[med-svn] r4031 - trunk/packages/infernal/trunk/debian
Andreas Tille
tille at alioth.debian.org
Sat Sep 26 07:05:42 UTC 2009
Author: tille
Date: 2009-09-26 07:05:38 +0000 (Sat, 26 Sep 2009)
New Revision: 4031
Added:
trunk/packages/infernal/trunk/debian/infernal-doc.doc-base
trunk/packages/infernal/trunk/debian/infernal-doc.install
trunk/packages/infernal/trunk/debian/infernal.manpages
Modified:
trunk/packages/infernal/trunk/debian/changelog
trunk/packages/infernal/trunk/debian/control
trunk/packages/infernal/trunk/debian/copyright
trunk/packages/infernal/trunk/debian/rules
Log:
Added infernal-doc package; I wonder whether ftpmaster might accept the conclusion that if the Userguide.pdf is really the source ist is also covered by the license terms GPL inside the LICENSE file. We should probably ask explicitely for the license.
Modified: trunk/packages/infernal/trunk/debian/changelog
===================================================================
--- trunk/packages/infernal/trunk/debian/changelog 2009-09-26 06:28:16 UTC (rev 4030)
+++ trunk/packages/infernal/trunk/debian/changelog 2009-09-26 07:05:38 UTC (rev 4031)
@@ -5,10 +5,20 @@
[ Andreas Tille ]
* New upstream version
- * Standards-Version: 3.8.3 (no changes needed)
- * Added myself to uploaders
- * s/Debian-Med/Debian Med/
- * debhelper 7
+ * debian/control:
+ - Standards-Version: 3.8.3 (no changes needed)
+ - Added myself to uploaders
+ - s/Debian-Med/Debian Med/
+ - Build-Depends: debhelper (>= 7.1) autotools-dev
+ - Package: infernal-doc
+ * debian/rules: removed deprecated -k option from dh_clean
+ * debian/copyright:
+ - added myself to Copyright holders of debian/*
+ - squid is not part of the upstream tarball anymore so this
+ paragraph was deleted
+ - files/Userguide.pdf: Copied comment about PDF = source from
+ README.Debian
+ * debian/infernal-doc.doc-base
-- Andreas Tille <tille at debian.org> Fri, 25 Sep 2009 15:17:22 +0200
Modified: trunk/packages/infernal/trunk/debian/control
===================================================================
--- trunk/packages/infernal/trunk/debian/control 2009-09-26 06:28:16 UTC (rev 4030)
+++ trunk/packages/infernal/trunk/debian/control 2009-09-26 07:05:38 UTC (rev 4031)
@@ -6,7 +6,7 @@
Uploaders: Steffen Moeller <moeller at debian.org>,
Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 7.1)
+Build-Depends: debhelper (>= 7.1), autotools-dev
Standards-Version: 3.8.3
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/infernal/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/infernal/trunk/
@@ -30,3 +30,21 @@
Users of this package should cite:
"Query-Dependent Banding (QDB) for Faster RNA Similarity Searches."
E. P. Nawrocki, S. R. Eddy. PLoS Comput. Biol., 3:e56, 2007.
+
+Package: infernal-doc
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: inference of RNA secondary structural alignments
+ Infernal ("INFERence of RNA ALignment") is for searching DNA sequence
+ databases for RNA structure and sequence similarities. It is an
+ implementation of a special case of profile stochastic context-free
+ grammars called covariance models (CMs). A CM is like a sequence
+ profile, but it scores a combination of sequence consensus and RNA
+ secondary structure consensus, so in many cases, it is more capable of
+ identifying RNA homologs that conserve their secondary structure more
+ than their primary sequence.
+ .
+ The tool is an integral component of the Rfam database.
+ .
+ This package provides the documentation which is shipped with the
+ code of infernal.
Modified: trunk/packages/infernal/trunk/debian/copyright
===================================================================
--- trunk/packages/infernal/trunk/debian/copyright 2009-09-26 06:28:16 UTC (rev 4030)
+++ trunk/packages/infernal/trunk/debian/copyright 2009-09-26 07:05:38 UTC (rev 4031)
@@ -12,7 +12,8 @@
Files: debian/*
Copyright: © 2007-2008 Steffen Moeller <moeller at debian.org>
- © 2007-2008 Charles Plessy <charles-debian-nospam at plessy.org>
+ © 2007-2008 Charles Plessy <plessy at debian.org>
+ © 2009 Andreas Tille <tille at debian.org>
License: GPL-2+
@@ -55,31 +56,11 @@
Files: Userguide.pdf
-X-Comment: Deleted in the Debian source package (no source available)
+X-Comment: The PDFs that are coming with the sources from which the userguide is
+ built are indeed upstream's original sources. They are edited with a PDF
+ editor. Upstream, Dr Eddy, was consulted in this issue.
-Files: squid/*
-Copyright: © 1992-2002 Washington University School of Medicine
-License: most likely GPL-2+
- In squid/00README, it is written:
- .
- " If you have any questions about redistributing squid or using
- squid code in your own work, see the files:
- COPYRIGHT -- copyright notice, and information on my distribution policy
- LICENSE -- version 2 of the GNU Public License (see COPYRIGHT)"
- .
- However:
- - There are no COPYRIGHT and LICENSE files in the squid directory but the
- source files indicate to be distributed under the terms of the GPL;
- - ../COPYRIGHT ../LICENSE indicate the GNU GPL "version 2 or (at your option)
- any later version", upstream behaved well in not distributing the same
- files twice;
- - squid is of the same author as it is infernal.
- - a more recent but "incompatible" version (upstream) of the squid library,
- distributed in Debian's biosquid package, is also disributed under version
- 2 or later.
-
-
Files: *
Copyright: © 2001-2007 HHMI Janelia Farm
© 1991-2007 Sean R. Eddy
Added: trunk/packages/infernal/trunk/debian/infernal-doc.doc-base
===================================================================
--- trunk/packages/infernal/trunk/debian/infernal-doc.doc-base (rev 0)
+++ trunk/packages/infernal/trunk/debian/infernal-doc.doc-base 2009-09-26 07:05:38 UTC (rev 4031)
@@ -0,0 +1,16 @@
+Document: infernal-doc
+Title: INFERNAL User’s Guide
+Author: Diana Kolbe, Eric Nawrocki, Sean Eddy
+Abstract: Sequence analysis using profiles of RNA secondary structure consensus
+ Infernal ("INFERence of RNA ALignment") is for searching DNA sequence
+ databases for RNA structure and sequence similarities. It is an
+ implementation of a special case of profile stochastic context-free
+ grammars called covariance models (CMs). A CM is like a sequence
+ profile, but it scores a combination of sequence consensus and RNA
+ secondary structure consensus, so in many cases, it is more capable of
+ identifying RNA homologs that conserve their secondary structure more
+ than their primary sequence.
+Section: Science/Biology
+
+Format: pdf
+Index: /usr/share/doc/infernal/Userguide.pdf
Added: trunk/packages/infernal/trunk/debian/infernal-doc.install
===================================================================
--- trunk/packages/infernal/trunk/debian/infernal-doc.install (rev 0)
+++ trunk/packages/infernal/trunk/debian/infernal-doc.install 2009-09-26 07:05:38 UTC (rev 4031)
@@ -0,0 +1 @@
+Userguide.pdf usr/share/doc/infernal
Added: trunk/packages/infernal/trunk/debian/infernal.manpages
===================================================================
--- trunk/packages/infernal/trunk/debian/infernal.manpages (rev 0)
+++ trunk/packages/infernal/trunk/debian/infernal.manpages 2009-09-26 07:05:38 UTC (rev 4031)
@@ -0,0 +1 @@
+documentation/manpages/*
Modified: trunk/packages/infernal/trunk/debian/rules
===================================================================
--- trunk/packages/infernal/trunk/debian/rules 2009-09-26 06:28:16 UTC (rev 4030)
+++ trunk/packages/infernal/trunk/debian/rules 2009-09-26 07:05:38 UTC (rev 4031)
@@ -71,7 +71,7 @@
install-indep:
#dh_testdir
#dh_testroot
- #dh_clean -k -i
+ #dh_clean -i
#dh_installdirs -i
# Add here commands to install the indep part of the package into
# debian/<package>-doc.
@@ -88,7 +88,7 @@
install-arch: cm2hmm.1
dh_testdir
dh_testroot
- dh_clean -k -s
+ dh_clean -s
dh_installdirs -s
# Add here commands to install the arch part of the package into
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