[med-svn] [sspace] 02/02: Add some packaging skeleton

Andreas Tille tille at debian.org
Wed Jun 1 14:51:05 UTC 2016 

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository sspace.

commit c756e0e2483b51ec63f1f8fdd2bf3801a11bb44a
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jun 1 16:50:25 2016 +0200

    Add some packaging skeleton
---
 debian/README.Debian     | 22 ++++++++++++++++++++++
 debian/bin/sspace        | 10 ++++++++++
 debian/changelog         |  5 +++++
 debian/compat            |  1 +
 debian/control           | 25 +++++++++++++++++++++++++
 debian/copyright         | 17 +++++++++++++++++
 debian/install           |  5 +++++
 debian/rules             | 11 +++++++++++
 debian/source/format     |  1 +
 debian/upstream/metadata | 12 ++++++++++++
 debian/watch             |  4 ++++
 11 files changed, 113 insertions(+)

diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..f403678
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,22 @@
+SSPACE for Debian
+_________________
+
+
+SSPACE tracks in memory all contigs. That means that the memory usage 
+will increase drastically with the size of your contig data set. In
+addition, during contig extension single reads are extracted and mapped
+to the contigs. Unmapped reads are stored in memory. Again, the more
+reads that can not map, the bigger the dataset and the more memory is
+used. Just be aware of these limitations and don't be surprised if you
+observe a lot of data swapping to disk if you attempt to run SSPACE on a
+machine with little RAM.
+
+Contig extension might not be suited to work with 454-type read pair 
+libraries. Simply because recurring base insertions/deletions errors,
+such as those commonly seen in homopolymeric regions, will not cluster
+well in the context of the SSAKE contig extension algorithm scheme. In
+addition, long 454 reads are less likely to map against the contigs,
+thus less read pairs are found and scaffolding is based on less read
+pairs. One possibility is to allow gaps during mapping using the æ-gÆ
+parameter.
+
diff --git a/debian/bin/sspace b/debian/bin/sspace
new file mode 100644
index 0000000..e3e0cdd
--- /dev/null
+++ b/debian/bin/sspace
@@ -0,0 +1,10 @@
+#!/bin/sh
+# Wrapper for SSPACE Perl script.
+# It is not sufficient to simply provide a symlink
+# Because the script uses
+#     use FindBin qw($Bin);
+# to detect the PATH from where it was started and
+# relies on this dir to find other modules and
+# executables
+#
+/usr/share/sspace/SSPACE_Basic_v2.0.pl $@
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..34d17c5
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+sspace (2.1.1+dfsg-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Wed, 01 Jun 2016 13:56:05 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..fc8bb7d
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,25 @@
+Source: sspace
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+               recode
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/sspace.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/sspace.git
+Homepage: http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/
+
+Package: sspace
+Architecture: all
+Depends: ${perl:Depends},
+         ${misc:Depends},
+         bowtie
+Description: scaffolding pre-assemblies after contig extension
+ Scaffolding Pre-Assemblies After Contig Extension (SSPACE) is a script
+ able to extend and scaffold pre-assembled contigs using one or more mate
+ pairs or paired-end libraries, or even a combination.
+ .
+ SSPACE is built based on SSAKE. Code of SSAKE is changed to be able to
+ extend and scaffold pre-assembled contigs for multiple paired reads
+ libraries.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..9460826
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,17 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: SSPACE
+Upstream-Contact: Walter Pirovano <walter.pirovano at baseclear.nl>
+Source: https://github.com/nsoranzo/sspace_basic/releases
+Files-Excluded: *.pdf
+
+Files: *
+Copyright: 2010-2011 Marten Boetzer and Walter Pirovano
+License: <license>
+
+Files: dotlib/*
+Copyright:  2002, 2003, The Institute for Genomic Research (TIGR)
+License:
+
+Files: debian/*
+Copyright: 2014 Andreas Tille <tille at debian.org>
+License: <license>
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..a13187b
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,5 @@
+*.pl			usr/share/sspace
+dotlib			usr/share/sspace
+bin			usr/share/sspace
+tools			usr/share/sspace
+debian/bin/*		usr/bin
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..91b7b89
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,11 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+	dh $@
+
+override_dh_install:
+	dh_install
+	find debian -name "*.pl" -exec recode ibmpc.. \{\} \;
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..2777172
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+  Author: "Marten Boetzer and Christiaan V. Henkel and Hans J. Jansen and Derek Butler and Walter Pirovano"
+  Title: "Scaffolding pre-assembled contigs using SSPACE"
+  Journal: Bioinformatics
+  Year: 2010
+  Volume: 27
+  Number: 4
+  Pages: 578-579
+  DOI: 10.1093/bioinformatics/btq683
+  PMID: 21149342
+  URL: http://bioinformatics.oxfordjournals.org/content/27/4/578
+  eprint: http://bioinformatics.oxfordjournals.org/content/27/4/578.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..37cbda8
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+   https://github.com/nsoranzo/sspace_basic/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)

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