[med-svn] r15263 - trunk/packages/seqan/trunk/debian
Andreas Tille
tille at moszumanska.debian.org
Sat Nov 23 17:36:56 UTC 2013
Author: tille
Date: 2013-11-23 17:36:56 +0000 (Sat, 23 Nov 2013)
New Revision: 15263
Added:
trunk/packages/seqan/trunk/debian/generate_manpages
trunk/packages/seqan/trunk/debian/seqan-apps.install
Removed:
trunk/packages/seqan/trunk/debian/dfi.1
trunk/packages/seqan/trunk/debian/micro_razers.1
trunk/packages/seqan/trunk/debian/pair_align.1
trunk/packages/seqan/trunk/debian/razers.1
trunk/packages/seqan/trunk/debian/seqan-apps.dirs
trunk/packages/seqan/trunk/debian/seqan-apps.links
trunk/packages/seqan/trunk/debian/seqan_tcoffee.1
trunk/packages/seqan/trunk/debian/seqcons.1
trunk/packages/seqan/trunk/debian/tree_recon.1
Modified:
trunk/packages/seqan/trunk/debian/changelog
trunk/packages/seqan/trunk/debian/control
trunk/packages/seqan/trunk/debian/rules
trunk/packages/seqan/trunk/debian/seqan-dev.docs
trunk/packages/seqan/trunk/debian/seqan-dev.install
Log:
Doing a bit of reorganisation how files are installed; create manpages automatically using help2man
Modified: trunk/packages/seqan/trunk/debian/changelog
===================================================================
--- trunk/packages/seqan/trunk/debian/changelog 2013-11-23 08:29:34 UTC (rev 15262)
+++ trunk/packages/seqan/trunk/debian/changelog 2013-11-23 17:36:56 UTC (rev 15263)
@@ -18,6 +18,9 @@
- Add Upstream-Contact according to latest discussion
- Update Source to actual download tarball
* debian/rules: cdbs -> dh
+ * debian/seqan-apps.links -> seqan-apps.install: Install applications
+ directly to /usr/bin
+ * debian/generate_manpages: use help2man to autogenerate manpages
-- Andreas Tille <tille at debian.org> Fri, 22 Nov 2013 10:06:25 +0100
Modified: trunk/packages/seqan/trunk/debian/control
===================================================================
--- trunk/packages/seqan/trunk/debian/control 2013-11-23 08:29:34 UTC (rev 15262)
+++ trunk/packages/seqan/trunk/debian/control 2013-11-23 17:36:56 UTC (rev 15263)
@@ -8,7 +8,9 @@
cmake,
zlib1g-dev,
libbam-dev,
- libboost-dev
+ libboost-dev,
+ dh-exec,
+ help2man
Standards-Version: 3.9.5
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/seqan/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/seqan/trunk/
Deleted: trunk/packages/seqan/trunk/debian/dfi.1
===================================================================
--- trunk/packages/seqan/trunk/debian/dfi.1 2013-11-23 08:29:34 UTC (rev 15262)
+++ trunk/packages/seqan/trunk/debian/dfi.1 2013-11-23 17:36:56 UTC (rev 15263)
@@ -1,44 +0,0 @@
-.TH DFI "1" "September 2009" "DFI version 2.0 20090715 [4670]" "User Commands"
-.SH NAME
-DFI \- The Deferred Frequency Index
-.SH SYNOPSIS
-.B dfi
-[\fIOPTION\fR]... \fI--minmax <min_1> <max_1> <database 1> \fR... \fI--minmax <min_m> <max_m> <database m>\fR
-.SH DESCRIPTION
-DFI \- The Deferred Frequency Index
-.TP
-dfi [OPTION]... \fB\-\-growth\fR <rho_s> <rho_g> <database 1> <database 2>
-.TP
-dfi [OPTION]... \fB\-\-entropy\fR <rho_s> <alpha> <database 1> <database 2> ... <database m>
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-displays this help message
-.TP
-\fB\-V\fR, \fB\-\-version\fR
-print version information
-.TP
-\fB\-f\fR, \fB\-\-minmax\fR NUM1 NUM2
-solve Frequent Pattern Mining Problem
-.TP
-\fB\-g\fR, \fB\-\-growth\fR NUM1 NUM2
-solve Emerging Substring Mining Problem
-.TP
-\fB\-e\fR, \fB\-\-entropy\fR NUM1 NUM2
-solve Entropy Mining Problem
-.TP
-\fB\-p\fR, \fB\-\-protein\fR
-use AminoAcid alphabet (for proteomes)
-.TP
-\fB\-d\fR, \fB\-\-dna\fR
-use DNA alphabet (for genomes)
-.TP
-\fB\-m\fR, \fB\-\-maximal\fR
-output only left and right maximal substrings
-The default is byte alphabet
-.SH AUTHOR
-.br
-dfi was written by David Weese and Marcel H. Schulz.
-.PP
-This manual page was generated using html2man and polished by
-Soeren Sonnenburg <sonne at debian.org>, for the Debian project
-(but may be used by others).
Added: trunk/packages/seqan/trunk/debian/generate_manpages
===================================================================
--- trunk/packages/seqan/trunk/debian/generate_manpages (rev 0)
+++ trunk/packages/seqan/trunk/debian/generate_manpages 2013-11-23 17:36:56 UTC (rev 15263)
@@ -0,0 +1,17 @@
+#!/bin/sh
+# generate manpages using help2man
+
+pkg=`dpkg-parsechangelog | sed -n 's/^Source: //p'`-apps
+version=`dpkg-parsechangelog -ldebian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d-`
+bindir=`pwd`/debian/${pkg}/usr/bin
+mandir=`pwd`/debian/${pkg}/usr/share/man/man1
+
+set -x
+mkdir -p ${mandir}
+for bin in `ls ${bindir}`; do
+ help2man --no-info --name="XXX remove this line" --version-string="${version}" ${bindir}/${bin} | \
+ sed -e '/XXX remove this line/d' \
+ -e '/^\.SH DESCRIPTION$/d' \
+ -e '/^============\+$/d' \
+ > ${mandir}/${bin}.1
+done
Property changes on: trunk/packages/seqan/trunk/debian/generate_manpages
___________________________________________________________________
Added: svn:executable
+ *
Deleted: trunk/packages/seqan/trunk/debian/micro_razers.1
===================================================================
--- trunk/packages/seqan/trunk/debian/micro_razers.1 2013-11-23 08:29:34 UTC (rev 15262)
+++ trunk/packages/seqan/trunk/debian/micro_razers.1 2013-11-23 17:36:56 UTC (rev 15263)
@@ -1,82 +0,0 @@
-.TH MICRORAZERS "1" "September 2009" "MicroRazerS version 0.1 20090710 (prerelease)" "User Commands"
-.SH NAME
-MicroRazerS \- Rapid Alignment of Small RNA Reads
-.SH SYNOPSIS
-.B micro_razers
-[\fIOPTION\fR]... \fI<GENOME FILE> <READS FILE>\fR
-.SH DESCRIPTION
-MicroRazerS \- Rapid Alignment of Small RNA Reads
-.SS "Main Options:"
-.TP
-\fB\-o\fR, \fB\-\-output\fR FILE
-change output filename (default <READS FILE>.result)
-.TP
-\fB\-sL\fR, \fB\-\-seed\-length\fR NUM
-seed length (default 16)
-.TP
-\fB\-sE\fR, \fB\-\-seed\-error\fR
-allow for one error in the seed (default off)
-.TP
-\fB\-rr\fR, \fB\-\-recognition\-rate\fR
-set lower bound of sensitivity level for one\-error matches (default 100)
-.TP
-\fB\-f\fR, \fB\-\-forward\fR
-only compute forward matches
-.TP
-\fB\-r\fR, \fB\-\-reverse\fR
-only compute reverse complement matches
-.TP
-\fB\-mN\fR, \fB\-\-match\-N\fR
-\&'N' matches with all other characters
-.TP
-\fB\-m\fR, \fB\-\-max\-hits\fR NUM
-output only NUM of the best hits (default 100)
-.TP
-\fB\-pa\fR, \fB\-\-purge\-ambiguous\fR
-purge reads with more than max\-hits best matches
-.TP
-\fB\-lm\fR, \fB\-\-low\-memory\fR
-may decrease memory usage at the expense of runtime
-.TP
-\fB\-v\fR, \fB\-\-verbose\fR
-verbose mode
-.TP
-\fB\-vv\fR, \fB\-\-vverbose\fR
-very verbose mode
-.TP
-\fB\-V\fR, \fB\-\-version\fR
-print version number
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-print this help
-.SS "Output Format Options:"
-.TP
-\fB\-a\fR, \fB\-\-alignment\fR
-dump the alignment for each match
-.TP
-\fB\-gn\fR, \fB\-\-genome\-naming\fR NUM
-select how genomes are named
-0 = use Fasta id (default)
-1 = enumerate beginning with 1
-.TP
-\fB\-rn\fR, \fB\-\-read\-naming\fR NUM
-select how reads are named
-0 = use Fasta id (default)
-1 = enumerate beginning with 1
-2 = use the read sequence (only for short reads!)
-.TP
-\fB\-so\fR, \fB\-\-sort\-order\fR NUM
-select how matches are sorted
-0 = 1. read number, 2. genome position (default)
-1 = 1. genome position, 2. read number
-.TP
-\fB\-pf\fR, \fB\-\-position\-format\fR
-0 = gap space (default)
-1 = position space
-.SH AUTHOR
-.br
-MicroRazerSwas written by Anne-Katrin Emde.
-.PP
-This manual page was generated using html2man and polished by
-Soeren Sonnenburg <sonne at debian.org>, for the Debian project
-(but may be used by others).
Deleted: trunk/packages/seqan/trunk/debian/pair_align.1
===================================================================
--- trunk/packages/seqan/trunk/debian/pair_align.1 2013-11-23 08:29:34 UTC (rev 15262)
+++ trunk/packages/seqan/trunk/debian/pair_align.1 2013-11-23 17:36:56 UTC (rev 15263)
@@ -1,73 +0,0 @@
-.TH PAIRALIGN "1" "September 2009" "Version 1.0 (15. July 2009) Revision: 4566" "User Commands"
-.SH NAME
-pair_align \- Pairwise alignment
-.SH SYNOPSIS
-.B pair_align
-\fI-s <FASTA sequence file> \fR[\fIOptions\fR]
-.SH DESCRIPTION
-Pairwise alignment \- PairAlign
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-displays this help message
-.TP
-\fB\-V\fR, \fB\-\-version\fR
-print version information
-.SS "Main Options:"
-.TP
-\fB\-s\fR, \fB\-\-seq\fR <FASTA Sequence File>
-file with 2 sequences
-.TP
-\fB\-a\fR, \fB\-\-alphabet\fR [protein | dna | rna]
-sequence alphabet (default protein)
-.TP
-\fB\-m\fR, \fB\-\-method\fR [nw, gotoh, sw, lcs]
-alignment method (default gotoh)
-nw = Needleman\-Wunsch
-gotoh = Gotoh
-sw = Smith\-Waterman
-lcs = Longest common subsequence
-.TP
-\fB\-o\fR, \fB\-\-outfile\fR <Filename>
-output filename (default out.fasta)
-.TP
-\fB\-f\fR, \fB\-\-format\fR [fasta | msf]
-output format (default fasta)
-.SS "Scoring Options:"
-.TP
-\fB\-g\fR, \fB\-\-gop\fR <Int>
-gap open penalty (default \fB\-11\fR)
-.TP
-\fB\-e\fR, \fB\-\-gex\fR <Int>
-gap extension penalty (default \fB\-1\fR)
-.TP
-\fB\-ma\fR, \fB\-\-matrix\fR <Matrix file>
-score matrix (default Blosum62)
-.TP
-\fB\-ms\fR, \fB\-\-msc\fR <Int>
-match score (default 5)
-.TP
-\fB\-mm\fR, \fB\-\-mmsc\fR <Int>
-mismatch penalty (default \fB\-4\fR)
-.SS "Banded Alignment Options:"
-.TP
-\fB\-lo\fR, \fB\-\-low\fR <Int>
-lower diagonal
-.TP
-\fB\-hi\fR, \fB\-\-high\fR <Int>
-upper diagonal
-.SS "DP Matrix Configuration Options:"
-.TP
-\fB\-c\fR, \fB\-\-config\fR [ffff | ... | tttt]
-alignment configuration (default ffff)
-tfff = First row with 0's
-ftff = First column with 0's
-fftf = Search last column for max
-ffft = Search last row for max
-All combinations are allowed.
-.SH AUTHOR
-.br
-pair_align was written by Tobias Rausch.
-.PP
-This manual page was generated using html2man and polished by
-Soeren Sonnenburg <sonne at debian.org>, for the Debian project
-(but may be used by others).
Deleted: trunk/packages/seqan/trunk/debian/razers.1
===================================================================
--- trunk/packages/seqan/trunk/debian/razers.1 2013-11-23 08:29:34 UTC (rev 15262)
+++ trunk/packages/seqan/trunk/debian/razers.1 2013-11-23 17:36:56 UTC (rev 15263)
@@ -1,128 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.36.
-.TH RAZERS "1" "September 2009" "RazerS version 1.0 20090710 [4739]" "User Commands"
-.SH NAME
-RazerS \- Fast Read Mapping with Sensitivity Control
-.SH SYNOPSIS
-.B razers
-[\fIOPTION\fR]... \fI<GENOME FILE> <READS FILE>\fR
-.SH DESCRIPTION
-RazerS \- Fast Read Mapping with Sensitivity Control
-.IP
-razers [OPTION]... <GENOME FILE> <MP\-READS FILE1> <MP\-READS FILE2>
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-displays this help message
-.TP
-\fB\-V\fR, \fB\-\-version\fR
-print version information
-.SS "Main Options:"
-.TP
-\fB\-f\fR, \fB\-\-forward\fR
-only compute forward matches
-.TP
-\fB\-r\fR, \fB\-\-reverse\fR
-only compute reverse complement matches
-.TP
-\fB\-i\fR, \fB\-\-percent\-identity\fR NUM
-set the percent identity threshold (default 92)
-.TP
-\fB\-rr\fR, \fB\-\-recognition\-rate\fR NUM
-set the percent recognition rate (default 99)
-.TP
-\fB\-pd\fR, \fB\-\-param\-dir\fR DIR
-folder containing user\-computed parameter files (optional)
-.TP
-\fB\-id\fR, \fB\-\-indels\fR
-allow indels (default: mismatches only)
-.TP
-\fB\-ll\fR, \fB\-\-library\-length\fR NUM
-mate\-pair library length (default 220)
-.TP
-\fB\-le\fR, \fB\-\-library\-error\fR NUM
-mate\-pair library length tolerance (default 50)
-.TP
-\fB\-m\fR, \fB\-\-max\-hits\fR NUM
-output only NUM of the best hits (default 100)
-.TP
-\fB\-\-unique\fR
-output only unique best matches (\fB\-m\fR 1 \fB\-dr\fR 0 \fB\-pa\fR)
-.TP
-\fB\-tr\fR, \fB\-\-trim\-reads\fR NUM
-trim reads to given length (default off)
-.TP
-\fB\-o\fR, \fB\-\-output\fR FILE
-change output filename (default <READS FILE>.result)
-.TP
-\fB\-v\fR, \fB\-\-verbose\fR
-verbose mode
-.TP
-\fB\-vv\fR, \fB\-\-vverbose\fR
-very verbose mode
-.SS "Output Format Options:"
-.TP
-\fB\-a\fR, \fB\-\-alignment\fR
-dump the alignment for each match
-.TP
-\fB\-pa\fR, \fB\-\-purge\-ambiguous\fR
-purge reads with more than max\-hits best matches
-.TP
-\fB\-dr\fR, \fB\-\-distance\-range\fR NUM
-only consider matches with at most NUM more errors compared to the best (default output all)
-.TP
-\fB\-of\fR, \fB\-\-output\-format\fR NUM
-set output format (default 0)
-0 = Razer format
-1 = enhanced Fasta format
-2 = Eland format
-3 = GFF format
-.TP
-\fB\-gn\fR, \fB\-\-genome\-naming\fR NUM
-select how genomes are named (default 0)
-0 = use Fasta id
-1 = enumerate beginning with 1
-.TP
-\fB\-rn\fR, \fB\-\-read\-naming\fR NUM
-select how reads are named (default 0)
-0 = use Fasta id
-1 = enumerate beginning with 1
-2 = use the read sequence (only for short reads!)
-.TP
-\fB\-so\fR, \fB\-\-sort\-order\fR NUM
-select how matches are sorted (default 0)
-0 = 1. read number, 2. genome position
-1 = 1. genome position, 2. read number
-.TP
-\fB\-pf\fR, \fB\-\-position\-format\fR NUM
-select begin/end position numbering (default 0)
-0 = gap space
-1 = position space
-.SS "Filtration Options:"
-.TP
-\fB\-s\fR, \fB\-\-shape\fR BITSTRING
-set k\-mer shape (default 11111111111)
-.TP
-\fB\-t\fR, \fB\-\-threshold\fR NUM
-set minimum k\-mer threshold (default 1)
-.TP
-\fB\-oc\fR, \fB\-\-overabundance\-cut\fR NUM
-set k\-mer overabundance cut ratio (default 1)
-.TP
-\fB\-rl\fR, \fB\-\-repeat\-length\fR NUM
-set simple\-repeat length threshold (default 1000)
-.TP
-\fB\-tl\fR, \fB\-\-taboo\-length\fR NUM
-set taboo length (default 1)
-.SS "Verification Options:"
-.TP
-\fB\-mN\fR, \fB\-\-match\-N\fR
-\&'N' matches with all other characters
-.TP
-\fB\-ed\fR, \fB\-\-error\-distr\fR FILE
-write error distribution to FILE
-.SH AUTHOR
-.br
-razers was written by David Weese.
-.PP
-This manual page was generated using html2man and polished by
-Soeren Sonnenburg <sonne at debian.org>, for the Debian project
-(but may be used by others).
Modified: trunk/packages/seqan/trunk/debian/rules
===================================================================
--- trunk/packages/seqan/trunk/debian/rules 2013-11-23 08:29:34 UTC (rev 15262)
+++ trunk/packages/seqan/trunk/debian/rules 2013-11-23 17:36:56 UTC (rev 15263)
@@ -20,26 +20,29 @@
cp -a $$header orig/$${header} ; \
done
-#override_dh_auto_install:
-# dh_auto_install
-__install/seqan-apps:: debian/stamp-install-seqan-apps
-__debian/stamp-install-seqan-apps:
- #install binaries
- for APP in `find $(CURDIR)/obj*/apps -mindepth 1 -maxdepth 1 -executable -type f` ; do \
- cp -a $$APP $(CURDIR)/debian/seqan-apps/usr/lib/sequan/bin/ ; done
- #install readmes
- for APP in `find apps -name README` ; do \
- app=`echo $$APP | sed 's?.*apps/\(.\+\)/README?\1?'` ; \
- echo $$app ; \
- cp -a $$APP $(CURDIR)/debian/seqan-apps/usr/share/doc/seqan-apps/README.$$app ; \
- done
+override_dh_install:
+ dh_install
+ # Formerly binaries were installed into usr/lib/sequan/bin/
+ # and only some of them were made available in /usr/bin via dh_link
+ # Since there is no obvious reason for this neither is there any
+ # documentation that explains the motivation this is commented here.
+ #for APP in `find $(CURDIR)/obj*/apps -mindepth 1 -maxdepth 1 -executable -type f` ; do \
+ # cp -a $$APP $(CURDIR)/debian/seqan-apps/usr/lib/sequan/bin/ ; done
+ # ------------------------------------------------------------------
+ # Formerly readmes were named README.app. It seems more consistent
+ # to keep upstream documentation layout which in addition contains
+ # some example files. So the old code is commented here.
+ #for APP in `find apps -name README` ; do \
+ # app=`echo $$APP | sed 's?.*apps/\(.\+\)/README?\1?'` ; \
+ # echo $$app ; \
+ # cp -a $$APP $(CURDIR)/debian/seqan-apps/usr/share/doc/seqan-apps/README.$$app ; \
+ #done
+ # ------------------------------------------------------------------
+ # Delete additional LICENSE files
+ find $(CURDIR)/debian/seqan-apps -type f -name LICENSE -delete
+ # Delete *.pyc files that somehow end up in seqan-dev documentation
+ find $(CURDIR)/debian/seqan-dev -type f -name "*.pyc" -delete
-# Delete extra license files
-__install/seqan-dev::
- @echo "This should be post-install action after installing files for seqan-dev ... but the doc is lying :-("
- find debian -type f -name LICENSE -delete
- # FIXME: Anybody able to convince cdbs to do what the doc is promising and remove the unneeded LICENSE files?
-
override_dh_auto_clean:
dh_auto_clean
find . -type f -name "*.pyc" -delete
@@ -50,6 +53,9 @@
fi
rm -rf orig
+override_dh_installman:
+ $(CURDIR)/debian/generate_manpages
+
get-orig-source:
uscan --verbose --force-download
Deleted: trunk/packages/seqan/trunk/debian/seqan-apps.dirs
===================================================================
--- trunk/packages/seqan/trunk/debian/seqan-apps.dirs 2013-11-23 08:29:34 UTC (rev 15262)
+++ trunk/packages/seqan/trunk/debian/seqan-apps.dirs 2013-11-23 17:36:56 UTC (rev 15263)
@@ -1,2 +0,0 @@
-usr/share/doc/seqan-apps
-usr/lib/sequan/bin
Added: trunk/packages/seqan/trunk/debian/seqan-apps.install
===================================================================
--- trunk/packages/seqan/trunk/debian/seqan-apps.install (rev 0)
+++ trunk/packages/seqan/trunk/debian/seqan-apps.install 2013-11-23 17:36:56 UTC (rev 15263)
@@ -0,0 +1,2 @@
+usr/bin/* usr/bin
+usr/share/doc/* usr/share/doc/seqan-apps
Deleted: trunk/packages/seqan/trunk/debian/seqan-apps.links
===================================================================
--- trunk/packages/seqan/trunk/debian/seqan-apps.links 2013-11-23 08:29:34 UTC (rev 15262)
+++ trunk/packages/seqan/trunk/debian/seqan-apps.links 2013-11-23 17:36:56 UTC (rev 15263)
@@ -1,7 +0,0 @@
-usr/lib/sequan/bin/dfi usr/bin/dfi
-usr/lib/sequan/bin/micro_razers usr/bin/micro_razers
-usr/lib/sequan/bin/pair_align usr/bin/pair_align
-usr/lib/sequan/bin/razers usr/bin/razers
-usr/lib/sequan/bin/seqan_tcoffee usr/bin/seqan_tcoffee
-usr/lib/sequan/bin/seqcons usr/bin/seqcons
-usr/lib/sequan/bin/tree_recon usr/bin/tree_recon
Modified: trunk/packages/seqan/trunk/debian/seqan-dev.docs
===================================================================
--- trunk/packages/seqan/trunk/debian/seqan-dev.docs 2013-11-23 08:29:34 UTC (rev 15262)
+++ trunk/packages/seqan/trunk/debian/seqan-dev.docs 2013-11-23 17:36:56 UTC (rev 15263)
@@ -1 +1,2 @@
-core/demos
+#! /usr/bin/dh-exec
+obj-${DEB_BUILD_GNU_TYPE}/docs/html
Modified: trunk/packages/seqan/trunk/debian/seqan-dev.install
===================================================================
--- trunk/packages/seqan/trunk/debian/seqan-dev.install 2013-11-23 08:29:34 UTC (rev 15262)
+++ trunk/packages/seqan/trunk/debian/seqan-dev.install 2013-11-23 17:36:56 UTC (rev 15263)
@@ -1,2 +1,2 @@
-docs/* usr/share/doc/seqan-dev/html
-# seqan usr/include
+docs/* usr/share/doc/seqan-dev/html
+core/include/seqan usr/include
Deleted: trunk/packages/seqan/trunk/debian/seqan_tcoffee.1
===================================================================
--- trunk/packages/seqan/trunk/debian/seqan_tcoffee.1 2013-11-23 08:29:34 UTC (rev 15262)
+++ trunk/packages/seqan/trunk/debian/seqan_tcoffee.1 2013-11-23 17:36:56 UTC (rev 15263)
@@ -1,90 +0,0 @@
-.TH SEQAN_TCOFFEE "1" "September 2009" "Version 1.11 (30. July 2009) Revision: 4637" "User Commands"
-.SH NAME
-seqan_tcoffee \- Multiple sequence alignment
-.SH SYNOPSIS
-.B seqan_tcoffee
-\fI-s <FASTA sequence file> \fR[\fIOptions\fR]
-.SH DESCRIPTION
-Multiple sequence alignment \- SeqAn::T\-Coffee
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-displays this help message
-.TP
-\fB\-V\fR, \fB\-\-version\fR
-print version information
-.SS "Main Options:"
-.TP
-\fB\-s\fR, \fB\-\-seq\fR <FASTA Sequence File>
-file with sequences
-.TP
-\fB\-a\fR, \fB\-\-alphabet\fR [protein | dna | rna]
-sequence alphabet (default protein)
-.TP
-\fB\-o\fR, \fB\-\-outfile\fR <Filename>
-output filename (default out.fasta)
-.TP
-\fB\-f\fR, \fB\-\-format\fR [fasta | msf]
-output format (default fasta)
-.SS "Segment Match Generation Options:"
-.TP
-\fB\-m\fR, \fB\-\-method\fR
-list of match generation methods
-\fR global = Global alignments
-\fR local = Local alignments
-\fR overlap = Overlap alignments
-\fR lcs = Longest common subsequence
-\fR Default: global,local
-\IP No spaces in\-between.
-.TP
-\fB\-bl\fR, \fB\-\-blast\fR <File1>,<File2>,...
-list of BLAST match files
-.TP
-\fB\-mu\fR, \fB\-\-mummer\fR <File1>,<File2>,...
-list of MUMmer match files
-.TP
-\fB\-al\fR, \fB\-\-aln\fR <File1>,<File2>,...
-list of FASTA align files
-.TP
-\fB\-li\fR, \fB\-\-lib\fR <File1>,<File2>,...
-list of T\-Coffee libraries
-.SS "Scoring Options:"
-.TP
-\fB\-g\fR, \fB\-\-gop\fR <Int>
-gap open penalty (default \fB\-13\fR)
-.TP
-\fB\-e\fR, \fB\-\-gex\fR <Int>
-gap extension penalty (default \fB\-1\fR)
-.TP
-\fB\-ma\fR, \fB\-\-matrix\fR <Matrix file>
-score matrix (default Blosum62)
-.TP
-\fB\-ms\fR, \fB\-\-msc\fR <Int>
-match score (default 5)
-.TP
-\fB\-mm\fR, \fB\-\-mmsc\fR <Int>
-mismatch penalty (default \fB\-4\fR)
-.SS "Guide Tree Options:"
-.TP
-\fB\-u\fR, \fB\-\-usetree\fR <Newick guide tree>
-tree filename
-.TP
-\fB\-b\fR, \fB\-\-build\fR [nj, min, max, avg, wavg]
-tree building method (default nj)
-\fR nj = Neighbor\-joining
-\fR min = UPGMA single linkage
-\fR max = UPGMA complete linkage
-\fR avg = UPGMA average linkage
-\fR wavg = UPGMA weighted average linkage
-.IP
-Neighbor\-joining creates an unrooted tree. We root that tree at the last joined pair.
-.SS "Alignment Evaluation Options:"
-.TP
-\fB\-i\fR, \fB\-\-infile\fR <FASTA alignment file>
-alignment file
-.SH AUTHOR
-.br
-seqan_tcoffee was written by Tobias Rausch.
-.PP
-This manual page was generated using html2man and polished by
-Soeren Sonnenburg <sonne at debian.org>, for the Debian project
-(but may be used by others).
Deleted: trunk/packages/seqan/trunk/debian/seqcons.1
===================================================================
--- trunk/packages/seqan/trunk/debian/seqcons.1 2013-11-23 08:29:34 UTC (rev 15262)
+++ trunk/packages/seqan/trunk/debian/seqcons.1 2013-11-23 17:36:56 UTC (rev 15263)
@@ -1,69 +0,0 @@
-.TH SEQCONS "1" "September 2009" "Version 0.22 (06. August 2009) Revision: 4663" "User Commands"
-.SH NAME
-seqcons \- Multi\-read alignment
-.SH SYNOPSIS
-.B seqcons
-\fI-r <FASTA file with reads> \fR[\fIOptions\fR]
-.SH DESCRIPTION
-Multi\-read alignment \- SeqCons
-.IP
-seqcons \fB\-a\fR <AMOS message file> [Options]
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-displays this help message
-.TP
-\fB\-V\fR, \fB\-\-version\fR
-print version information
-.SS "Main Options:"
-.TP
-\fB\-r\fR, \fB\-\-reads\fR <FASTA reads file>
-file with reads
-.TP
-\fB\-a\fR, \fB\-\-afg\fR <AMOS afg file>
-message file
-.TP
-\fB\-o\fR, \fB\-\-outfile\fR <Filename>
-output filename (default align.txt)
-.TP
-\fB\-f\fR, \fB\-\-format\fR [seqan | afg]
-output format (default afg)
-.TP
-\fB\-m\fR, \fB\-\-method\fR [realign | msa]
-alignment method (default realign)
-.TP
-\fB\-b\fR, \fB\-\-bandwidth\fR <Int>
-bandwidth (default 8)
-.TP
-\fB\-n\fR, \fB\-\-noalign\fR
-no align, only convert input
-.SS "MSA Method Options:"
-.TP
-\fB\-ma\fR, \fB\-\-matchlength\fR <Int>
-min. overlap length (default 15)
-.TP
-\fB\-qu\fR, \fB\-\-quality\fR <Int>
-min. overlap precent identity (default 80)
-.TP
-\fB\-ov\fR, \fB\-\-overlaps\fR <Int>
-min. number of overlaps per read (default 3)
-.TP
-\fB\-wi\fR, \fB\-\-window\fR <Int>
-window size (default 0)
-/*If this parameter is > 0 then all
-.IP
-overlaps within a given window
-are computed.*/
-.SS "ReAlign Method Options:"
-.TP
-\fB\-in\fR, \fB\-\-include\fR
-include contig sequence
-.TP
-\fB\-rm\fR, \fB\-\-rmethod\fR [nw | gotoh]
-realign method (default gotoh)
-.SH AUTHOR
-.br
-seqcons was written by Tobias Rausch
-.PP
-This manual page was generated using html2man and polished by
-Soeren Sonnenburg <sonne at debian.org>, for the Debian project
-(but may be used by others).
Deleted: trunk/packages/seqan/trunk/debian/tree_recon.1
===================================================================
--- trunk/packages/seqan/trunk/debian/tree_recon.1 2013-11-23 08:29:34 UTC (rev 15262)
+++ trunk/packages/seqan/trunk/debian/tree_recon.1 2013-11-23 17:36:56 UTC (rev 15263)
@@ -1,43 +0,0 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.36.
-.TH VERSION "1" "September 2009" "Version 1.01 (18. August 2009) Revision: 4692" "User Commands"
-.SH NAME
-Version \- Tree reconstrucion
-.SH SYNOPSIS
-.B tree_recon
-\fI-m <Phylip distance matrix> \fR[\fIOptions\fR]
-.SH DESCRIPTION
-Tree reconstrucion \- TreeRecon
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-displays this help message
-.TP
-\fB\-V\fR, \fB\-\-version\fR
-print version information
-.SS "Main Options:"
-.TP
-\fB\-m\fR, \fB\-\-matrix\fR <Phylip distance matrix>
-file with distance matrix
-At least 3 species required.
-.TP
-\fB\-b\fR, \fB\-\-build\fR [nj, min, max, avg, wavg]
-tree building method (default nj)
-\fR nj = Neighbor\-joining
-\fR min = UPGMA single linkage
-\fR max = UPGMA complete linkage
-\fR avg = UPGMA average linkage
-\fR wavg = UPGMA weighted average linkage
-.IP
-Neighbor\-joining creates an unrooted tree. We root that tree at the last joined pair.
-.TP
-\fB\-o\fR, \fB\-\-outfile\fR <Filename>
-output filename (default tree.dot)
-.TP
-\fB\-f\fR, \fB\-\-format\fR [dot | newick]
-output format (default dot)
-.SH AUTHOR
-.br
-tree_recon was written by Tobias Rausch.
-.PP
-This manual page was generated using html2man and polished by
-Soeren Sonnenburg <sonne at debian.org>, for the Debian project
-(but may be used by others).
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