[med-svn] r12359 - in trunk/packages/concavity: . trunk/debian trunk/debian/patches

[Laszlo Kajan]

Author: lkajan-guest
Date: 2012-10-10 14:26:48 +0000 (Wed, 10 Oct 2012)
New Revision: 12359

Modified:
   trunk/packages/concavity/
   trunk/packages/concavity/trunk/debian/README.source
   trunk/packages/concavity/trunk/debian/control
   trunk/packages/concavity/trunk/debian/patches/manpage
   trunk/packages/concavity/trunk/debian/rules
Log:
updated config with new related package conservation-code


Property changes on: trunk/packages/concavity
___________________________________________________________________
Added: svn:ignore
   + build-area
tarballs


Modified: trunk/packages/concavity/trunk/debian/README.source
===================================================================
--- trunk/packages/concavity/trunk/debian/README.source	2012-10-10 13:43:21 UTC (rev 12358)
+++ trunk/packages/concavity/trunk/debian/README.source	2012-10-10 14:26:48 UTC (rev 12359)
@@ -11,13 +11,9 @@
 Upstream (as of 20120928) does not version the downloadable tarball. The version (v0.1) is mentioned on the home page, but the downloadable is simply concavity_distr.tar.gz .
 A watch file will be created when upstream introduces version numbers to the name of the downloadable archive.
 
-Missing man page for concavity
-------------------------------
-The man page is planned, but not yet ready. Fellow developer asked for an early upload, regardless of the man page.
-
 Static linking to GAPS library
 ------------------------------
 These are the files in pkg/. In a personal communication the author (Thomas Funkhouser <funk at CS.Princeton.EDU>) did not endorse the separate packaging of this library, although the license would allow this.
 His argument is roughly that GAPS is handled very dynamically by its developers and its versions are not expected to be compatible.
 
-# vim:et:ts=2:
+# vim:et:ts=4:

Modified: trunk/packages/concavity/trunk/debian/control
===================================================================
--- trunk/packages/concavity/trunk/debian/control	2012-10-10 13:43:21 UTC (rev 12358)
+++ trunk/packages/concavity/trunk/debian/control	2012-10-10 14:26:48 UTC (rev 12359)
@@ -13,7 +13,7 @@
 Package: concavity
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
-Suggests: pymol
+Suggests: conservation-code, pymol
 Description: predictor of protein ligand binding sites from structure and conservation
  ConCavity predicts protein ligand binding sites by combining evolutionary
  sequence conservation and 3D structure.
@@ -34,6 +34,9 @@
  'Capra JA, Laskowski RA, Thornton JM, Singh M, and Funkhouser TA(2009)
  Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence
  Conservation and 3D Structure. PLoS Comput Biol, 5(12).'.
+ .
+ score_conservation(1) from the conservation-code package can be used to
+ calculate evolutionary sequence conservation for concavity.
 
 Package: concavity-dbg
 Section: debug

Modified: trunk/packages/concavity/trunk/debian/patches/manpage
===================================================================
--- trunk/packages/concavity/trunk/debian/patches/manpage	2012-10-10 13:43:21 UTC (rev 12358)
+++ trunk/packages/concavity/trunk/debian/patches/manpage	2012-10-10 14:26:48 UTC (rev 12359)
@@ -3,7 +3,7 @@
 Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-October/017343.html
 --- /dev/null
 +++ b/concavity.1.pod
-@@ -0,0 +1,192 @@
+@@ -0,0 +1,195 @@
 +=pod
 +
 +=head1 NAME
@@ -86,7 +86,8 @@
 +Pre-computed conservation files available for almost the entire PQS on
 +the ConCavity web site.  If you'd like to compute sequence
 +conservation values for your own alignments, we recommend the JSD
-+algorithm: http://compbio.cs.princeton.edu/conservation/
++algorithm: L<http://compbio.cs.princeton.edu/conservation/>,
++available as score_conservation(1) from the conservation-code package.
 +
 +=back
 +
@@ -193,6 +194,8 @@
 +
 +=item Concavity Homepage L<http://compbio.cs.princeton.edu/concavity/>
 +
++=item score_conservation(1)
++
 +=back
 +
 +=cut

Modified: trunk/packages/concavity/trunk/debian/rules
===================================================================
--- trunk/packages/concavity/trunk/debian/rules	2012-10-10 13:43:21 UTC (rev 12358)
+++ trunk/packages/concavity/trunk/debian/rules	2012-10-10 14:26:48 UTC (rev 12359)
@@ -20,7 +20,7 @@
 	t=$$(mktemp -d) || exit 1; \
 	trap "rm -rf -- '$$t'" EXIT; \
 	pwd; \
-	wget -O $$t/concavity_0.1.orig.tar.gz --quiet http://compbio.cs.princeton.edu/concavity/concavity_distr.tar.gz; \
+	wget -O $$t/concavity_$(VERSION).orig.tar.gz --quiet http://compbio.cs.princeton.edu/concavity/concavity_distr.tar.gz; \
 	( cd "$$t"; \
 		gunzip *.tar.gz; \
 		tar --owner=root --group=root --mode=a+rX --delete -f *.tar --wildcards 'concavity_distr/pkgs/freeglut'; \
@@ -33,9 +33,7 @@
 
 .PHONY: man
 man:
-	set
-	export
-	$(MAKE) man
+	$(MAKE) man VERSION=$(VERSION) prefix=$(prefix)
 
 .PHONY: override_dh_strip
 override_dh_strip: