[med-svn] [abyss] 02/20: Manpage, rules, get-orig-source
Andreas Tille
tille at debian.org
Thu Sep 21 20:46:13 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to annotated tag upstream/1.3.1
in repository abyss.
commit 27a83885cd366bb5a888519d1c19f017a1b23054
Author: Andreas Tille <tille at debian.org>
Date: Fri Mar 18 18:47:31 2011 +0000
Manpage, rules, get-orig-source
---
debian/abacas.1 | 104 +++++++++++++++++++++++++++++++++++++++++++++++++
debian/changelog | 3 +-
debian/compat | 2 +-
debian/control | 2 +-
debian/get-orig-source | 38 ++++++++++++++++++
debian/install | 1 +
debian/manpages | 1 +
debian/rules | 11 ++++++
debian/watch | 3 +-
9 files changed, 160 insertions(+), 5 deletions(-)
diff --git a/debian/abacas.1 b/debian/abacas.1
new file mode 100644
index 0000000..a67c317
--- /dev/null
+++ b/debian/abacas.1
@@ -0,0 +1,104 @@
+.TH ABACAS "1" "2011-02-11" "1.3.1" "User Commands"
+.SH NAME
+abacas \- Algorithm Based Automatic Contiguation of Assembled Sequences
+.SH SYNOPSIS
+.B abacas
+\fB\-r\fR \fIref\fR \fB\-q\fR \fIqs\fR \fB\-p\fR \fIprog\fR [OPTIONS]
+.PP
+OR
+.PP
+.B abacas
+\fB\-r\fR \fIref\fR \fB\-q\fR \fIpsf\fR \fB\-e\fR
+.PP
+.TP
+\fIref\fR
+reference sequence in a single fasta file
+.TP
+\fIqs\fR
+contigs in multi\-fasta format
+.TP
+\fI\prog\fR
+MUMmer program to use: 'nucmer' or 'promer'
+.TP
+\fIpsf\fR
+pseudomolecule/ordered sequence file in fasta format
+.PP
+\fBOPTIONS\fR
+.TP
+\fB\-h\fR
+print usage
+.TP
+\fB\-d\fR
+use default nucmer/promer parameters
+.TP
+\fB\-s\fR
+int minimum length of exact matching word (nucmer default = 12, promer default = 4)
+.TP
+\fB\-m\fR
+print ordered contigs to file in multifasta format
+.TP
+\fB\-b\fR
+print contigs in bin to file
+.TP
+\fB\-N\fR
+print a pseudomolecule without "N"s
+.TP
+\fB\-i\fR
+int mimimum percent identity [default 40]
+.TP
+\fB\-v\fR
+int mimimum contig coverage [default 40]
+.TP
+\fB\-V\fR
+int minimum contig coverage difference [default 1]
+.TP
+\fB\-l\fR
+int minimum contig length [default 1]
+.TP
+\fB\-t\fR
+run tblastx on contigs that are not mapped
+.TP
+\fB\-g\fR
+string (file name) print uncovered regions (gaps) on reference to file name
+.TP
+\fB\-a\fR
+append contigs in bin to the pseudomolecule
+.TP
+\fB\-o\fR
+prefix output files will have this prefix
+.TP
+\fB\-P\fR
+pick primer sets to close gaps
+.TP
+\fB\-f\fR
+int number of flanking bases on either side of a gap for primer design (default 350)
+.TP
+\fB\-R\fR
+int Run mummer [default 1, use \fB\-R\fR 0 to avoid running mummer]
+.TP
+\fB\-e\fR
+Escape contig ordering i.e. go to primer design
+.TP
+\fB\-c\fR
+Reference sequence is circular
+
+.SH DESCRIPTION
+ABACAS is intended to rapidly contiguate (align, order, orientate),
+visualize and design primers to close gaps on shotgun assembled contigs
+based on a reference sequence.
+.PP
+ABACAS uses MUMmer to find alignment positions and identify syntenies
+of assembled contigs against the reference. The output is then processed
+to generate a pseudomolecule taking overlapping contigs and gaps in to
+account. ABACAS generates a comparision file that can be used to
+visualize ordered and oriented contigs in ACT. Synteny is represented by
+red bars where colour intensity decreases with lower values of percent
+identity between comparable blocks. Information on contigs such as the
+orientation, percent identity, coverage and overlap with other contigs
+can also be visualized by loading the outputted feature file on ACT.
+
+.SH AUTHOR
+ABACAS IS Copyright (C) 2008-10 The Wellcome Trust Sanger Institute, Cambridge, UK.
+.PP
+This manual page was written by Andreas Tille <tille at debian.org>,
+for the Debian project (and may be used by others).
diff --git a/debian/changelog b/debian/changelog
index f25d0f6..3e1b948 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,5 @@
abacas (1.3.1-1) unstable; urgency=low
* Initial release (Closes: #????)
- PACKAGING NOT FINISHED - FEEL FREE TO TAKE OVER
- -- Andreas Tille <tille at debian.org> Mon, 11 Feb 2011 12:02:43 +0100
+ -- Andreas Tille <tille at debian.org> Mon, 07 Feb 2011 12:02:43 +0100
diff --git a/debian/compat b/debian/compat
index 7f8f011..45a4fb7 100644
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-7
+8
diff --git a/debian/control b/debian/control
index 5fea68e..a5b8efc 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 7.1)
+Build-Depends: debhelper (>= 8)
Standards-Version: 3.9.1
Homepage: http://abacas.sourceforge.net/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/abacas/trunk/?rev=0&sc=0
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100644
index 0000000..0ae9ac7
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,38 @@
+#!/bin/sh
+# creating source tarbal for abacas which comes as plain Perl file
+# and needs to be putin to a tarball
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+
+if ! echo $@ | grep -q upstream-version ; then
+ # if called manually run uscan to obtain file and version number
+ # VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
+ VERSION=`uscan --verbose --force-download | \
+ grep "Newest version on remote site is .* local version is .*" | \
+ head -n 1 | \
+ sed "s/Newest version on remote site is \([-0-9.]\+\),.*/\1/"`
+else
+ # If called by uscan
+ VERSION=`echo $@ | sed 's?^.*--upstream-version \([0-9.]\+\) .*download.html.*?\1?'`
+ if echo "$VERSION" | grep -q "upstream-version" ; then
+ echo "Unable to parse version number"
+ exit
+ fi
+fi
+
+if [ "$VERSION" = "" ] ; then
+ VERSION=`ls ../${PKG}.*.pl | sed "s/.*$PKG\.\(.*\)\.pl/\1/"`
+fi
+
+mkdir -p ../tarballs/${PKG}-${VERSION}
+cd ../tarballs
+
+# Rename perl file (without .pl suffix) and fix perl path
+sed -e '1s?/usr/local/bin/perl?/usr/bin/perl?' \
+ -e "s/^${PKG}.pl/${PKG}/" \
+ ../${PKG}.${VERSION}.pl > ${PKG}-${VERSION}/${PKG}
+touch -r ../${PKG}.${VERSION}.pl ${PKG}-${VERSION}/${PKG}
+rm -f ../${PKG}.${VERSION}.pl
+
+GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "$PKG"-"$VERSION"
+rm -rf "$PKG"-"$VERSION"
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..77afc00
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+abacas usr/bin
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..100c68c
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,11 @@
+#!/usr/bin/make -f
+# debian/rules for abacas
+# Andreas Tille <tille at debian.org>
+# GPL
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
+
diff --git a/debian/watch b/debian/watch
index ec13f28..6a4c879 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,2 +1,3 @@
version=3
-http://sf.net/abacas/abacas\.([\d\.]+)\.pl
+http://sf.net/abacas/abacas\.([\d\.]+)\.pl \
+ debian debian/get-orig-source
--
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