[med-svn] r1375 - trunk/packages/infernal/trunk/debian

[smoe-guest at alioth.debian.org]

Author: smoe-guest
Date: 2008-02-14 13:48:11 +0000 (Thu, 14 Feb 2008)
New Revision: 1375

Modified:
   trunk/packages/infernal/trunk/debian/README.Debian
   trunk/packages/infernal/trunk/debian/rules
Log:
* added get-orig-source
* added additional comments to the README


Modified: trunk/packages/infernal/trunk/debian/README.Debian
===================================================================
--- trunk/packages/infernal/trunk/debian/README.Debian	2008-02-14 04:07:04 UTC (rev 1374)
+++ trunk/packages/infernal/trunk/debian/README.Debian	2008-02-14 13:48:11 UTC (rev 1375)
@@ -10,16 +10,22 @@
 from source - although Debian most likely provide the tools at least to
 prepare some of the figures, e.g., a sequence alignment.  Other figures
 would be more difficult to prepare. As an interim solution it was decided
-to leave the documentation out and users are requested to address the
+to leave that documentation out and users are requested to address the
 web pages of the upstream developers in this matter.
 
 The directory "squid" that is distributed with the source of infernal
-differs slightly from the biosquid Debian package. This redundancy
-needs to be investigated further and talked back about with the upstream
-developer.  Either the biosquid package needs to be updated or infernal
-will get dynamically linked against it. Until this issue is resolved,
-the package shall remain in experimental.
+differs slightly from the biosquid Debian package. Upstream was contacted
+about this redundancy to his own software and the answer was to please
+leave with that situation since the two are not safely substituted for
+another.
 
+Infernal offers to be compiled for LAM-MPI. Please contact us if there
+is respective demand.
+
+Infernal optionally uses the CFSQP library which is non-free. This is
+not supported by this Debian package. Please address the Userguide for
+instructions of a manual self-compilation and -installation.
+
 The packaging has become part of the Debian-Med Custom Debian Distribution
 and everyone interested is invited to join in for maintaining it.
 

Modified: trunk/packages/infernal/trunk/debian/rules
===================================================================
--- trunk/packages/infernal/trunk/debian/rules	2008-02-14 04:07:04 UTC (rev 1374)
+++ trunk/packages/infernal/trunk/debian/rules	2008-02-14 13:48:11 UTC (rev 1375)
@@ -126,5 +126,21 @@
 binary-arch: build-arch install-arch
 	$(MAKE) -f debian/rules DH_OPTIONS=-s binary-common
 
+get-orig-source:
+	VERSION=`head -1 debian/changelog  | cut -f1 -d- | cut -f2 -d\( | tr -d '\n'` ; \
+	URL="ftp://selab.janelia.org/pub/software/infernal/infernal.tar.gz"; \
+	cd ..; \
+	wget -nc $$URL && tar xzvf infernal.tar.gz; \
+	p=`pwd`; \
+	if [ -d infernal-$$VERSION ]; then \
+		cd infernal-$$VERSION && rm -rf ./easel/documentation Userguide.pdf ; \
+	else \
+		echo "Please check debian/changelog, the version you have downloaded is apparently newer than expected." ; \
+		exit -1 ; \
+	fi; \
+	cd $$p ; \
+	tar czvf infernal_$${VERSION}.orig.tar.gz infernal-$$VERSION && rm -rf infernal-$$VERSION
+
+
 binary: binary-arch
 .PHONY: build clean binary-indep binary-arch binary install install-indep install-arch