[med-svn] r15162 - in trunk/packages/snap/trunk/debian: . mans
Andreas Tille
tille at alioth.debian.org
Fri Nov 8 23:13:12 UTC 2013
Author: tille
Date: 2013-11-08 23:13:12 +0000 (Fri, 08 Nov 2013)
New Revision: 15162
Added:
trunk/packages/snap/trunk/debian/manpages
trunk/packages/snap/trunk/debian/mans/
trunk/packages/snap/trunk/debian/mans/TODO
trunk/packages/snap/trunk/debian/mans/exonpairs.1
trunk/packages/snap/trunk/debian/mans/fathom.1
trunk/packages/snap/trunk/debian/mans/forge.1
trunk/packages/snap/trunk/debian/mans/hmm-assembler.pl.1
trunk/packages/snap/trunk/debian/mans/hmm-info.1
trunk/packages/snap/trunk/debian/mans/patch-hmm.pl.1
trunk/packages/snap/trunk/debian/mans/snap.1
trunk/packages/snap/trunk/debian/mans/zoe-loop.1
Modified:
trunk/packages/snap/trunk/debian/changelog
trunk/packages/snap/trunk/debian/rules
Log:
Enhancing manpages
Modified: trunk/packages/snap/trunk/debian/changelog
===================================================================
--- trunk/packages/snap/trunk/debian/changelog 2013-11-08 23:10:37 UTC (rev 15161)
+++ trunk/packages/snap/trunk/debian/changelog 2013-11-08 23:13:12 UTC (rev 15162)
@@ -14,11 +14,14 @@
- deleted useless comment
- Work around self-made build system and save original files
before configuration and restore these in clean target
- - Use help2man to create simple man pages where possible
+ * debian/mans: create simple man pages by polishing help2man output
* debian/bin/snap: wrapper to set environment variable ZOE to implement
hint given in 00README installation instructions
* debian/patches/hardening.patch: Propagate hardening options
+ *** TODO: cds-trainer.pl
+ Needs: IK.pm, FAlite.pm, DataBrowser.pm
+
-- Andreas Tille <tille at debian.org> Fri, 25 Oct 2013 16:39:26 +0200
snap (2010-07-28-1~lucid1) lucid; urgency=low
Added: trunk/packages/snap/trunk/debian/manpages
===================================================================
--- trunk/packages/snap/trunk/debian/manpages (rev 0)
+++ trunk/packages/snap/trunk/debian/manpages 2013-11-08 23:13:12 UTC (rev 15162)
@@ -0,0 +1 @@
+debian/mans/*.1
Added: trunk/packages/snap/trunk/debian/mans/TODO
===================================================================
--- trunk/packages/snap/trunk/debian/mans/TODO (rev 0)
+++ trunk/packages/snap/trunk/debian/mans/TODO 2013-11-08 23:13:12 UTC (rev 15162)
@@ -0,0 +1,11 @@
+# These *.pl do not run:
+# cds-trainer.pl
+# noncoding-trainer.pl
+#
+# This *.pl does some magic without printing help
+# zff2gff3.pl
+
+W: snap: binary-without-manpage usr/bin/cds-trainer.pl
+W: snap: binary-without-manpage usr/bin/noncoding-trainer.pl
+W: snap: binary-without-manpage usr/bin/patch-hmm.pl
+W: snap: binary-without-manpage usr/bin/zff2gff3.pl
Added: trunk/packages/snap/trunk/debian/mans/exonpairs.1
===================================================================
--- trunk/packages/snap/trunk/debian/mans/exonpairs.1 (rev 0)
+++ trunk/packages/snap/trunk/debian/mans/exonpairs.1 2013-11-08 23:13:12 UTC (rev 15162)
@@ -0,0 +1,42 @@
+.TH EXONPAIRS "1" "October 2013" "exonpairs 2010-07-28" "User Commands"
+.SH NAME
+exonpairs \- SNAP module exonpairs
+.SH SYNOPSIS
+.B exonpairs
+[\fIoptions\fR] <\fBHMM file\fR> <\fBFASTA file\fR> [\fIoptions\fR]
+.SH OPTIONS
+.TP
+\fB\-min\-intron\fR <int>
+minimum Intron length [30]
+.TP
+\fB\-max\-intron\fR <int>
+maximum Intron length [10000]
+.TP
+\fB\-einit\-length\fR <int>
+minimum Einit length in bp [10]
+.TP
+\fB\-eterm\-length\fR <int>
+minimum Eterm length in bp [10]
+.TP
+\fB\-exon\-length\fR <int>
+minimum Exon length in bp [30]
+.HP
+\fB\-intron\-score\fR <float> minimum Intron score in bits [\-5]
+.TP
+\fB\-einit\-score\fR <float>
+minimum Einit score in bits [\-5]
+.TP
+\fB\-eterm\-score\fR <float>
+minimum Eterm score in bits [\-5]
+.TP
+\fB\-exon\-score\fR <float>
+minimum Exon score in bits [\-5]
+.TP
+\fB\-pair\-score\fR <float>
+minimum pair score (exon\-intron\-exon) [10]
+.TP
+\fB\-flank\-length\fR <int>
+length of flanking sequence per exon [20]
+.TP
+\fB\-lcmask\fR
+treat lowercase as N
Added: trunk/packages/snap/trunk/debian/mans/fathom.1
===================================================================
--- trunk/packages/snap/trunk/debian/mans/fathom.1 (rev 0)
+++ trunk/packages/snap/trunk/debian/mans/fathom.1 2013-11-08 23:13:12 UTC (rev 15162)
@@ -0,0 +1,32 @@
+.TH FATHOM "1" "October 2013" "fathom 2010-07-28" "User Commands"
+.SH NAME
+fathom \- sequence and annotation tool
+.SH SYNOPSIS
+.B fathom
+<\fBann\fR> <\fBdna\fR> <\fBcommands\fR>
+.SH OPTIONS
+.TP
+\fB\-help\fR
+report useful information
+.HP
+\fB\-validate\fR [\-quiet]
+.HP
+\fB\-gene\-stats\fR [\-errors\-ok \fB\-nucleotide\fR \fB\-dinucleotide]\fR
+.HP
+\fB\-categorize\fR <int>
+.HP
+\fB\-export\fR <int> [\-plus \fB\-errors\-ok]\fR
+.HP
+\fB\-extract\fR <feature> \fB\-length\fR <int> \fB\-offset\fR <int>
+.HP
+\fB\-exon\-intron\fR
+.HP
+\fB\-split\fR <\-number <int> | \fB\-training\fR <float> | \fB\-GC\fR <float> | \fB\-repeat\fR <float>>
+.HP
+\fB\-ace\-format\fR <\-gene\-method <string> [\-dna \fB\-extra\fR <string>]>
+.HP
+\fB\-compare\-genes\fR <predictions> [\-details]
+.HP
+\fB\-score\-genes\fR <hmm> [\-errors\-ok]
+.HP
+\fB\-filter\-genes\fR <hmm> \fB\-min\-score\fR <float> \fB\-min\-length\fR <int>
Added: trunk/packages/snap/trunk/debian/mans/forge.1
===================================================================
--- trunk/packages/snap/trunk/debian/mans/forge.1 (rev 0)
+++ trunk/packages/snap/trunk/debian/mans/forge.1 2013-11-08 23:13:12 UTC (rev 15162)
@@ -0,0 +1,47 @@
+.TH FORGE "1" "October 2013" "forge 2010-07-28" "User Commands"
+.SH NAME
+forge \- training program for SNAP
+.SH SYNOPSIS
+.B forge
+[\fIoptions\fR] <\fBann\fR> <\fBdna\fR> [\fIoptions\fR]
+.SH OPTIONS
+.HP
+\fB\-help\fR
+.HP
+\fB\-verbose\fR
+.TP
+\fB\-pseudocount\fR <float>
+[1] (absolute number for all models)
+.HP
+\fB\-pseudoCoding\fR <float> [0.0] (eg. 0.05)
+.HP
+\fB\-pseudoIntron\fR <float> [0.0]
+.TP
+\fB\-pseudoInter\fR <float>
+[0.0]
+.TP
+\fB\-min\-counts\fR
+[0]
+.HP
+\fB\-lcmask\fR [\-fragmentN]
+.TP
+\fB\-utr5\-length\fR <int>
+[50]
+.TP
+\fB\-utr5\-offset\fR <int>
+[10]
+.TP
+\fB\-utr3\-length\fR <int>
+[50]
+.TP
+\fB\-utr3\-offset\fR <int>
+[10]
+.TP
+\fB\-explicit\fR <int>
+[250]
+.TP
+\fB\-min\-intron\fR <int>
+[30]
+.TP
+\fB\-boost\fR <file>
+(file of ID <int>)
Added: trunk/packages/snap/trunk/debian/mans/hmm-assembler.pl.1
===================================================================
--- trunk/packages/snap/trunk/debian/mans/hmm-assembler.pl.1 (rev 0)
+++ trunk/packages/snap/trunk/debian/mans/hmm-assembler.pl.1 2013-11-08 23:13:12 UTC (rev 15162)
@@ -0,0 +1,77 @@
+.TH HMM-ASSEMBLER.PL "1" "November 2013" "hmm-assembler.pl 2010-07-28" "User Commands"
+.SH NAME
+hmm-assembler.pl \- SNAP module hmm-assembler.pl
+.SH SYNOPSIS
+.B hmm-assembler.pl
+[\fI-OPTIONS \fR[\fI-MORE_OPTIONS\fR]] [\fI--\fR] [\fIPROGRAM_ARG1 \fR...]
+.SH OPTIONS
+.SS "The following single-character options are accepted:"
+.PP
+With arguments: \fB\-i\fR \fB\-e\fR \fB\-A\fR \fB\-D\fR \fB\-M\fR \fB\-S\fR \fB\-C\fR \fB\-I\fR \fB\-N\fR \fB\-a\fR \fB\-3\fR \fB\-5\fR \fB\-Z\fR \fB\-c\fR
+.PP
+Boolean (without arguments): \fB\-r\fR \fB\-o\fR \fB\-x\fR \fB\-p\fR \fB\-t\fR \fB\-1\fR
+.PP
+Options may be merged together. \fB\-\-\fR stops processing of options.
+Space is not required between options and their arguments.
+.PP
+Options:
+.TP
+\fB\-i\fR
+<length> [500]
+.TP
+\fB\-e\fR
+<length> [1000]
+.TP
+\fB\-A\fR
+<order:length> [0:30]
+.TP
+\fB\-D\fR
+<order:length> [0:9]
+.TP
+\fB\-M\fR
+<order:length> [0:15]
+.TP
+\fB\-S\fR
+<order:length> [0:9]
+.TP
+\fB\-C\fR
+<order> [4]
+.TP
+\fB\-I\fR
+<order> [4]
+.TP
+\fB\-N\fR
+<order> [4]
+.TP
+\fB\-3\fR
+<order:length> [] include 3'UTR model, requires \fB\-a\fR
+.TP
+\fB\-a\fR
+<order:length> [] include PolyA model, requires \fB\-3\fR
+.TP
+\fB\-5\fR
+<order:length> [] include 5'UTR moel, requires \fB\-p\fR
+.TP
+\fB\-p\fR
+include generic promoter model, requires \fB\-5\fR
+.TP
+\fB\-r\fR
+include generic repeat model
+.TP
+\fB\-o\fR
+include reverse ORF model
+.TP
+\fB\-x\fR
+use explicit duration intron model
+.TP
+\fB\-t\fR
+include C.elegans trans\-splicing, requires \fB\-p\fR, \fB\-5\fR
+.TP
+\fB\-Z\fR
+<clade> sets clade\-specific values (worm, fly, plant)
+.TP
+\fB\-1\fR
+single gene model
+.TP
+\fB\-c\fR <score>
+include GC\-AG splice donor model
Added: trunk/packages/snap/trunk/debian/mans/hmm-info.1
===================================================================
--- trunk/packages/snap/trunk/debian/mans/hmm-info.1 (rev 0)
+++ trunk/packages/snap/trunk/debian/mans/hmm-info.1 2013-11-08 23:13:12 UTC (rev 15162)
@@ -0,0 +1,13 @@
+.TH HMM-INFO "1" "October 2013" "hmm-info 2010-07-28" "User Commands"
+.SH NAME
+hmm-info \- SNAP module hmm-info
+.SH SYNOPSIS
+.B hmm\-info
+[\fIoptions\fR] <\fBhmm file\fR>
+.SH OPTIONS
+.HP
+\fB\-models\fR
+.HP
+\fB\-general\fR
+.HP
+\fB\-durations\fR <length>
Added: trunk/packages/snap/trunk/debian/mans/patch-hmm.pl.1
===================================================================
--- trunk/packages/snap/trunk/debian/mans/patch-hmm.pl.1 (rev 0)
+++ trunk/packages/snap/trunk/debian/mans/patch-hmm.pl.1 2013-11-08 23:13:12 UTC (rev 15162)
@@ -0,0 +1,7 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3.
+.TH PATCH-HMM.PL "1" "October 2013" "patch-hmm.pl 2010-07-28" "User Commands"
+.SH NAME
+patch-hmm.pl \- SNAP module patch-hmm.pl
+.SH SYNOPSIS
+.B patch\-hmm.pl\fP
+<hmm> <model> <model> <etc>
Added: trunk/packages/snap/trunk/debian/mans/snap.1
===================================================================
--- trunk/packages/snap/trunk/debian/mans/snap.1 (rev 0)
+++ trunk/packages/snap/trunk/debian/mans/snap.1 2013-11-08 23:13:12 UTC (rev 15162)
@@ -0,0 +1,41 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3.
+.TH SNAP "1" "October 2013" "snap 2010-07-28" "User Commands"
+.SH NAME
+snap \- Semi-HMM-based Nucleic Acid Parser
+.SH SYNOPSIS
+.B snap
+[\fIoptions\fR] <\fBHMM file\fR> <\fBFASTA file\fR> [\fIoptions\fR]
+.SH OPTIONS
+.TP
+\fB\-help\fR
+report useful information
+.TP
+\fB\-lcmask\fR
+treat lowercase as N
+.TP
+\fB\-plus\fR
+predict on plus strand only
+.TP
+\fB\-minus\fR
+predict on minus strand only
+.TP
+\fB\-gff\fR
+output annotation as GFF
+.TP
+\fB\-ace\fR
+output annotation as ACED
+.TP
+\fB\-quiet\fR
+do not send progress to STDERR
+.TP
+\fB\-aa\fR <file>
+create FASTA file of proteins
+.TP
+\fB\-tx\fR <file>
+create FASTA file of transcripts
+.TP
+\fB\-xdef\fR <file>
+external definitions
+.TP
+\fB\-name\fR <string>
+name for the gene [default snap]
Added: trunk/packages/snap/trunk/debian/mans/zoe-loop.1
===================================================================
--- trunk/packages/snap/trunk/debian/mans/zoe-loop.1 (rev 0)
+++ trunk/packages/snap/trunk/debian/mans/zoe-loop.1 2013-11-08 23:13:12 UTC (rev 15162)
@@ -0,0 +1,26 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3.
+.TH ZOE-LOOP "1" "October 2013" "zoe-loop 2010-07-28" "User Commands"
+.SH NAME
+zoe-loop \- SNAP module zoe-loop
+.SH SYNOPSIS
+.B zoe\-loop
+<\fBtest\fR> [\fIiterations \- default 1000\fR]
+.SH OPTIONS
+.HP
+\fB\-all\fR
+.HP
+\fB\-Vec\fR, \fB\-IVec\fR, \fB\-FVec\fR, \fB\-TVec\fR, \fB\-Hash\fR \fB\-Xtree\fR
+.HP
+\fB\-Feature\fR, \fB\-FeatureVec\fR
+.HP
+\fB\-FastaFile\fR, \fB\-DNA\fR, \fB\-Protein\fR, \fB\-Alignment\fR \fB\-CDS\fR \fB\-Palign\fR
+.HP
+\fB\-Distribution\fR, \fB\-Duration\fR, \fB\-State\fR, \fB\-Transition\fR
+.PP
+The following tests are not part of \fB\-all\fR and require files
+.HP
+\fB\-FeatureTable\fR <file>
+.HP
+\fB\-Model\fR, \fB\-Scanner\fR, \fB\-Counter\fR
+.HP
+\fB\-HMM\fR <file>
Modified: trunk/packages/snap/trunk/debian/rules
===================================================================
--- trunk/packages/snap/trunk/debian/rules 2013-11-08 23:10:37 UTC (rev 15161)
+++ trunk/packages/snap/trunk/debian/rules 2013-11-08 23:13:12 UTC (rev 15162)
@@ -27,40 +27,9 @@
override_dh_auto_build:
dh_auto_build CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
-override_dh_installman:
- mkdir -p $(mandir)
- help2man --no-info --no-discard-stderr -h "" \
- --version-string="$(version)" \
- --name="Semi-HMM-based Nucleic Acid Parser" \
- $(libdir)/snap > $(mandir)/snap.1
- help2man --no-info --no-discard-stderr -h "" \
- --version-string="$(version)" \
- $(bindir)/exonpairs > $(mandir)/exonpairs.1
- help2man --no-info --no-discard-stderr -h "" \
- --version-string="$(version)" \
- --name="sequence and annotation tool" \
- $(bindir)/fathom > $(mandir)/fathom.1
- help2man --no-info --no-discard-stderr -h "" \
- --version-string="$(version)" \
- --name="training program for SNAP" \
- $(bindir)/forge > $(mandir)/forge.1
- help2man --no-info --no-discard-stderr -h "" \
- --version-string="$(version)" \
- $(bindir)/hmm-info > $(mandir)/hmm-info.1
- help2man --no-info --no-discard-stderr -h "" \
- --version-string="$(version)" \
- $(bindir)/zoe-loop > $(mandir)/zoe-loop.1
- # Not sure whether we should leave .pl extension
- help2man --no-info --no-discard-stderr -h "" \
- --version-string="$(version)" \
- $(bindir)/hmm-assembler.pl > $(mandir)/hmm-assembler.pl.1
- help2man --no-info --no-discard-stderr -h "" \
- --version-string="$(version)" \
- $(bindir)/patch-hmm.pl > $(mandir)/patch-hmm.pl.1
- #
- # These *.pl do not run:
- # cds-trainer.pl
- # noncoding-trainer.pl
- #
- # This *.pl does some magic without printing help
- # zff2gff3.pl
+override_dh_install:
+ dh_install
+ # cds-trainer.pl needs the following Perl modules:
+ # IK.pm, FAlite.pm, DataBrowser.pm
+ # since these are not available in Debian there is no point in installing this script
+ find debian -name cds-trainer.pl -delete
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