[med-svn] r1763 - trunk/packages/ncbi-epcr/trunk/debian
tille at alioth.debian.org
tille at alioth.debian.org
Tue Apr 15 13:42:08 UTC 2008
Author: tille
Date: 2008-04-15 13:42:07 +0000 (Tue, 15 Apr 2008)
New Revision: 1763
Added:
trunk/packages/ncbi-epcr/trunk/debian/e-PCR.1
trunk/packages/ncbi-epcr/trunk/debian/fahash.1
trunk/packages/ncbi-epcr/trunk/debian/re-PCR.1
Removed:
trunk/packages/ncbi-epcr/trunk/debian/e-PCR.sgml
Modified:
trunk/packages/ncbi-epcr/trunk/debian/changelog
trunk/packages/ncbi-epcr/trunk/debian/control
trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.manpages
trunk/packages/ncbi-epcr/trunk/debian/rules
Log:
Do not build ncbi-epcr-data package any more because there are no data to ship inside the upstream tarball, wrote man pages for binaries (one further has to be written)
PLEASE TEST
Modified: trunk/packages/ncbi-epcr/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/changelog 2008-04-15 05:43:27 UTC (rev 1762)
+++ trunk/packages/ncbi-epcr/trunk/debian/changelog 2008-04-15 13:42:07 UTC (rev 1763)
@@ -16,6 +16,9 @@
* Patches using quilt
* Use cdbs
* Updated long description according to text on web Homepage
+ * Just use (and fix) the docbook-to-man output rather than live with
+ the broken output
+ * Wrote man pages for re-PCR and fahash
-- Andreas Tille <tille at debian.org> Mon, 14 Apr 2008 13:13:05 +0200
@@ -25,6 +28,7 @@
also go to Lamont Jones) (Closes: #239733).
* data package is now architecture-independent (Closes: #233421).
-- Steffen Moeller <moeller at pzr.uni-rostock.de> Thu, 20 Feb 2004 12:50:19 +0100
+
epcr (1.2.0-2) unstable; urgency=low
* Corrected structure of man page
Modified: trunk/packages/ncbi-epcr/trunk/debian/control
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/control 2008-04-15 05:43:27 UTC (rev 1762)
+++ trunk/packages/ncbi-epcr/trunk/debian/control 2008-04-15 13:42:07 UTC (rev 1763)
@@ -25,7 +25,7 @@
The new version of e-PCR implements a fuzzy matching strategy. To reduce
likelihood that a true STS will be missed due to mismatches, multiple
discontigous words may be used instead of a single exact word. Each of this
- word has groups of significant positions seperated by 'wildcard' positions
+ word has groups of significant positions separated by 'wildcard' positions
that are not required to match. In addition, it is also possible to allow
gaps in the primer alignments.
.
Added: trunk/packages/ncbi-epcr/trunk/debian/e-PCR.1
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/e-PCR.1 (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/e-PCR.1 2008-04-15 13:42:07 UTC (rev 1763)
@@ -0,0 +1,106 @@
+.TH "E-PCR" "1" "February 2004"
+.SH "NAME"
+e-PCR \(em Find sequence tagged sites (STS) in DNA sequences
+.SH "SYNOPSIS"
+.PP
+\fBe-PCR [-hV] [posix-options] stsfile [fasta ...]\fR [\fB\fIcompat-options\fR\fP]
+.SH "DESCRIPTION"
+.PP
+The program substitutes blast in the location of pairs primers on the
+genome that may yield a PCR product.
+
+.SH "OPTIONS"
+.PP
+posix-options are:
+.IP "\fB-m=\fI##\fR\fP " 10
+Margin (default 50)
+.IP "\fB-w=\fI##\fR\fP " 10
+Wordsize (default 7)
+.IP "\fB-n=\fI##\fR\fP " 10
+Max mismatches allowed (default 0)
+.IP "\fB-g=\fI##\fR\fP " 10
+Max indels allowed (default 0)
+.IP "\fB-f=\fI##\fR\fP " 10
+Use ## discontiguos words, slow if ##>1
+.IP "\fB-o=\fI##\fR\fP " 10
+Set output file
+.IP "\fB-t=\fI##\fR\fP " 10
+Set output format:
+.IP "" 10
+1 - classic, range (pos1..pos2)
+.IP "" 10
+2 - classic, midpoint
+.IP "" 10
+3 - tabular
+.IP "" 10
+4 - tabular with alignment in comments (slow)
+.IP "\fB-d=\fI##-##\fR\fP " 10
+Set default size range (default 100-350)
+.IP "\fB-p=\fI+-\fR\fP " 10
+Turn hits postprocess on/off
+.IP "\fB-v=\fI##\fR\fP " 10
+Verbosity flags
+.IP "\fB-a=\fIa|f\fR\fP " 10
+Use presize alignmens (only if gaps>0), slow
+.IP "" 10
+a - Allways or f - as Fallback
+.IP "\fB-x=\fI+-\fR\fP " 10
+Use 5'-end lowercase masking of primers (default -)
+.IP "\fB-u=\fI+-\fR\fP " 10
+Uppercase all primers (default -)
+
+.P
+compat-options (duplicate posix-options) are
+.IP "\fBM=\fI##\fR\fP " 10
+Margin (default 50)
+.IP "\fBW=\fI##\fR\fP " 10
+Wordsize (default 7)
+.IP "\fBN=\fI##\fR\fP " 10
+Number of mismatches allowed (default 0)
+.IP "\fBG=\fI##\fR\fP " 10
+Max indels allowed (default 0)
+.IP "\fBF=\fI##\fR\fP " 10
+Use ## discontinuos words
+.IP "\fBO=\fI##\fR\fP " 10
+Set output file to ##
+.IP "\fBT=\fI##\fR\fP " 10
+Set output format (1..3)
+.IP "\fBD=\fI##-##\fR\fP " 10
+Set default size range
+.IP "\fBP=\fI+-\fR\fP " 10
+Postprocess hits on/off
+.IP "\fBV=\fI##\fR\fP " 10
+Verbosity flags
+.IP "\fBA=\fIa|f\fR\fP " 10
+Use presize alignmens (only if gaps>0), slow
+.IP "" 10
+a - Allways or f - as Fallback
+.IP "\fBX=\fI+-\fR\fP " 10
+Use 5'-end lowercase masking of primers (default -)
+.IP "\fBU=\fI+-\fR\fP " 10
+Uppercase all primers (default -)
+.IP "\fB-mid\fP " 10
+Same as T=2
+
+.P
+For information about further options just call \fBe-PCR\fR
+without any options.
+
+.SH "SEE ALSO"
+.PP
+bioperl(1), re-pcr(1)
+.PP
+/usr/share/doc/ncbi-epcr
+.PP
+.SH "AUTHORS"
+.PP
+This manual page was written by Steffen Moeller <moeller at debian.org>
+and Andreas Tille <tille at debian.org> for
+the \fBDebian\fP system (but may be used by others). Permission is
+granted to copy, distribute and/or modify this document under
+the terms of the GNU General Public License, Version 2 any
+later version published by the Free Software Foundation.
+
+.PP
+On Debian systems, the complete text of the GNU General Public
+License can be found in /usr/share/common-licenses/GPL.
Deleted: trunk/packages/ncbi-epcr/trunk/debian/e-PCR.sgml
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/e-PCR.sgml 2008-04-15 05:43:27 UTC (rev 1762)
+++ trunk/packages/ncbi-epcr/trunk/debian/e-PCR.sgml 2008-04-15 13:42:07 UTC (rev 1763)
@@ -1,146 +0,0 @@
-<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
-
-<!-- Process this file with docbook-to-man to generate an nroff manual
- page: `docbook-to-man manpage.sgml > manpage.1'. You may view
- the manual page with: `docbook-to-man manpage.sgml | nroff -man |
- less'. A typical entry in a Makefile or Makefile.am is:
-
-manpage.1: manpage.sgml
- docbook-to-man $< > $@
-
-
- The docbook-to-man binary is found in the docbook-to-man package.
- Please remember that if you create the nroff version in one of the
- debian/rules file targets (such as build), you will need to include
- docbook-to-man in your Build-Depends control field.
-
- -->
-
- <!-- Fill in your name for FIRSTNAME and SURNAME. -->
- <!ENTITY dhfirstname "<firstname>FIRSTNAME</firstname>">
- <!ENTITY dhsurname "<surname>SURNAME</surname>">
- <!-- Please adjust the date whenever revising the manpage. -->
- <!ENTITY dhdate "<date>November 20, 2003</date>">
- <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
- allowed: see man(7), man(1). -->
- <!ENTITY dhsection "<manvolnum>SECTION</manvolnum>">
- <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
- <!ENTITY dhusername "Steffen Moeller">
- <!ENTITY dhucpackage "<refentrytitle>E-PCR</refentrytitle>">
- <!ENTITY dhpackage "e-PCR">
-
- <!ENTITY debian "<productname>Debian</productname>">
- <!ENTITY gnu "<acronym>GNU</acronym>">
- <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
-]>
-
-<refentry>
- <refentryinfo>
- <address>
- &dhemail;
- </address>
- <author>
- &dhfirstname;
- &dhsurname;
- </author>
- <copyright>
- <year>2003</year>
- <holder>&dhusername;</holder>
- </copyright>
- &dhdate;
- </refentryinfo>
- <refmeta>
- &dhucpackage;
-
- &dhsection;
- </refmeta>
- <refnamediv>
- <refname>&dhpackage;</refname>
-
- <refpurpose>Find sequence tagged sites (STS) in DNA sequences</refpurpose>
- </refnamediv>
-
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>&dhpackage; stsfile seqfile</command>
-
- <arg><option><replaceable>options</replaceable></option></arg>
- </cmdsynopsis>
- </refsynopsisdiv>
- <refsect1>
- <title>DESCRIPTION</title>
- <para>
- The program substitutes blast in the location of pairs primers on the genome that may yield a PCR product.
- </para>
- </refsect1>
- <refsect1>
- <title>OPTIONS</title>
- <para>
- </para>
- <variablelist>
- <varlistentry>
- <term><option>M=<replaceable>##</replaceable></option>
- </term>
- <listitem>
- <para>Margin (default 50)</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>N=<replaceable>##</replaceable></option>
- </term>
- <listitem>
- <para>Number of mismatches allowed (default 0)</para>
- </listitem>
- </varlistentry>
- <varlistentry>
- <term><option>-mid</option>
- </term>
- <listitem>
- <para>Show midpoint of STS location instead of range</para>
- </listitem>
- </varlistentry>
- </variablelist>
- </refsect1>
- <refsect1>
- <title>SEE ALSO</title>
-
- <para>bioperl (1)</para>
- <para>/usr/share/doc/ncbi-epcr</para>
- <para>/usr/share/ncbi/e-PCR/db/<sequence tag data> in ncbi-epcr-data</para>
- <para>/usr/share/ncbi/e-PCR/samples/<sequences from genbank> in ncbi-epcr-data</para>
- </refsect1>
- <refsect1>
- <title>AUTHOR</title>
-
- <para>This manual page was written by &dhusername; &dhemail; for
- the &debian; system (but may be used by others). Permission is
- granted to copy, distribute and/or modify this document under
- the terms of the &gnu; General Public License, Version 2 any
- later version published by the Free Software Foundation.
- </para>
- <para>
- On Debian systems, the complete text of the GNU General Public
- License can be found in /usr/share/common-licenses/GPL.
- </para>
-
- </refsect1>
-</refentry>
-
-<!-- Keep this comment at the end of the file
-Local variables:
-mode: sgml
-sgml-omittag:t
-sgml-shorttag:t
-sgml-minimize-attributes:nil
-sgml-always-quote-attributes:t
-sgml-indent-step:2
-sgml-indent-data:t
-sgml-parent-document:nil
-sgml-default-dtd-file:nil
-sgml-exposed-tags:nil
-sgml-local-catalogs:nil
-sgml-local-ecat-files:nil
-End:
--->
-
-
Added: trunk/packages/ncbi-epcr/trunk/debian/fahash.1
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/fahash.1 (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/fahash.1 2008-04-15 13:42:07 UTC (rev 1763)
@@ -0,0 +1,55 @@
+.TH FAHASH "1" "April 2008"
+.SH NAME
+fahash \- build hash-file, and output word usage statistics for re-PCR
+.SH DESCRIPTION
+fahash [\-hV] \fB\-b\fR hash\-file [\-w wdsize] [\-f period] [\-F fragment_min,fragment_max] [\-k] [\-c cachesize] [\-v 1|2] famap\-file ...
+.PP
+fahash [\-hV] \fB\-T\fR hash\-file [\-o outfile]
+.SS "where:"
+.TP
+\fB\-b\fR hash\-file
+Build hash tables (hash\-file) from sequence files,
+.TP
+\fB\-T\fR hash\-file
+Print word usage statistics for hash\-file
+.TP
+\fB\-o\fR outfile
+Write output to file `outfile'
+
+.SS "build-options:"
+.TP
+\fB\-w\fR wordsize
+Set word size when building hash tables
+.TP
+\fB\-f\fR period
+Set discontiguity when building hash tables
+.TP
+\fB\-k\fR
+Skip repeats when building hash\-file
+.TP
+\fB\-F\fR min,max
+Set watermarks for fragment size (in Mb) (version 1 only)
+.TP
+\fB\-c\fR cachesize
+Set cache size (version 2 only)
+.TP
+\fB\-v\fR ver
+Use format version (1|2, 2 is default)
+
+.SH "SEE ALSO"
+.PP
+bioperl(1), e-pcr(1), re-pcr(1)
+.PP
+/usr/share/doc/ncbi-epcr
+.PP
+.SH "AUTHORS"
+.PP
+This manual page was written by Andreas Tille <tille at debian.org> for
+the \fBDebian\fP system (but may be used by others). Permission is
+granted to copy, distribute and/or modify this document under
+the terms of the GNU General Public License, Version 2 any
+later version published by the Free Software Foundation.
+
+.PP
+On Debian systems, the complete text of the GNU General Public
+License can be found in /usr/share/common-licenses/GPL.
Modified: trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.manpages
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.manpages 2008-04-15 05:43:27 UTC (rev 1762)
+++ trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.manpages 2008-04-15 13:42:07 UTC (rev 1763)
@@ -1 +1 @@
-debian/e-PCR.1
+debian/*.1
Added: trunk/packages/ncbi-epcr/trunk/debian/re-PCR.1
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/re-PCR.1 (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/re-PCR.1 2008-04-15 13:42:07 UTC (rev 1763)
@@ -0,0 +1,69 @@
+.TH "RE-PCR" "1" "April 2008"
+.SH "NAME"
+re-PCR \(em Find sequence tagged sites (STS) in DNA sequences
+.SH "SYNOPSIS"
+.PP
+\fBre-PCR [-hV] -p hash-file [-g gaps] [-n mism] [-lq] [primer ...]
+
+\fBre-PCR [-hV] -P hash-file [-g gaps] [-n mism] [-l] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [primers-file ...]
+
+\fBre-PCR [-hV] -s hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-o outfile] [-r+|-] [left right lo[-hi] [...]]
+
+\fBre-PCR [-hV] -S hash-file [-g gaps] [-n mism] [-lq] [-m margin] [-O+|-] [-C batchcnt] [-o outfile] [-r+|-] [stsfile ...]
+
+.SH "DESCRIPTION"
+.PP
+Implements reverse searching (called Reverse e-PCR) to make it feasible
+to search the human genome sequence and other large genomes.
+
+.SH "OPTIONS"
+.PP
+.IP "\fB-p=\fIhash-file\fR\fP " 10
+Perform primer lookup using hash-file
+.IP "\fB-P=\fIhash-file\fR\fP " 10
+Perform primer lookup using hash-file
+.IP "\fB-s=\fIhash-file\fR\fP " 10
+Perform STS lookup using hash-file
+.IP "\fB-S=\fIhash-file\fR\fP " 10
+Perform STS lookup using hash-file
+.IP "\fB-n=\fImism\fR\fP " 10
+Set max allowed mismatches per primer for lookup
+.IP "\fB-g=\fIgaps\fR\fP " 10
+Set max allowed indels per primer for lookup
+.IP "\fB-m=\fImargin\fR\fP " 10
+Set variability for STS size for lookup
+.IP "\fB-l\fP " 10
+Use presize alignments (only if gaps>0)
+.IP "\fB-G\fP " 10
+Print alignments in comments
+.IP "\fB-d=\fImin-max\fR\fP " 10
+Set default STS size
+.IP "\fB-r=\fI+|-\fR\fP " 10
+Enable/disable reverse STS lookup
+.IP "\fB-O=\fI+|-\fR\fP " 10
+Enable/disable syscall optimisation
+.IP "\fB-C=\fIbatchcnt\fR\fP " 10
+Set number of STSes per batch
+.IP "\fB-o=\fIoutfile\fR\fP " 10
+Set output file name
+.IP "\fB-q\fP " 10
+Quiet (no progress indicator)
+
+
+.SH "SEE ALSO"
+.PP
+bioperl(1), e-pcr(1)
+.PP
+/usr/share/doc/ncbi-epcr
+.PP
+.SH "AUTHORS"
+.PP
+This manual page was written by Andreas Tille <tille at debian.org> for
+the \fBDebian\fP system (but may be used by others). Permission is
+granted to copy, distribute and/or modify this document under
+the terms of the GNU General Public License, Version 2 any
+later version published by the Free Software Foundation.
+
+.PP
+On Debian systems, the complete text of the GNU General Public
+License can be found in /usr/share/common-licenses/GPL.
Modified: trunk/packages/ncbi-epcr/trunk/debian/rules
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/rules 2008-04-15 05:43:27 UTC (rev 1762)
+++ trunk/packages/ncbi-epcr/trunk/debian/rules 2008-04-15 13:42:07 UTC (rev 1763)
@@ -11,11 +11,7 @@
rm -f epcr
rm -f libepcr.a
rm -f e-PCR famap fahash re-PCR
- rm -f debian/e-PCR.1
DEB_OPT_FLAG += -I. -g2 -DDEALLOCATE=0 `getconf LFS_CFLAGS` -DVERSION=\\\"2.3.9\\\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=9 -DSTANDALONE=1
LDFLAGS += `getconf LFS_LDFLAGS` `getconf LFS_LIBS` -L.
-
-build/ncbi-epcr::
- /usr/bin/docbook-to-man debian/e-PCR.sgml > debian/e-PCR.1
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