[med-svn] r908 - in trunk/packages: . gnumed-client/trunk/debian mafft/trunk/debian seaview/trunk/debian t-coffee/trunk/debian

Thu Dec 20 19:15:58 UTC 2007

Author: smoe-guest
Date: 2007-12-20 19:15:58 +0000 (Thu, 20 Dec 2007)
New Revision: 908

Added:
   trunk/packages/mgltools/
Modified:
   trunk/packages/gnumed-client/trunk/debian/control
   trunk/packages/mafft/trunk/debian/control
   trunk/packages/seaview/trunk/debian/control
   trunk/packages/t-coffee/trunk/debian/rules
   trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base
Log:
I am a bit uncertain at the moment what all my changes exactly
were about, mostly typos or other bits that annoyed me in the 
original package description of packages that I translated to
German.

My main motivation for this upload though is to prepare the
repository for packages of the MGLTools. These are preparing
the protein for docking experiments with AutoDock, an ultimate
requirement for following any of the tutorials for docking.



Modified: trunk/packages/gnumed-client/trunk/debian/control
===================================================================

--- trunk/packages/gnumed-client/trunk/debian/control	2007-12-19 16:56:34 UTC (rev 907)
+++ trunk/packages/gnumed-client/trunk/debian/control	2007-12-20 19:15:58 UTC (rev 908)
@@ -7,6 +7,8 @@
 Build-Depends: debhelper (>= 5.0.37.2)
 Build-Depends-Indep: po-debconf, python-support (>= 0.3.8), python-all-dev (>= 2.3.5-11)
 Standards-Version: 3.7.2
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gnumed-client/trunk/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/gnumed-client
 Homepage: http://gnumed.org/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gnumed-client/
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/gnumed-client/

Modified: trunk/packages/mafft/trunk/debian/control
===================================================================
--- trunk/packages/mafft/trunk/debian/control	2007-12-19 16:56:34 UTC (rev 907)
+++ trunk/packages/mafft/trunk/debian/control	2007-12-20 19:15:58 UTC (rev 908)
@@ -16,7 +16,7 @@
 Depends: ${shlibs:Depends}, ${misc:Depends}
 Suggests: ruby, lynx, blast2
 Description: Multiple alignment program for amino acid or nucleotide sequences
- MAFFT is a multiple sequence alignment program, which offers three
+ MAFFT is a multiple sequence alignment program which offers three
  accuracy-oriented methods:
   * L-INS-i (probably most accurate; recommended for <200 sequences;
     iterative refinement method incorporating local pairwise alignment
@@ -26,7 +26,7 @@
     pairwise alignment information),
   * E-INS-i (suitable for sequences containing large unalignable regions;
     recommended for <200 sequences),
-    and five speed-oriented methods:
+ and five speed-oriented methods:
   * FFT-NS-i (iterative refinement method; two cycles only),
   * FFT-NS-i (iterative refinement method; max. 1000 iterations),
   * FFT-NS-2 (fast; progressive method),

Modified: trunk/packages/seaview/trunk/debian/control
===================================================================
--- trunk/packages/seaview/trunk/debian/control	2007-12-19 16:56:34 UTC (rev 907)
+++ trunk/packages/seaview/trunk/debian/control	2007-12-20 19:15:58 UTC (rev 908)
@@ -17,11 +17,14 @@
 Suggests: muscle, clustalw
 Description: Multiple sequence alignment editor
  SeaView is a graphical multiple sequence alignment editor developed by Manolo
- Gouy. SeaView is able to read and write various alignment formats (NEXUS, MSF,
- CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and
- also to run DOT-PLOT or MUSCLE programs to locally improve the alignment.
+ Gouy. Multiple alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE)
+ are supported for reading and writing. Alignments can be manually edited.
+ The user is further supported by an integration of external programs,
+ i.e., to run DOT-PLOT or MUSCLE, to locally improve the alignment.
  .
- If you use SeaView in a published work, please cite the following
- reference: Galtier, N., Gouy, M. and Gautier, C. (1996) SeaView and
+ When using SeaView for investigations that lead to a publication, please
+ cite the following reference:
+ .
+ Galtier, N., Gouy, M. and Gautier, C. (1996) "SeaView and
  Phylo_win, two graphic tools for sequence alignment and molecular
- phylogeny. Comput. Applic. Biosci., 12, 543-548.
+ phylogeny." Comput. Applic. Biosci. 12:543-548.

Modified: trunk/packages/t-coffee/trunk/debian/rules
===================================================================
--- trunk/packages/t-coffee/trunk/debian/rules	2007-12-19 16:56:34 UTC (rev 907)
+++ trunk/packages/t-coffee/trunk/debian/rules	2007-12-20 19:15:58 UTC (rev 908)
@@ -37,7 +37,7 @@
 	# circumventing a hen-and-egg problem
 	# the fix to clean the source even if not necessary is only applied after the clean
 	[ -r t_coffee_source/util_dp_drivers.o ] && $(MAKE) -C t_coffee_source clean || echo No need to clean the source
-	dh_clean  bin/t_coffee
+	dh_clean  bin/t_coffee `find example/ -size 0` doc/t_coffee.pdf
 
 install: install-arch install-indep
 

Modified: trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base
===================================================================
--- trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base	2007-12-19 16:56:34 UTC (rev 907)
+++ trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base	2007-12-20 19:15:58 UTC (rev 908)
@@ -3,8 +3,10 @@
 Author: Cédric Notredame
 Abstract: A description of T-Coffee, the program
  for multiple sequence alignment, and sequence
- formats.
+ formats. The documentation entails both a technical
+ description and a tutorial for a novice's first
+ steps.
 Section: Applications/Science/Biology
 
-Format: pdf
-Files: /usr/share/doc/t-coffee-doc/t_coffee.pdf
+Format: text
+Files: /usr/share/doc/t-coffee-doc/t_coffee_tutorial.txt.gz /usr/share/doc/t-coffee-doc/t_coffee_technical.txt.gz


