[med-svn] [Git][med-team/genomethreader][master] 2 commits: add man page building
Sascha Steinbiss
gitlab at salsa.debian.org
Thu Jan 9 21:24:00 GMT 2020
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 <gordon at gremme.org>
(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 <gordon at gremme.org>
(c) 2003 Stefan Kurtz <kurtz at zbh.uni-hamburg.de>
(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
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