Commit fc1362fc authored by Christian Meesters's avatar Christian Meesters

new hints in help message

parent af5b6ae5
......@@ -18,7 +18,7 @@ module load tools/parallel
module load bio/BLAST+
# inherently loaded is python
SCRIPT_VERSION="0.3.1"
SCRIPT_VERSION="0.3.2"
# TODO: delete the following 3 functions, once sbcast is working
function queue {
......@@ -92,7 +92,7 @@ _arg_compress=off
print_help ()
{
echo "This script's help msg"
printf 'Usage: %s [-l|--runlimit <arg>] [-p|--partition <arg>] [-s|--splitup <arg>] [-N|--nodes <arg>] [--executable <arg>] [-m|--mem <arg>] [--blastparams <string>] [-r|--ramdisk <arg>] [--blastdir <arg>] [--(no-)test] [-h|--help] <FASTA> <DATABASE>\n' "$(basename $0)"
printf 'Usage: %s [-l|--runlimit <arg>] [-p|--partition <arg>] [-s|--splitup <arg>] [-N|--nodes <arg>] [--executable <arg>] [-m|--mem <arg>] [--blastparams <string>] [-r|--ramdisk <arg>] [--blastdir <arg>] [--(no-)test] [-h|--help] <FASTA> <DATABASE>\n' "$(basename $0)\n"
printf 'HINT: The FASTA and DATABASE items need to be full paths to files.'
printf "\t%s\n" "<FASTA>: path to the query FASTA file"
printf "\t%s\n" "<DATABASE>: path to the database file"
......@@ -114,12 +114,16 @@ print_help ()
printf "\t%s\n" "--credits,--version: Prints credits and a brief version history and exits"
printf "\t%s\n" "-h,--help: Prints help"
echo
echo "WARNING: BLAST parameters:"
echo "There are no BLAST default parameters, other than specifing XML output, the database and"
echo "queries as well as the numer of threads (all set by this script)."
echo "Detailed overview on parameters can be shown by entering <blastexecutable> -help"
echo
echo "NOTE: Currently only NCBI-BLAST+ executables are supported."
echo -e "\e[3mWARNINGS:\e[0m"
echo -e "\e[3m- BLAST parameters:\e[0m"
echo " There are no BLAST default parameters, other than specifing XML output, the database and"
echo " queries as well as the numer of threads (all set by this script)."
echo " Detailed overview on parameters can be shown by entering <blastexecutable> -help"
echo -e "\e[3m- Limitations:\e[0m"
echo " - Currently only NCBI-BLAST+ executables are supported."
echo " - References may be as big as 30G, 50G may also work."
echo " References beyond this this may or not work."
echo " Be sure to reserve sufficient RAM."
echo
echo "Planned features for upcoming versions:"
echo "- better, more stable user interface"
......@@ -132,7 +136,7 @@ print_help ()
echo "- automatic reference database generation in case of version mismatches or similar"
echo
echo "Minor improvements will be implemented as time permits. Yet, to make this possible,"
echo "you can request a collaboration (for minor add ons an acknowladegement by name will do)."
echo -e "\e[1myou can request a collaboration\e[0m (for minor add ons an acknowladegement by name will do)."
}
credits()
......@@ -707,7 +711,7 @@ trap "rm -f $cmd" EXIT
HOSTLIST=$(scontrol show hostname $SLURM_JOB_NODELIST | paste -d, -s )
#parallel --controlmaster --workdir --sshdelay 0.2 $PWD -S $HOSTLIST -j $(($SLURM_JOB_NUM_NODES*$SLURM_CPUS_ON_NODE/$SLURM_CPUS_PER_TASK)) --env run_blast run_blast ::: $(find -type f -name 'group*.fasta')
parallel --workdir $PWD --sshdelay 0.1 -S $HOSTLIST -j $(($SLURM_CPUS_ON_NODE / $SLURM_CPUS_PER_TASK)) $cmd ::: $(find -type f -name 'group*.fasta')
parallel --workdir $PWD --sshdelay 0.1 -S $HOSTLIST -j $(($SLURM_CPUS_ON_NODE / $SLURM_CPUS_PER_TASK)) $cmd ::: $(find $(pwd) -type f -name 'group*.fasta')
wait
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment