[med-svn] [pcma] 01/10: Take over information from task file

[Andreas Tille]

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tille pushed a commit to branch master
in repository pcma.

commit 4406d5b61ba576d13f1289adbea23a2008b6b466
Author: Andreas Tille <tille at debian.org>
Date:   Sun May 27 07:58:59 2012 +0000

    Take over information from task file
---
 debian/changelog |  5 +++++
 debian/compat    |  1 +
 debian/control   | 28 ++++++++++++++++++++++++++++
 debian/copyright | 14 ++++++++++++++
 debian/rules     |  6 ++++++
 debian/upstream  | 12 ++++++++++++
 6 files changed, 66 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..6acb5bb
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+pcma (2-1) unstable; urgency=low
+
+  * Initial release
+
+ -- DMPT <debian-med-packaging at lists.alioth.debian.org>  Thu, 24 May 2012 14:30:13 +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..fa83850
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,28 @@
+Source: pcma
+Section: science
+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 (>= 9)
+Standards-Version: 3.9.3
+Homepage: ftp://iole.swmed.edu/pub/PCMA/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/pcma/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/pcma/trunk/
+
+Package: pcma
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Enhances: t-coffee
+Description: fast and accurate multiple sequence alignment based on profile consistency
+ PCMA (profile consistency multiple sequence alignment) is a progressive
+ multiple sequence alignment program that combines two different
+ alignment strategies. Highly similar sequences are aligned in a fast way
+ as in ClustalW, forming pre-aligned groups. The T-Coffee strategy is
+ applied to align the relatively divergent groups based on
+ profile–profile comparison and consistency. The scoring function for
+ local alignments of pre-aligned groups is based on a novel
+ profile–profile comparison method that is a generalization of the
+ PSI-BLAST approach to profile–sequence comparison. PCMA balances speed
+ and accuracy in a flexible way and is suitable for aligning large
+ numbers of sequences.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..1b038dc
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,14 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: ftp://iole.swmed.edu/pub/PCMA/
+
+Files: *
+Copyright: © 2003-2004 Jimin Pei, Ruslan Sadreyev and Nick V. Grishin
+License: non-free for commercial
+Comment:  Check with authors about licensing, they adopted code from clustalw which is now
+ free.  Thus a change might be possible
+
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille at debian.org>
+License: LGPL-3+
+Comment: Take over license of recent ClustalW for the packaging
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..6055261
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+	dh $@
diff --git a/debian/upstream b/debian/upstream
new file mode 100644
index 0000000..3eeb5ee
--- /dev/null
+++ b/debian/upstream
@@ -0,0 +1,12 @@
+Reference:
+  Author: Jimin Pei and Ruslan Sadreyev and Nick V. Grishin
+  Title: "PCMA: fast and accurate multiple sequence alignment based on profile consistency"
+  Journal: Bioinformatics
+  Year: 2003
+  Volume: 19
+  Number: 3
+  Pages: 427-428
+  DOI: 10.1093/bioinformatics/btg008
+  PMID: 12584134
+  URL: http://bioinformatics.oxfordjournals.org/content/19/3/427.short
+  eprint: http://bioinformatics.oxfordjournals.org/content/19/3/427.full.pdf+html

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