[med-svn] r22807 - trunk/packages/python-cogent/trunk/debian

[Andreas Tille]

Author: tille
Date: 2016-09-15 13:17:33 +0000 (Thu, 15 Sep 2016)
New Revision: 22807

Modified:
   trunk/packages/python-cogent/trunk/debian/README.Debian
   trunk/packages/python-cogent/trunk/debian/changelog
Log:
Update d/README.Debian with todo list


Modified: trunk/packages/python-cogent/trunk/debian/README.Debian
===================================================================
--- trunk/packages/python-cogent/trunk/debian/README.Debian	2016-09-15 13:16:39 UTC (rev 22806)
+++ trunk/packages/python-cogent/trunk/debian/README.Debian	2016-09-15 13:17:33 UTC (rev 22807)
@@ -19,20 +19,29 @@
             Packaging prepared but licensing issues
 
 carnac:     http://bioinfo.lifl.fr/carnac/
+            Asket upstream about versioned tarball
 
 cmfinder:   http://bio.cs.washington.edu/yzizhen/CMfinder/
+            registration page
 
 comrna:     http://stormo.wustl.edu/comRNA/
+            needs contact about license: If you are a commercial user or want to commercialize it, please contact the authors.
 
 contrafold: http://contra.stanford.edu/contrafold/
 	    http://bioinformatics.oxfordjournals.org/content/22/14/e90.abstract
+            Packaging prepared at https://anonscm.debian.org/git/debian-med/contrafold.git
 
-covea:      ???
+covea:      not sure - may be part of (non-free) trnascan-se
+            https://anonscm.debian.org/git/debian-med/trnascan-se.git
 
 dynalign:   http://rna.urmc.rochester.edu/dynalign.html
             Mathews DH, Turner DH (2002). "Dynalign: an algorithm for finding the secondary structure common to two RNA sequences". J. Mol. Biol. 317 (2): 191–203. doi:10.1006/jmbi.2001.5351. PMID 11902836.
+            Note that Dynalign is now fully incorporated into the RNAstructure package
+              -->  http://rna.urmc.rochester.edu/RNAstructure.html<->(GPL, but registration)
 
-foldalign:  http://foldalign.ku.dk/software/
+foldalign:  http://rth.dk/resources/foldalign/
+            http://bioinformaticsreview.com/20160413/foldalign-a-tool-for-secondary-structure-alignment-of-rna/
+             == https://www.ncbi.nlm.nih.gov/pubmed/26704597
 
 guppy:      https://staff.aist.go.jp/yutaka.ueno/guppy/
 
@@ -46,9 +55,6 @@
 
 pplacer:    http://www.mybiosoftware.com/phylogenetic-analysis/5069
 
-rdp-classifier: Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rdp-classifier/trunk/
-            Packaging prepared, preconditions in new queue
-
 Fold.out    ???
 
 PETfold:    http://rth.dk/resources/petfold/download.html

Modified: trunk/packages/python-cogent/trunk/debian/changelog
===================================================================
--- trunk/packages/python-cogent/trunk/debian/changelog	2016-09-15 13:16:39 UTC (rev 22806)
+++ trunk/packages/python-cogent/trunk/debian/changelog	2016-09-15 13:17:33 UTC (rev 22807)
@@ -1,3 +1,9 @@
+python-cogent (1.9-5) UNRELEASED; urgency=medium
+
+  * Update d/README.Debian with todo list
+
+ -- Andreas Tille <tille at debian.org>  Thu, 15 Sep 2016 15:16:46 +0200
+
 python-cogent (1.9-4) unstable; urgency=medium
 
   * Need to exclude further tests on armhf and mips