[med-svn] r12794 - trunk/packages/meme/trunk/debian

[Andreas Tille]

Author: tille
Date: 2013-01-16 08:41:56 +0000 (Wed, 16 Jan 2013)
New Revision: 12794

Modified:
   trunk/packages/meme/trunk/debian/control
   trunk/packages/meme/trunk/debian/copyright
   trunk/packages/meme/trunk/debian/meme.install
   trunk/packages/meme/trunk/debian/rules
Log:
Meme contains a copy of readseq.  To avoid a conflict when installing meme, a "Depends: readseq" is included in debian/control and the code copy (with some changes, seems to be older than the Debian packaged version) is not used.


Modified: trunk/packages/meme/trunk/debian/control
===================================================================
--- trunk/packages/meme/trunk/debian/control	2013-01-15 11:00:22 UTC (rev 12793)
+++ trunk/packages/meme/trunk/debian/control	2013-01-16 08:41:56 UTC (rev 12794)
@@ -18,7 +18,7 @@
 
 Package: meme
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, csh
+Depends: ${shlibs:Depends}, ${misc:Depends}, csh, readseq
 Description: search for common motifs in DNA or protein sequences
  MEME (Multiple EM for Motif Elicitation) is a tool for discovering
  motifs in a group of related DNA or protein sequences.  A motif is a

Modified: trunk/packages/meme/trunk/debian/copyright
===================================================================
--- trunk/packages/meme/trunk/debian/copyright	2013-01-15 11:00:22 UTC (rev 12793)
+++ trunk/packages/meme/trunk/debian/copyright	2013-01-16 08:41:56 UTC (rev 12794)
@@ -34,6 +34,21 @@
  *	THE USE OF THE MATERIAL WILL NOT INFRINGE ANY PATENT, 		*
  *	TRADEMARK OR OTHER RIGHTS.  					*
 
+Files: src/readseq src/ureadseq.[ch]
+Copyright: 1990 D. G. Gilbert, Biology Dept., Indiana University, Bloomington, in 47405
+        <gilbertd at bio.indiana.edu>
+License: PD
+ This program may be freely copied and used by anyone.
+ Developers are encourged to incorporate parts in their
+ programs, rather than devise their own private sequence
+ format.
+Remark: The copyright file of Debian's readseq package contains an
+ additional statement where the author explicitely mentioned public
+ domain.
+ .
+ This code is not used anyway because it would conflict with the
+ readseq package.  The binary package rather depends from readseq.
+
 Files: debian/*
 Copyright: © 2005 Steffen Moeller <moeller at pzr.uni-rostock.de>
            © 2011-2012 Andreas Tille <tille at debian.org>

Modified: trunk/packages/meme/trunk/debian/meme.install
===================================================================
--- trunk/packages/meme/trunk/debian/meme.install	2013-01-15 11:00:22 UTC (rev 12793)
+++ trunk/packages/meme/trunk/debian/meme.install	2013-01-16 08:41:56 UTC (rev 12794)
@@ -1,8 +1,11 @@
 #only usable with website: usr/bin/metameme
 #use all tools: usr/bin/meme*
 etc/*
-usr/bin/[a-fh-z]*
+usr/bin/[a-fh-qs-z]*
 usr/bin/g[eo]*
+usr/bin/read_fasta*
+usr/bin/re[b-z]*
+usr/bin/r[a-df-z]*
 usr/share/doc/meme
 usr/share/perl5/Meme
 var

Modified: trunk/packages/meme/trunk/debian/rules
===================================================================
--- trunk/packages/meme/trunk/debian/rules	2013-01-15 11:00:22 UTC (rev 12793)
+++ trunk/packages/meme/trunk/debian/rules	2013-01-16 08:41:56 UTC (rev 12794)
@@ -6,7 +6,7 @@
 
 DBPATH=/var/lib/meme
 LOGPATH=/var/log/meme
-MODULES=alphtype ama ama-qvalues ame beadstring beeml2meme cat_max centrimo ceqlogo changetoweb chen2meme clustalw-io clustalw2fasta clustalw2phylip compare_dates compute-prior-dist compute-uniform-priors download draw-mhmm dreme dust fasta-center fasta-dinucleotide-shuffle fasta-dinucleotide-shuffle.py fasta-fetch fasta-get-markov fasta-hamming-enrich fasta-hamming-enrich.py fasta-io fasta-make-index fasta-shuffle-letters fasta-subsample fasta-unique-names fimo fitevd gendb get_db_csv getsize gomo gomo_highlight hart2meme-bkg hartemink2psp hypergeometric.py iupac2meme jaspar2meme llr log-hmm mast mast2txt mcast meme meme-chip meme-get-motif meme-xml-html meme.bin meme2images meme2meme meme_p metameme mhmm mhmm-io mhmm2html mhmme mhmms mhmmscan motiph nmica2meme oldmeme2meme plotgen pmp_bf prior_utils.pl priority2meme psp-gen purge qvalue ramen ranksum_test read_fasta_file.pl readseq reconcile-tree-alignment reduce-alignment remove-alignment-gaps rna2meme scpd2meme sd sequence.py shadow spamo taipale2meme tamo2meme tomtom transfac2meme tree uniprobe2meme update_db update_meme_tests xsltproc_lite
+MODULES=alphtype ama ama-qvalues ame beadstring beeml2meme cat_max centrimo ceqlogo changetoweb chen2meme clustalw-io clustalw2fasta clustalw2phylip compare_dates compute-prior-dist compute-uniform-priors download draw-mhmm dreme dust fasta-center fasta-dinucleotide-shuffle fasta-dinucleotide-shuffle.py fasta-fetch fasta-get-markov fasta-hamming-enrich fasta-hamming-enrich.py fasta-io fasta-make-index fasta-shuffle-letters fasta-subsample fasta-unique-names fimo fitevd gendb get_db_csv getsize gomo gomo_highlight hart2meme-bkg hartemink2psp hypergeometric.py iupac2meme jaspar2meme llr log-hmm mast mast2txt mcast meme meme-chip meme-get-motif meme-xml-html meme.bin meme2images meme2meme meme_p metameme mhmm mhmm-io mhmm2html mhmme mhmms mhmmscan motiph nmica2meme oldmeme2meme plotgen pmp_bf prior_utils.pl priority2meme psp-gen purge qvalue ramen ranksum_test read_fasta_file.pl reconcile-tree-alignment reduce-alignment remove-alignment-gaps rna2meme scpd2meme sd sequence.py shadow spamo taipale2meme tamo2meme tomtom transfac2meme tree uniprobe2meme update_db update_meme_tests xsltproc_lite
 
 %:
 	dh $@ --with autoreconf,python2