From: Sasha Sherstnev Date: Fri, 2 Aug 2013 10:32:09 +0000 (+0100) Subject: JWS-67 configuration and manual file for jpred 3.0.1 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d58f92e0f06498d2f18d9b40c932989cb038f3de;p=jabaws.git JWS-67 configuration and manual file for jpred 3.0.1 --- diff --git a/conf/settings/JpredLimits.xml b/conf/settings/JpredLimits.xml new file mode 100644 index 0000000..3180ec5 --- /dev/null +++ b/conf/settings/JpredLimits.xml @@ -0,0 +1,13 @@ + + + compbio.runner.predictors.Jpred + + 2000 + 1000 + + + # LocalEngineExecutionLimit # + 30 + 500 + + diff --git a/conf/settings/JpredParameters.xml b/conf/settings/JpredParameters.xml new file mode 100644 index 0000000..03c6906 --- /dev/null +++ b/conf/settings/JpredParameters.xml @@ -0,0 +1,71 @@ + + + compbio.runner.predictors.Jpred + + + Prediction without PSI-BLAST hits + + Toggle allowing Jpred to make predictions even when there are no + PSI-BLAST hits. + + -pred-nohits + prog_docs/jpred.txt + + + + + + UNIREF database + + Path to UNIREF database for PSI-BLAST querying + + -dbpath + prog_docs/jpred.txt + . + + + + UNIREF database name + + Number of (combined guide tree/HMM) iterations + + -dbname + prog_docs/jpred.txt + ported_db + uniref90 + ported_db + cluster + + + + + Number of CPUs + + Number of CPU used by jpred.pl. Maximum value is 8 + + -ncpu + prog_docs/jpred.txt + 1 + + Integer + 1 + 8 + + + + + PSI-BLAST output file + + Path to a PSI-BLAST output file + + -psi + prog_docs/jpred.txt + + + diff --git a/conf/settings/JpredPresets.xml b/conf/settings/JpredPresets.xml new file mode 100644 index 0000000..51f3d30 --- /dev/null +++ b/conf/settings/JpredPresets.xml @@ -0,0 +1,28 @@ + + + compbio.runner.predictors.Jpred + + + cluser configuration + + Dundee cluser configuration + + + + + + + + + laptop configuration + + My 4-core laptop configuration + + + + + + + + + diff --git a/website/prog_docs/jpred.txt b/website/prog_docs/jpred.txt new file mode 100644 index 0000000..7ef389f --- /dev/null +++ b/website/prog_docs/jpred.txt @@ -0,0 +1,45 @@ +Usage: + ./jpred.pl -in/-sequence [-out/-output ] [-dbname + ] [-dbpath ] [-ncpu NNN] [-psi ] + [-pred-nohits] [-verbose] [-debug] [-help] [-man] + +Options: + -in/-sequence FILE + The path to the sequence file (in FASTA format) you want to + predict. + + -out/-output FILEPREFIX + A prefix to the filenames created by Jpred, defaults to the value + set by -sequence/-in. + + -dbpath PATH + Path to the uniref database used for PSI-BLAST querying. + Default: . + + -dbname database + Database to use for PSI-BLAST querying. This only accepts databases + from a list which is pre-defined in the code. + Default: uniref90 + + -psi path + Path to a PSI-BLAST output file. + + -ncpu NNN + Number of CPU used by jpred.pl. Maximum value is 8 + Default: NNN = 1 + + -pred-nohits + Toggle allowing Jpred to make predictions even when there are no + PSI-BLAST hits. + + -verbose + Verbose mode. Print more information while running jpred. + + -debug + Debug mode. Print debugging information while running jpred. + + -help + Gives help on the programs usage. + + -man Displays this man page. +