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Commit 08266d80 authored by Julien  GUGLIELMINI's avatar Julien GUGLIELMINI
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Automatic -a parameter; option to skip memory check; output improvement

parent 8419f412
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...@@ -27,19 +27,19 @@ display_usage() { ...@@ -27,19 +27,19 @@ display_usage() {
echo "${bold}OPTIONS:${normal}" echo "${bold}OPTIONS:${normal}"
echo " -p <string> Path to the mmseqs executable." echo " -p <string> Path to the mmseqs executable."
echo " e.g. /usr/local/bin" echo " e.g. /usr/local/bin"
echo " by default the mmseqs binary found in the \"\$PATH\" environment variable will" echo " By default the mmseqs binary found in the \"\$PATH\" environment variable will"
echo " be used, if there is one." echo " be used, if there is one."
echo " If wGRR is used on Maestro, MMSeqs will be automatically loaded." echo " If wGRR is used on Maestro, MMSeqs will be automatically loaded."
echo " -o <string> Base name for the output files." echo " -o <string> Base name for the output files."
echo " by default a random string will be used." echo " By default a random string will be used."
echo " -t <integer> Number of threads to use." echo " -t <integer> Number of threads to use."
echo " default: 1" echo " default: 1"
echo " recommended: at least 4" echo " recommended: at least 4"
echo " Note: if wGRR is run on Maestro via sbatch, this number only applies to the" echo " Note: if wGRR is run on Maestro via sbatch, this number only applies to the"
echo " MMseqs step" echo " MMseqs step"
echo " -a <integer> Number of genomes comparisons to be performed in each thread." echo " -a <integer> Number of genomes comparisons to be performed in each thread."
echo " Increasing this will decrease the number of tasks to be performed" echo " Increasing this will decrease the number of tasks to be performed"
echo " but each task will take longer and use more RAM." echo " but each task will take longer and use more RAM."
echo " default: auto" echo " default: auto"
echo " -m <integer> Max number of simulteaneous tasks." echo " -m <integer> Max number of simulteaneous tasks."
echo " Only applicable to Maestro, for the wGRR calculation step." echo " Only applicable to Maestro, for the wGRR calculation step."
...@@ -73,7 +73,7 @@ fi ...@@ -73,7 +73,7 @@ fi
if [ $# -lt 1 ] ; then if [ $# -lt 1 ] ; then
display_usage display_usage
exit 1 exit 0
fi fi
## Functions ## Functions
......
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