo
echo " Please submit this issue via Git Hub: "
echo " https://github.com/cgat-developers/cgat-apps/issues "
echo
print_env_vars
fi # if-$?
# revert setup.py if downloaded with git
[[ $CODE_DOWNLOAD_TYPE -ge 1 ]] && git checkout -- setup.py
# go back to old working directory
cd $OLDWD
} # install_cgat_core
# test code with conda install
conda_test() {
log "starting conda_test"
# get environment variables: CGAT_HOME, CONDA_INSTALL_DIR, CONDA_INSTALL_TYPE_PIPELINES
get_cgat_env
#setup_env_vars
# setup environment and run tests
if [[ $TRAVIS_INSTALL ]] || [[ $JENKINS_INSTALL ]] ; then
# activate cgat environment
is_env_enabled
# show conda environment used for testing
conda env list
log "conda env export"
conda env export
# install cgat-core
install_cgat_core
# install cgat-apps
install_cgat_apps
# python preparation
log "install CGAT code into conda environment"
cd $CGAT_HOME
# Python preparation
sed -i'' -e 's/CGATScripts/scripts/g' setup.py
sed -i'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py
sed -i'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py
python setup.py develop
log "starting tests"
# run nosetests
if [[ $TEST_ALL ]] ; then
log "test_style.py" && nosetests -v tests/test_style.py && \
log "test_import.py" && nosetests -v tests/test_import.py && \
echo -e "restrict:\n manifest:\n" > tests/_test_commandline.yaml && \
log "test_commandline" && nosetests -v tests/test_commandline.py && \
log "test_scripts" && nosetests -v tests/test_scripts.py ;
elif [[ $TEST_IMPORT ]] ; then
nosetests -v tests/test_import.py ;
elif [[ $TEST_STYLE ]] ; then
nosetests -v tests/test_style.py ;
elif [[ $TEST_CMDLINE ]] ; then
echo -e "restrict:\n manifest:\n" > tests/_test_commandline.yaml
nosetests -v tests/test_commandline.py ;
elif [[ $TEST_PRODUCTION_SCRIPTS ]] ; then
echo -e "restrict:\n manifest:\n" > tests/_test_scripts.yaml
nosetests -v tests/test_scripts.py ;
else
nosetests -v tests/test_scripts.py ;
fi
else
if [[ $CONDA_INSTALL_TYPE_PIPELINES ]] ; then
# activate cgat environment
is_env_enabled
# show conda environment used for testing
conda env list
log "conda env export"
conda env export
# make sure you are in the CGAT_HOME/cgat-flow folder
cd $CGATFLOW_REPO
OUTPUT_DIR=`pwd`
# run tests, note: OSX has no options (no -v, -o)
/usr/bin/time nosetests -v tests/test_import.py
if [[ $? -eq 0 ]] ; then
echo
echo " test_import.py passed successfully! "
echo
else
echo
echo " test_import.py failed. Please see $OUTPUT_DIR/test_import.out file for detailed output. "
echo
print_env_vars
fi
/usr/bin/time nosetests -v tests/test_scripts.py
if [[ $? -eq 0 ]] ; then
echo
echo " test_scripts.py passed successfully! "
echo
else
echo
echo " test_scripts.py failed. Please see $OUTPUT_DIR/test_scripts.out file for detailed output. "
echo
print_env_vars
fi
else
echo
echo " There was an error running the tests. "
echo " Execution aborted. "
echo
print_env_vars
exit 1
fi
fi # if travis or jenkins
} # conda_test
# update conda installation
conda_update() {
# get environment variables: CGAT_HOME, CONDA_INSTALL_DIR, CONDA_INSTALL_TYPE_PIPELINES
get_cgat_env
# activate cgat environment
is_env_enabled
conda update --all
if [[ ! $? -eq 0 ]] ; then
echo
echo " There was a problem updating the installation. "
echo
echo " Please submit this issue via Git Hub: "
echo " https://github.com/cgat-developers/cgat-flow/issues "
echo
else
echo
echo " All packages were succesfully updated. "
echo
fi
} # conda_update
# unistall CGAT code collection
uninstall() {
detect_cgat_installation
if [[ -z "$UNINSTALL_DIR" ]] ; then
echo
echo " The location of the CGAT code was not found. "
echo " Please uninstall manually."
echo
exit 1
else
rm -rf $UNINSTALL_DIR
if [[ $? -eq 0 ]] ; then
echo
echo " CGAT code successfully uninstalled."
echo
exit 0
else
echo
echo " There was a problem uninstalling the CGAT code."
echo " Please uninstall manually."
echo
exit 1
fi
fi
}
# test whether --git and --git-ssh download is doable
test_git() {
git --version >& /dev/null || GIT_AVAIL=$?
if [[ $GIT_AVAIL -ne 0 ]] ; then
echo
echo " Git is not available but --git or --git-ssh option was given."
echo " Please rerun this script on a computer with git installed "
echo " or try again without --git or --git-ssh"
report_error " "
fi
}
# test whether --git-ssh download is doable
test_git_ssh() {
ssh-add -L >& /dev/null || SSH_KEYS_LOADED=$?
if [[ $SSH_KEYS_LOADED -ne 0 ]] ; then
echo
echo " Please load your ssh keys for GitHub before proceeding!"
echo
echo " Try: "
echo " 1. eval \$(ssh-agent)"
echo " 2. ssh-add ~/.ssh/id_rsa # or the file where your private key is"
report_error " and run this script again. "
fi
}
# don't mix branch and release options together
test_mix_branch_release() {
# don't mix branch and release options together
if [[ $RELEASE ]] ; then
if [[ "$CGATFLOW_BRANCH" != "master" ]] || [[ $CGATAPPS_BRANCH != "master" ]] ; then
echo
echo " You cannot mix git branches and releases for the installation."
echo
echo " Your input was: "$SCRIPT_PARAMS
report_error " Please either use branches or releases but not both."
fi
fi
}
# test whether a branch exists in the cgat-core repository
# https://stackoverflow.com/questions/12199059/how-to-check-if-an-url-exists-with-the-shell-and-probably-curl
test_core_branch() {
RELEASE_TEST=0
curl --output /dev/null --silent --head --fail https://raw.githubusercontent.com/cgat-developers/cgat-core/${CGATCORE_BRANCH}/README.md || RELEASE_TEST=$?
if [[ ${RELEASE_TEST} -ne 0 ]] ; then
echo
echo " The branch provided for cgat-core does not exist: ${CGATCORE_BRANCH}"
echo
echo " Please have a look at valid branches here: "
echo " https://github.com/cgat-developers/cgat-core/branches"
echo
report_error " Please use a valid branch and try again."
fi
}
# test whether a branch exists in the cgat-apps repository
# https://stackoverflow.com/questions/12199059/how-to-check-if-an-url-exists-with-the-shell-and-probably-curl
test_apps_branch() {
RELEASE_TEST=0
curl --output /dev/null --silent --head --fail https://raw.githubusercontent.com/cgat-developers/cgat-apps/${CGATAPPS_BRANCH}/README.rst || RELEASE_TEST=$?
if [[ ${RELEASE_TEST} -ne 0 ]] ; then
echo
echo " The branch provided for cgat-apps does not exist: ${CGATAPPS_BRANCH}"
echo
echo " Please have a look at valid branches here: "
echo " https://github.com/cgat-developers/cgat-apps/branches"
echo
report_error " Please use a valid branch and try again."
fi
}
# test whether a release exists or not
# https://stackoverflow.com/questions/12199059/how-to-check-if-an-url-exists-with-the-shell-and-probably-curl
test_release() {
RELEASE_PIPELINES=0
# check pipelines
curl --output /dev/null \
--silent --head --fail \
https://raw.githubusercontent.com/cgat-developers/cgat-flow/${RELEASE}/README.rst || RELEASE_PIPELINES=$?
if [[ ${RELEASE_PIPELINES} -ne 0 ]] ; then
echo
echo " The release number provided for the pipelines does not exist: ${RELEASE}"
echo
echo " Please have a look at valid releases here: "
echo " https://github.com/cgat-developers/cgat-flow/releases"
echo
echo " An example of valid release is: --release v0.4.0"
report_error " Please use a valid release and try again."
fi
RELEASE_SCRIPTS=0
# check scripts
curl --output /dev/null \
--silent --head --fail \
https://raw.githubusercontent.com/cgat-developers/cgat-apps/${RELEASE}/README.rst || RELEASE_SCRIPTS=$?
if [[ ${RELEASE_SCRIPTS} -ne 0 ]] ; then
echo
echo " The release number provided for the scripts does not exist: ${RELEASE}"
echo
echo " Please have a look at valid releases here: "
echo " https://github.com/cgat-developers/cgat-apps/releases"
echo
echo " An example of valid release is: --release v0.4.0"
report_error " Please use a valid release and try again."
fi
}
# test whether a C/C++ compiler is available
test_compilers() {
which gcc &> /dev/null || report_error " C compiler not found "
which g++ &> /dev/null || report_error " C++ compiler not found "
}
# clean up environment
# deliberately use brute force
cleanup_env() {
set +e
conda deactivate >& /dev/null || true
conda deactivate >& /dev/null || true
unset -f conda || true
unset PYTHONPATH || true
# Next actions disabled. Please see:
# https://github.com/cgat-developers/cgat-core/issues/44
#module purge >& /dev/null || true
#mymodule purge >& /dev/null || true
set -e
}
# function to display help message
help_message() {
cat << EOF
usage="$(basename "$0") cgatflow install script
where:
-h/--help show this help text. The following options are supported:
--install-repo install cgatflow from repository. This will also install
conda and the conda environment.
--install-pipeline-dependencies install dependencies for running the pipelines
included in the cgat-flow repository.
--clone-from-repo clone a fresh copy from git for the install. Please specify
either --clone-from-repo or --use-repo.
--use-repo PATH install from an existing repository in PATH, see above.
--location PATH installation PATH for the conda environment. Must not exist.
--cgatflow-branch BRANCH branch to use for cgatflow repository checkout. Default
is master.
--cgatapps-branch BRANCH branch to install from cgatapps. Default is master.
--cgatcore-branch BRANCH branch to install from cgatapps. Default is master.
--env-name NAME name of conda environment. Default is 'cgat-flow'
Examples:
For an install from a clone in the current directory into a new conda installation, type:
./install-devel.sh
--install-repo
--install-pipeline-dependencies
--use-repo .
--location </full/path/to/folder/without/trailing/slash>
To install a specific branch of the code on GitHub from scratch:
curl -O https://raw.githubusercontent.com/cgat-developers/cgat-flow/master/install-devel.sh
./install-devel.sh
--install-repo
--install-pipeline-dependencies
--clone-from-repo
--cgatflow-branch <branch>
--location </full/path/to/folder/without/trailing/slash>
Please submit any issues via Git Hub:
https://github.com/cgat-developers/cgat-flow/issues
EOF
} # help_message
# the script starts here
cleanup_env
test_compilers
if [[ $# -eq 0 ]] ; then
help_message
fi
# conda installation type. If set to 1, cgat-core and cgat-apps
# will be installed from repository.