Sascha Steinbiss pushed to branch master at Debian Med / genomethreader
Commits: 1b0b8408 by Sascha Steinbiss at 2020-01-09T22:10:38+01:00 add man page building - - - - - f30ceda8 by Sascha Steinbiss at 2020-01-09T22:16:20+01:00 install manpages - - - - - 4 changed files: - debian/copyright - + debian/genomethreader.manpages - + debian/man_src/gth.1.adoc - debian/rules Changes: ===================================== debian/copyright ===================================== @@ -39,7 +39,7 @@ Copyright: (c) 2003-2009 Gordon Gremme <[email protected]> (c) 2003-2008 Center for Bioinformatics, University of Hamburg License: ISC -File: src/gth/editoperation.h +Files: src/gth/editoperation.h Copyright: (c) 2003-2009 Gordon Gremme <[email protected]> (c) 2003 Stefan Kurtz <[email protected]> (c) 2003-2007 Center for Bioinformatics, University of Hamburg ===================================== debian/genomethreader.manpages ===================================== @@ -0,0 +1 @@ +debian/man/*.1 ===================================== debian/man_src/gth.1.adoc ===================================== @@ -0,0 +1,121 @@ +# gth(1) + +## NAME + +gth - calculate genome structures + +## SYNOPSIS + +*gth* [option ...] -genomic file [...] -cdna file [...] -protein file [...] + +## DESCRIPTION + +Computes similarity-based gene structure predictions (spliced alignments) +using cDNA/EST and/or protein sequences and assemble the resulting spliced +alignments to consensus spliced alignments. + +## OPTIONS + +-genomic specify input files containing genomic sequences + mandatory option +-cdna specify input files containing cDNA/EST sequences +-protein specify input files containing protein sequences +-species specify species to select splice site model which is most + appropriate; possible species: + "human" + "mouse" + "rat" + "chicken" + "drosophila" + "nematode" + "fission_yeast" + "aspergillus" + "arabidopsis" + "maize" + "rice" + "medicago" + default: undefined +-bssm read bssm parameter from file in the path given by the + environment variable BSSMDIR + default: undefined +-scorematrix read amino acid substitution scoring matrix from file in the + path given by the environment variable GTHDATADIR + default: BLOSUM62 +-translationtable set the codon translation table used for codon translation in + matching, DP, and output + default: 1 +-f analyze only forward strand of genomic sequences + default: no +-r analyze only reverse strand of genomic sequences + default: no +-cdnaforward align only forward strand of cDNAs + default: no +-frompos analyze genomic sequence from this position + requires -topos or -width; counting from 1 on + default: 0 +-topos analyze genomic sequence to this position + requires -frompos; counting from 1 on + default: 0 +-width analyze only this width of genomic sequence + requires -frompos + default: 0 +-v be verbose + default: no +-xmlout show output in XML format + default: no +-gff3out show output in GFF3 format + default: no +-md5ids show MD5 fingerprints as sequence IDs + default: no +-o redirect output to specified file + default: undefined +-gzip write gzip compressed output file + default: no +-bzip2 write bzip2 compressed output file + default: no +-force force writing to output file + default: no +-gs2out output in old GeneSeqer2 format + default: no +-minmatchlen specify minimum match length (cDNA matching) + default: 20 +-seedlength specify the seed length (cDNA matching) + default: 18 +-exdrop specify the Xdrop value for edit distance extension (cDNA + matching) + default: 2 +-prminmatchlen specify minimum match length (protein matches) + default: 24 +-prseedlength specify seed length (protein matching) + default: 10 +-prhdist specify Hamming distance (protein matching) + default: 4 +-gcmaxgapwidth set the maximum gap width for global chains + defines approximately the maximum intron length + set to 0 to allow for unlimited length + in order to avoid false-positive exons (lonely exons) at the + sequence ends, it is very important to set this parameter + appropriately! + default: 1000000 +-gcmincoverage set the minimum coverage of global chains regarding to the + reference sequence + default: 50 +-paralogs compute paralogous genes (different chaining procedure) + default: no +-introncutout enable the intron cutout technique + default: no +-fastdp use jump table to increase speed of DP calculation + default: no +-autointroncutout set the automatic intron cutout matrix size in megabytes and + enable the automatic intron cutout technique + default: 0 +-intermediate stop after calculation of spliced alignments and output + results in reusable XML format. Do not process this output + yourself, use the ``normal'' XML output instead! + default: no +-first set the maximum number of spliced alignments per genomic DNA + input. Set to 0 for unlimited number. + default: 0 +-help display help for basic options and exit +-help+ display help for all options and exit +-version display version information and exit ===================================== debian/rules ===================================== @@ -10,6 +10,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all override_dh_clean: dh_clean rm -rf bin/bssm debian/bssm bin/gthdata debian/gthdata + rm -rf $(CURDIR)/debian/man override_dh_auto_build: make licensemanager=no opt=yes 64bit=yes @@ -26,7 +27,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) endif override_dh_installman: - #mkdir -p $(CURDIR)/debian/man - #asciidoctor -a docdate='' -b manpage $(CURDIR)/debian/man_src/*.adoc - #cp $(CURDIR)/debian/man_src/*.? $(CURDIR)/debian/man + mkdir -p $(CURDIR)/debian/man + asciidoctor -a docdate='' -b manpage $(CURDIR)/debian/man_src/*.adoc + cp $(CURDIR)/debian/man_src/*.? $(CURDIR)/debian/man dh_installman -- View it on GitLab: https://salsa.debian.org/med-team/genomethreader/compare/205e56590886042ee3bc74df524597cbbc284a12...f30ceda835d1092e825b2091846aa8d7216c354f -- View it on GitLab: https://salsa.debian.org/med-team/genomethreader/compare/205e56590886042ee3bc74df524597cbbc284a12...f30ceda835d1092e825b2091846aa8d7216c354f You're receiving this email because of your account on salsa.debian.org.
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