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Option Type: PATH

Argument: 3didsql alndir altupc anchor blast+path blastdir blastpath blastpath+ buildpath clustalo clustalw datapath distdir docdir docsource domppidir dumpdir ensdat enspath fasdir fastapath fasttree forkdir forkprog fsa genpath gopherdir goseqdir haqdir hmmerpath homedir hprd hprdpath htmldir htmlpath ipipath iupath javascript jimdir locusdir mafft mapdir motalndir muscle newupc orth2tdt outdir pagan pamlpath phylip ppidir ppioutdir pridepath protalndir pypath qfasdir qpath randfdr randir resdir restoutdir revertdir rpath runpath slimdir slimpath sourcepath splitout stylepath taxdir teiresiaspath unifake unipath virusdir webdir xdir

Modules: bob extatic gatic gopherbench humsf09 orcfinder revert rje_aic rje_archive rje_embl rje_hivqsf rje_hm_html rje_hmm_V2 rje_mirna rje_omim rje_paml slimfrap slimjim spydarm file_monster rje_dbase rje_pattern_discovery rje_pydocs rje_seqgen seqforker slim_pickings gopher_V2 qslimfinder_V1.9 slimbench_V1 slimfinder_V4.9 slimprob_V1.4 rje_biogrid rje_blast_V2 rje_disorder rje_ensembl rje_forker rje_genbank rje_hmm_V1 rje_hpc rje_hprd rje_html rje_iridis rje_motiflist rje_obj rje_ppi rje_qsub rje_seq rje_slimcalc rje_slimcore rje_slimhtml rje_slimlist rje_taxonomy rje_tree rje_uniprot rje gablam gopher happi haqesac multihaq pingu_V3 pingu_V4 presto_V5 qslimfinder slimbench slimfarmer slimfinder slimmutant slimparser slimprob slimsearch

ModuleOptionDescriptionDefault
bob randfdr=PATH Path to FDR files from random datasets
bob resdir=PATH Path to SLiMFinder results directory
extatic resdir=PATH Path for results output ./
file_monster dumpdir=PATH Directory in which to dump redundant files (don't move if "None") ./Redundant/
file_monster dumpdir=PATH Directory in which to dump redundant files (don't move if "None") ./Redundant/
file_monster outdir=PATH Output directory for renamed/reorganised files ./Organised/
gablam blastdir=PATH Path for blast results file (best used with keepblast=T) ./
gablam blastpath+=PATH path for blast+ files c:/bioware/blast+/
gablam blastpath=PATH path for blast files c:/bioware/blast/
gablam fasdir=PATH Directory in which to save fasta files BLASTFAS/
gatic enspath=PATH Path to Ensembl files ./
gopher gopherdir=PATH Parent directory for output of files ./
gopher runpath=PATH Directory from which to run GOPHER. (NB. Will look for input here unless full paths given) ./
gopher_V2 runpath=PATH Specify parent directory in which to output files ./
gopherbench orth2tdt=PATH Directory of orthology files to convert into TDT file
happi htmlpath=PATH Path of parent html directory ./html
haqesac resdir=PATH Output directory for d>0 outputs ./HAQESAC/
humsf09 resdir=PATH Path to extra SLiMFinder results files (*.occ.csv)
multihaq haqdir=PATH Directory in which to output HAQESAC files and perform run seqin_HAQESAC
orcfinder buildpath=PATH Alternative path to look for existing intermediate files SLiMFinder/
orcfinder resdir=PATH Redirect individual output files to specified directory (and look for intermediates) SLiMFinder/
pingu_V3 domppidir=PATH Produce domain-based PPI files and output into PATH (No output if blank/none)
pingu_V3 ensdat=PATH Path to EnsDAT files to use for making combined PPI datasets None
pingu_V3 goseqdir=PATH Path to output full GO fasta files (No output if blank/none)
pingu_V3 hprd=PATH Path to HPRD flat files None
pingu_V3 ppioutdir=PATH Path to output combined PPI files (No output if blank/none)
pingu_V3 resdir=PATH Redirect output files to specified directory ./
pingu_V3 unipath=PATH Path to UniProt files UniProt/
pingu_V4 hprd=PATH Path to HPRD flat files None
pingu_V4 resdir=PATH Redirect output files/directories to specified directory ./
pingu_V4 sourcepath=PATH/ Will look in this directory for input files if not found 'SourceData/'
presto_V5 alndir=PATH Path to alignments of proteins containing motifs ./
presto_V5 iupath=PATH The full path to the IUPred exectuable c:/bioware/iupred/iupred.exe
presto_V5 protalndir=PATH Directory name for output of protein aligments ProteinAln/
qslimfinder buildpath=PATH Alternative path to look for existing intermediate files SLiMFinder/
qslimfinder resdir=PATH Redirect individual output files to specified directory (and look for intermediates) QSLiMFinder/
qslimfinder_V1.9 buildpath=PATH Alternative path to look for existing intermediate files SLiMFinder/
qslimfinder_V1.9 resdir=PATH Redirect individual output files to specified directory (and look for intermediates) QSLiMFinder/
revert blastdir=PATH BLAST directory for GABLAM BLAST files if keepblast=T RevertDir/BLAST/
revert fasdir=PATH Directory in which to save fasta files RevertDir/GABLAMFAS/genome/
revert revertdir=PATH/ Directory to output run files into. (Prefixes basefile for single runs.) REVERT/
revert taxdir=PATH/ Will look in this directory for taxonomy input files if not found 'SourceData/'
revert virusdir=PATH/ Will look in this directory for single viral gb files 'VirusGB/'
rje rpath=PATH Path to installation of R 'R'
rje runpath=PATH Run program from given path (log files and some programs only) path called from
rje_aic enspath=PATH Path to EnsEMBL files ./EnsEMBL/
rje_aic pridepath=PATH Path to XML downloads from PRIDE './PRIDE_XML/'
rje_archive homedir=PATH Home directory from which the archive script will be run '/home/z3452659'
rje_biogrid unipath=PATH Path to UniProt files UniProt/
rje_blast_V2 blast+path=PATH Path to BLAST+ programs (will use blastpath if not given) ''
rje_blast_V2 blastpath=PATH Path to BLAST programs ''
rje_blast_V2 qfasdir=PATH Output directory for QAssemble alignments ./QFAS/
rje_dbase enspath=PATH Path to EnsEMBL file EnsEMBL/
rje_dbase ipipath=PATH Path to IPI files IPI/
rje_dbase unipath=PATH Path to UniProt files UniProt/
rje_disorder anchor=PATH Full path to ANCHOR executable
rje_disorder iupath=PATH The full path to the IUPred executable c:/bioware/iupred/iupred.exe
rje_embl splitout=PATH If path given, will split output into individual files per entry into PATH
rje_ensembl enspath=PATH Path to EnsEMBL file EnsEMBL/
rje_ensembl hmmerpath=PATH Path for hmmer files /home/richard/Bioware/hmmer-2.3.2/src/
rje_ensembl unipath=PATH Path to UniProt files enspath=PATH/uniprot/
rje_forker forkdir=PATH Alternative directory for forking output. `./`
rje_genbank locusdir=PATH Directory in which to generate output by locus ./
rje_genbank taxdir=PATH Path to taxonomy files for species code extraction. (Will not use if blank or None) ./SourceData/
rje_hivqsf ppidir=PATH Path to human protein PPI files
rje_hm_html datapath=PATH Path to parent data directory ./
rje_hm_html htmlpath=PATH Path of parent html directory ./aa_ff
rje_hm_html unifake=PATH Path to UniFake dat file(s) ./unifake/
rje_hm_html unipath=PATH Path to real UniProt dat file(s) ./uniprot/
rje_hmm_V1 hmmerpath=PATH Path for hmmer files /home/richard/Bioware/hmmer-2.3.2/src/
rje_hmm_V2 hmmerpath=PATH Path for hmmer files /home/richard/Bioware/hmmer-2.3.2/src/
rje_hpc pypath=PATH Path to python modules '/home/re1u06/Serpentry/'
rje_hprd hprdpath=PATH Path to HPRD Flat Files ./
rje_hprd outdir=PATH The output directory for the files produced ./
rje_html javascript=PATH Path to javascript files for tabs etc. 'http://www.southampton.ac.uk/~re1u06/javascript/'
rje_iridis pypath=PATH Path to python modules '/home/re1u06/Serpentry/'
rje_mirna enspath=PATH Path to EnsLoci files /scratch/Databases/NewDB/EnsEMBL/
rje_motiflist alndir=PATH Path to alignments of proteins containing motifs ./
rje_motiflist iupath=PATH The full path to the IUPred exectuable c:/bioware/iupred/iupred.exe
rje_motiflist motalndir=PATH Output path for Motif Alignments
rje_motiflist protalndir=PATH Output path for Protein Alignments ProteinAln/
rje_obj rpath=PATH Path to installation of R 'R'
rje_obj runpath=PATH Run program from given path (log files and some programs only) path called from
rje_omim slimdir=PATH Directory where *.occ.csv files can be found
rje_paml pamlpath=PATH Path to PAML package exectuables ./
rje_paml resdir=PATH Directory for results output 'PAML/'
rje_pattern_discovery teiresiaspath=PATH Path to TEIRESIAS 'c:/bioware/Teiresias/teiresias_char.exe'
rje_ppi xdir=PATH Directory for XGMML output ./XGMML
rje_pydocs distdir=PATH Output directory for distribution directories '../packages/'
rje_pydocs docdir=PATH Output path for Python Module documentation '../docs/'
rje_pydocs docsource=PATH Input path for Python Module documentation (manuals etc.) '../docs/'
rje_pydocs pypath=PATH Path to python modules. Will also look in listed sourcedir subfolders. ../
rje_pydocs stylepath=PATH Path to style sheets and javascript code folder etc. http://www.southampton.ac.uk/~re1u06/
rje_pydocs webdir=PATH Directory containing webpage resources ../html/'
rje_qsub pypath=PATH Path for RJE Python scripts /rhome/re1u06/Serpentry/
rje_qsub qpath=PATH Path to change directory too current path
rje_seq blast+path=PATH Path to BLAST+ programs ''
rje_seq blastpath=PATH Path to BLAST programs ''
rje_seq clustalo=PATH Path to CLUSTAL Omega alignment program 'clustalo'
rje_seq clustalw=PATH Path to CLUSTALW program 'clustalw'
rje_seq fastapath=PATH Path to FASTA programs ''
rje_seq fsa=PATH Path to FSA alignment program 'fsa'
rje_seq mafft=PATH Path to MAFFT alignment program 'mafft'
rje_seq muscle=PATH Path to MUSCLE alignment program 'muscle'
rje_seq pagan=PATH Path to PAGAN alignment program 'pagan'
rje_seqgen teiresiaspath=PATH Path to TEIRESIAS 'c:/bioware/Teiresias/teiresias_char.exe'
rje_slimcalc alndir=PATH Path to pre-made alignment files ./
rje_slimcalc gopherdir=PATH Path from which to look for GOPHER alignments (if not found in alndir) and/or run GOPHER ./
rje_slimcalc iupath=PATH The full path to the IUPred exectuable c:/bioware/iupred/iupred.exe
rje_slimcore buildpath=PATH Alternative path to look for existing intermediate files SLiMFinder/
rje_slimcore randir=PATH Output path for creation of randomised datasets Random/
rje_slimcore resdir=PATH Redirect individual output files to specified directory (and look for intermediates) SLiMFinder/
rje_slimhtml datapath=PATH Path to parent data directory ./
rje_slimhtml htmlpath=PATH Path of parent html directory ./html
rje_slimhtml unifake=PATH Path to UniFake dat file(s) ./unifake/
rje_slimhtml unipath=PATH Path to real UniProt dat file(s) ./uniprot/
rje_slimlist alndir=PATH Path to alignments of proteins containing motifs ./
rje_slimlist iupath=PATH The full path to the IUPred exectuable c:/bioware/iupred/iupred.exe
rje_slimlist motalndir=PATH Output path for Motif Alignments
rje_slimlist protalndir=PATH Output path for Protein Alignments ProteinAln/
rje_taxonomy taxdir=PATH/ Will look in this directory for input files if not found './SourceData/'
rje_tree fasttree=PATH Path to FastTree (and including) program ''
rje_tree phylip=PATH Path to PHYLIP programs ''
rje_uniprot unipath=PATH Path to UniProt Datafile (looks here for DB Index file; url = use Web downloads) url
seqforker forkprog=PATH Common program system call for all forked splits of sequence file (e.g. program) None
slim_pickings alndir=PATH Path to alignments of proteins containing motifs [./] * Use forward slashes (/) Gopher/ALN/
slim_pickings iupath=PATH The full path to the IUPred exectuable c:/bioware/iupred/iupred.exe
slim_pickings outdir=PATH Directory into which extracted data will be placed. ./
slim_pickings slimpath=PATH Path to place (or find) index files. *Cannot be used for extraction if fullpath=F* ./
slimbench genpath=PATH Output path for datasets generated with SLiMBench file generator ./SLiMBenchDatasets/
slimbench randir=PATH Output path for creation of randomised datasets ./SLiMBenchDatasets/Random/
slimbench sourcepath=PATH/ Will look in this directory for input files if not found SourceData/
slimbench unipath=PATH Path to UniProt download. Will query website if "URL" URL
slimbench_V1 3didsql=PATH Path to 3DID sql data. Use rje_mysql sqldump to extract 3DID DMI data.
slimbench_V1 genpath=PATH Output path for datasets generated with SLiMBench file generator ./SLiMBenchDatasets/
slimbench_V1 randir=PATH Output path for creation of randomised datasets ./SLiMBenchDatasets/Random/
slimbench_V1 sourcepath=PATH/ Will look in this directory for input files if not found 'SourceData/'
slimfarmer pypath=PATH Path to python modules slimsuite home directoy
slimfarmer qpath=PATH Path to change directory too current path
slimfinder altupc=PATH Look for alternative UPC file and filter based on minocc None
slimfinder buildpath=PATH Alternative path to look for existing intermediate files SLiMFinder/
slimfinder newupc=PATH Look for alternative UPC file and calculate Significance using new clusters None
slimfinder randir=PATH Output path for creation of randomised datasets Random/
slimfinder resdir=PATH Redirect individual output files to specified directory (and look for intermediates) SLiMFinder/
slimfinder_V4.9 altupc=PATH Look for alternative UPC file and filter based on minocc None
slimfinder_V4.9 buildpath=PATH Alternative path to look for existing intermediate files SLiMFinder/
slimfinder_V4.9 newupc=PATH Look for alternative UPC file and calculate Significance using new clusters None
slimfinder_V4.9 randir=PATH Output path for creation of randomised datasets Random/
slimfinder_V4.9 resdir=PATH Redirect individual output files to specified directory (and look for intermediates) SLiMFinder/
slimfrap resdir=PATH Path to extra SLiMFinder results files (*.occ.csv)
slimjim alndir=PATH Path to orthologue alignments for those missing mapping.fas
slimjim htmldir=PATH Output path for HTML files html/
slimjim jimdir=PATH Output directory for generated PNG files ./
slimjim mapdir=PATH Output directory for intermediate composite *.mapping.fas files sjmap/
slimjim resdir=PATH Path to extra SLiMFinder results
slimjim unifake=PATH Path to indexed UniFake DAT file
slimjim unipath=PATH Path to indexed real UniProt DAT files
slimmutant buildpath=PATH Alternative path to look for existing intermediate files (e.g. *.upc) SLiMProb/
slimmutant resdir=PATH Location of output files. SLiMProb resdir should be in slimini SLiMMutant/ (and SLiMProb/)
slimmutant sourcepath=PATH/ Will look in this directory for input files if not found 'SourceData/'
slimparser restoutdir=PATH Path for output of parsed REST output ./
slimprob buildpath=PATH Alternative path to look for existing intermediate files SLiMProb/
slimprob resdir=PATH Redirect individual output files to specified directory (and look for intermediates) SLiMProb/
slimprob_V1.4 buildpath=PATH Alternative path to look for existing intermediate files SLiMProb/
slimprob_V1.4 resdir=PATH Redirect individual output files to specified directory (and look for intermediates) SLiMProb/
slimsearch buildpath=PATH Alternative path to look for existing intermediate files SLiMSearch/
slimsearch resdir=PATH Redirect individual output files to specified directory (and look for intermediates) SLiMSearch/
spydarm pypath=PATH Path to python modules. Will also look in listed sourcedir subfolders. ../
© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.