Commit 8dd24c44 by Eric Coissac

including lecaluke module on a non-luke computer raise an error.

By default register SCRATCH_DIR and SHARED_SCRATCH_DIR in the place
potentially usable for storing temp directories
parent 0621afc5
......@@ -17,27 +17,46 @@
include logging
logdebug "Load lecaluke package"
# Where is located the LECA_ENVIRONEMENT
LECA_ENVIRONEMENT=/nfs_scratch/LECA_ENVIRONEMENT
# Lock files are stored in a common place
LOCK_DIR="${LECA_ENVIRONEMENT}/locks"
# All the data shared among users can be stored here
DATA_DIR="${LECA_ENVIRONEMENT}/data"
# All the molecular public databases downloaded for users on the luke cluster
# will be downloaded here
BIODATA_DIR="${DATA_DIR}/biodatabase"
# Main directory for the NCBI taxonomy
TAXONOMY_DIR="${BIODATA_DIR}/taxonomy"
TREMBL_DIR="${BIODATA_DIR}/trembl"
SWISSPROT_DIR="${BIODATA_DIR}/swissprot"
function latest_taxonomy() {
echo "${TAXONOMY_DIR}/$(ls -ltr "${BIODATA_DIR}/taxonomy" | awk '/^d/ {print $NF}' | tail -1)"
}
include tempfile
if onluke; then
logdebug Script run on the LUKE cluster
# Register scratch_dir as place where to create temp directory
registertmpdir $SHARED_SCRATCH_DIR
registertmpdir $SCRATCH_DIR
# Where is located the LECA_ENVIRONEMENT
LECA_ENVIRONEMENT=/nfs_scratch/LECA_ENVIRONEMENT
# Load the LECA envoronement
. ${LECA_ENVIRONEMENT}/etc/bashrc
# Lock files are stored in a common place
LOCK_DIR="${LECA_ENVIRONEMENT}/locks"
# All the data shared among users can be stored here
DATA_DIR="${LECA_ENVIRONEMENT}/data"
# All the molecular public databases downloaded for users on the luke cluster
# will be downloaded here
BIODATA_DIR="${DATA_DIR}/biodatabase"
# Main directory for the NCBI taxonomy
TAXONOMY_DIR="${BIODATA_DIR}/taxonomy"
TREMBL_DIR="${BIODATA_DIR}/trembl"
SWISSPROT_DIR="${BIODATA_DIR}/swissprot"
function latest_taxonomy() {
echo "${TAXONOMY_DIR}/$(ls -ltr "${BIODATA_DIR}/taxonomy" | awk '/^d/ {print $NF}' | tail -1)"
}
else
logerror Script is not running on the LUKE cluster
exit 1
fi
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