diff --git a/Dockerfile b/Dockerfile index bdc2fca..8e18014 100644 --- a/Dockerfile +++ b/Dockerfile @@ -33,10 +33,10 @@ RUN tar xzf modules-${MODULE_VERSION}.tar.gz && \ && cd modules-${MODULE_VERSION} && ./configure && make -j 7 && make install \ && cd .. && rm -rf modules-${MODULE_VERSION} && rm -rf /usr/local/Modules/modulefiles/* RUN ["ln", "-s", "/usr/local/Modules/init/profile.sh", "/etc/profile.d/z00_module.sh"] -RUN echo "source /etc/profile.d/z00_module.sh" >> /etc/bashrc +#RUN echo "source /etc/profile.d/z00_module.sh" >> /etc/bashrc ADD devmodule/genpipes "/usr/local/Modules/modulefiles/." -RUN echo "source /etc/profile.d/z90_genpipe.sh" >> /etc/bashrc +#RUN echo "source /etc/profile.d/z90_genpipes.sh" >> /etc/bashrc RUN ["ln", "-s", "/usr/local/etc/genpiperc", "/etc/profile.d/z90_genpipes.sh"] ADD genpiperc /usr/local/etc/genpiperc diff --git a/genpiperc b/genpiperc index f680e04..409b274 100755 --- a/genpiperc +++ b/genpiperc @@ -1,5 +1,5 @@ -source /etc/bashrc -source ~/.bashrc +#source /etc/bashrc +#source ~/.bashrc if [ -z "${QUIET}" ]; then echo -e "\nWait while Genpipes module are loaded. This could take a while," echo -e " especially if the cvmfs cache is new\n" diff --git a/init_genpipes b/init_genpipes index e5999ab..a3d0380 100755 --- a/init_genpipes +++ b/init_genpipes @@ -6,7 +6,7 @@ # It also loads the lmod software to load mugqic modules export PARROT_ALLOW_SWITCHING_CVMFS_REPOSITORIES=yes -CVMFS_CONFIG_CC=cvmfs-s1-beluga.computecanada.ca:8000/cvmfs/cvmfs-config.computecanada.ca,pubkey=/etc/cvmfs/keys/cvmfs-config.computecanada.ca.pub;cvmfs-s1-arbutus.computecanada.ca:8000/cvmfs/cvmfs-config.computecanada.ca,pubkey=/etc/cvmfs/keys/cvmfs-config.computecanada.ca.pub;http://cvmfs-s1-east.computecanada.ca:8000/cvmfs/cvmfs-config.computecanada.ca,pubkey=/etc/cvmfs/keys/cvmfs-config.computecanada.ca.pub +CVMFS_CONFIG_CC="cvmfs-s1-beluga.computecanada.ca:8000/cvmfs/cvmfs-config.computecanada.ca,pubkey=/etc/cvmfs/keys/cvmfs-config.computecanada.ca.pub;cvmfs-s1-arbutus.computecanada.ca:8000/cvmfs/cvmfs-config.computecanada.ca,pubkey=/etc/cvmfs/keys/cvmfs-config.computecanada.ca.pub;cvmfs-s1-east.computecanada.ca:8000/cvmfs/cvmfs-config.computecanada.ca,pubkey=/etc/cvmfs/keys/cvmfs-config.computecanada.ca.pub" export PARROT_CVMFS_REPO="${CVMFS_CONFIG_CC}" export HTTP_PROXY='DIRECT' @@ -14,7 +14,6 @@ LOCAL_CONFIG_PATH=/etc/parrot PARROT_CVMFS_ALIEN_CACHE=/tmp/parrot.${UID} export MUGQIC_INSTALL_HOME=/cvmfs/soft.mugqic/CentOS6 -export QUIET='' usage (){ echo -e "\nUsage: $0 [-c ] [-a ] [-p ] [ -d ] [-V ] [ ] " 1>&2; @@ -29,12 +28,13 @@ usage (){ echo -e "\t the soft.mugqic repo's version (developer's mode)" echo -e "\t-V Genpipes version (will default to latest release)" echo -e "\t-e Execute specific command and exit" - echo -e "\t-q keep the parrot quiet" + echo -e "\t-v vebose mode, makes the parrot talk" echo } +export QUIET="-d clear" -while getopts ":a:d:c:p:qV:" opt; do +while getopts ":a:d:c:p:vV:" opt; do case $opt in a) echo "Setting parrot alien cache to $OPTARG" @@ -47,8 +47,8 @@ while getopts ":a:d:c:p:qV:" opt; do p) MUGQIC_INSTALL_HOME=${OPTARG} ;; - q) - export QUIET="-d clear" + v) + unset QUIET ;; V) export PIPELINE_VERSION=/${OPTARG} @@ -76,7 +76,6 @@ done shift $((OPTIND-1)) # move the execline to a script if [ $# -gt 0 ] ; then - echo $# function finish { rm ${genpipe_script} }