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HPC - JGU - Life Sciences
seq-analysis
Commits
14739780
Commit
14739780
authored
Aug 21, 2019
by
Christian Meesters
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reduced the number of split files for the default
parent
60bb252f
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blast/parallel_BLAST/LA_Wrapper
blast/parallel_BLAST/LA_Wrapper
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blast/parallel_BLAST/LA_Wrapper
View file @
14739780
...
...
@@ -175,10 +175,14 @@ credits()
{
echo
"The original implementation (2013/2014) was written by Christoph Martin (ZDV, UNIX group)"
echo
"Benjamin Rieger (Institut für Molekulargenetik) contributed a perl implementation"
echo
"of a format conform splitting of FASTA files."
echo
"of a format conform splitting of FASTA files
, which is not used, anymore
."
echo
"The original implemenation was a LSF chain job. It was eventually adopted and maintained by"
echo
"Christian Meesters (ZDV, HPC group) from 2017 onwards."
echo
echo
"I am particularly grateful for their feedback to:"
echo
"- Lukas Hellman (AG Hankeln)"
echo
"- Benjamin Rieger (NGS Facility)"
echo
echo
"History of the re-implementation:"
echo
"- v0.1 -- 27. Sep. 2017 -- release of the re-implementation for SLURM supporting the"
echo
" ability to compute accross nodes."
...
...
@@ -201,7 +205,7 @@ credits()
echo
"- v0.3.2 -- 16. Jan. 2019 -- hot fix for new ramdisk and slurmstepd support"
echo
"- v0.4 -- 06. Mar. 2019 -- refactored version:"
echo
" - executables now pluggable"
echo
"- v0.5 -- 1
7
. Aug. 2019 -- fix: parser did not work for '--mem'-arg properly"
echo
"- v0.5 --
2
1. Aug. 2019 -- fix: parser did not work for '--mem'-arg properly"
echo
" update: - clearer UI"
echo
" - better default memory settings"
echo
" - faster stage-in for reference data"
...
...
@@ -494,10 +498,10 @@ if [ $_arg_splitup_per_queryfile -ne 0 ]; then # the user thinks differently?
error
"There would be more than '
$nsplits
' files in scratch."
exit
1
elif
[
$nsplits
-gt
15000
]
;
then
warning
"There will be '
$nsplits
' files in scratch."
warning
"There will be '
$nsplits
' files in scratch
-- resulting in poor performance
."
fi
else
# infer the value
_arg_splitup_per_queryfile
=
$((
nentries
/
10
000
))
_arg_splitup_per_queryfile
=
$((
nentries
/
5
000
))
fi
# default values, see:
...
...
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