[med-svn] r15209 - in trunk/packages/snap/trunk/debian: . mans mans.pl
Andreas Tille
tille at moszumanska.debian.org
Wed Nov 20 22:01:55 UTC 2013
Author: tille
Date: 2013-11-20 22:01:55 +0000 (Wed, 20 Nov 2013)
New Revision: 15209
Added:
trunk/packages/snap/trunk/debian/mans.pl/
trunk/packages/snap/trunk/debian/mans.pl/hmm-assembler.pl.1
trunk/packages/snap/trunk/debian/mans.pl/patch-hmm.pl.1
trunk/packages/snap/trunk/debian/mans.pl/zff2gff3.pl.1
Removed:
trunk/packages/snap/trunk/debian/mans/TODO
trunk/packages/snap/trunk/debian/mans/hmm-assembler.pl.1
trunk/packages/snap/trunk/debian/mans/patch-hmm.pl.1
Modified:
trunk/packages/snap/trunk/debian/README.Debian
trunk/packages/snap/trunk/debian/changelog
trunk/packages/snap/trunk/debian/rules
trunk/packages/snap/trunk/debian/snap.install
Log:
Mass commit 2010-07-28-2
Modified: trunk/packages/snap/trunk/debian/README.Debian
===================================================================
--- trunk/packages/snap/trunk/debian/README.Debian 2013-11-20 22:01:13 UTC (rev 15208)
+++ trunk/packages/snap/trunk/debian/README.Debian 2013-11-20 22:01:55 UTC (rev 15209)
@@ -1,4 +1,19 @@
snap for Debian
---------------
- -- Steffen Moeller <moeller at debian.org> Fri, 17 Jun 2011 00:52:12 +0200
+The Perl scripts cds-trainer.pl and noncoding-trainer.pl are needing the
+following Perl modules:
+
+ IK.pm, FAlite.pm, DataBrowser.pm
+
+A web search leads to
+
+ https://github.com/KorfLab/LearnGit
+
+which is a bit mysterious because it is a "Git learning" project and no
+serious bio informatics Perl module. Since this all seems a bit strange
+it was decided to drop the two Perl scripts with unavailable Perl
+modules and the user who might really need these is asked to provide
+more detailed information.
+
+ -- Andreas Tille <tille at debian.org> Fri, 25 Oct 2013 16:39:26 +0200
Modified: trunk/packages/snap/trunk/debian/changelog
===================================================================
--- trunk/packages/snap/trunk/debian/changelog 2013-11-20 22:01:13 UTC (rev 15208)
+++ trunk/packages/snap/trunk/debian/changelog 2013-11-20 22:01:55 UTC (rev 15209)
@@ -1,9 +1,11 @@
-snap (2010-07-28-2) UNRELEASED; urgency=low
+snap (2010-07-28-2) unstable; urgency=low
* debian/upstream: Added citation information
* debian/copyright: DEP5 issues
- * debian/README.Debian: Removed information which is not intended
- for users
+ * debian/README.Debian:
+ - Removed information which is not intended for users
+ - Added information about scripts which are not included into the
+ package since some requriements are not yet fullfilled
* debian/control:
- cme fix dpkg-control
- canonical Vcs fields
@@ -19,9 +21,6 @@
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
Deleted: trunk/packages/snap/trunk/debian/mans/TODO
===================================================================
--- trunk/packages/snap/trunk/debian/mans/TODO 2013-11-20 22:01:13 UTC (rev 15208)
+++ trunk/packages/snap/trunk/debian/mans/TODO 2013-11-20 22:01:55 UTC (rev 15209)
@@ -1,11 +0,0 @@
-# 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
Deleted: trunk/packages/snap/trunk/debian/mans/hmm-assembler.pl.1
===================================================================
--- trunk/packages/snap/trunk/debian/mans/hmm-assembler.pl.1 2013-11-20 22:01:13 UTC (rev 15208)
+++ trunk/packages/snap/trunk/debian/mans/hmm-assembler.pl.1 2013-11-20 22:01:55 UTC (rev 15209)
@@ -1,77 +0,0 @@
-.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
Deleted: trunk/packages/snap/trunk/debian/mans/patch-hmm.pl.1
===================================================================
--- trunk/packages/snap/trunk/debian/mans/patch-hmm.pl.1 2013-11-20 22:01:13 UTC (rev 15208)
+++ trunk/packages/snap/trunk/debian/mans/patch-hmm.pl.1 2013-11-20 22:01:55 UTC (rev 15209)
@@ -1,7 +0,0 @@
-.\" 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.pl/hmm-assembler.pl.1
===================================================================
--- trunk/packages/snap/trunk/debian/mans.pl/hmm-assembler.pl.1 (rev 0)
+++ trunk/packages/snap/trunk/debian/mans.pl/hmm-assembler.pl.1 2013-11-20 22:01:55 UTC (rev 15209)
@@ -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.pl/patch-hmm.pl.1
===================================================================
--- trunk/packages/snap/trunk/debian/mans.pl/patch-hmm.pl.1 (rev 0)
+++ trunk/packages/snap/trunk/debian/mans.pl/patch-hmm.pl.1 2013-11-20 22:01:55 UTC (rev 15209)
@@ -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
+<hmm> <model> <model> <etc>
Added: trunk/packages/snap/trunk/debian/mans.pl/zff2gff3.pl.1
===================================================================
--- trunk/packages/snap/trunk/debian/mans.pl/zff2gff3.pl.1 (rev 0)
+++ trunk/packages/snap/trunk/debian/mans.pl/zff2gff3.pl.1 2013-11-20 22:01:55 UTC (rev 15209)
@@ -0,0 +1,7 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3.
+.TH ZFF2GFF3.PL "1" "October 2013" "SNAP 2010-07-28" "User Commands"
+.SH NAME
+zff2gff3.pl \- SNAP module zff2gff3.pl
+.SH SYNOPSIS
+.B zff2gff3.pl
+<files>
Modified: trunk/packages/snap/trunk/debian/rules
===================================================================
--- trunk/packages/snap/trunk/debian/rules 2013-11-20 22:01:13 UTC (rev 15208)
+++ trunk/packages/snap/trunk/debian/rules 2013-11-20 22:01:55 UTC (rev 15209)
@@ -29,7 +29,8 @@
override_dh_install:
dh_install
- # cds-trainer.pl needs the following Perl modules:
+ # cds-trainer.pl and noncoding-trainer.pl are needing 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
+ find debian -name noncoding-trainer.pl -delete
Modified: trunk/packages/snap/trunk/debian/snap.install
===================================================================
--- trunk/packages/snap/trunk/debian/snap.install 2013-11-20 22:01:13 UTC (rev 15208)
+++ trunk/packages/snap/trunk/debian/snap.install 2013-11-20 22:01:55 UTC (rev 15209)
@@ -1,14 +1,16 @@
-exonpairs usr/bin
-hmm-info usr/bin
-forge usr/bin
-fathom usr/bin
-snap usr/lib/snap
-debian/bin/snap usr/bin
-cds-trainer.pl usr/bin
+exonpairs usr/bin
+hmm-info usr/bin
+forge usr/bin
+fathom usr/bin
+snap usr/lib/snap
+debian/bin/snap usr/bin
+cds-trainer.pl usr/bin
hmm-assembler.pl usr/bin
noncoding-trainer.pl usr/bin
-patch-hmm.pl usr/bin
-zff2gff3.pl usr/bin
-HMM usr/share/snap
-Zoe/zoe-loop usr/bin
-Zoe/blosum62 usr/share/snap/Zoe
+patch-hmm.pl usr/bin
+zff2gff3.pl usr/bin
+HMM usr/share/snap
+Zoe/zoe-loop usr/bin
+Zoe/blosum62 usr/share/snap/Zoe
+# dh_installmans is to intelligent and moves these manpages to /usr/share/man/pl/man1 which is prevented by this trick
+debian/mans.pl/* usr/share/man/man1
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