[med-svn] r9916 - in trunk/packages/hhsuite/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Wed Mar 7 09:28:07 UTC 2012
Author: lkajan-guest
Date: 2012-03-07 09:28:06 +0000 (Wed, 07 Mar 2012)
New Revision: 9916
Modified:
trunk/packages/hhsuite/trunk/debian/changelog
trunk/packages/hhsuite/trunk/debian/control
trunk/packages/hhsuite/trunk/debian/patches/Makefile
Log:
new upstream release; bumped Standards-Version to 3.9.3
Modified: trunk/packages/hhsuite/trunk/debian/changelog
===================================================================
--- trunk/packages/hhsuite/trunk/debian/changelog 2012-03-07 08:53:07 UTC (rev 9915)
+++ trunk/packages/hhsuite/trunk/debian/changelog 2012-03-07 09:28:06 UTC (rev 9916)
@@ -1,3 +1,9 @@
+hhsuite (2.0.13-1) UNRELEASED; urgency=low
+
+ * New upstream release
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 07 Mar 2012 09:35:48 +0100
+
hhsuite (2.0.12-1) unstable; urgency=low
* Initial release (Closes: #656626)
Modified: trunk/packages/hhsuite/trunk/debian/control
===================================================================
--- trunk/packages/hhsuite/trunk/debian/control 2012-03-07 08:53:07 UTC (rev 9915)
+++ trunk/packages/hhsuite/trunk/debian/control 2012-03-07 09:28:06 UTC (rev 9916)
@@ -4,7 +4,7 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Laszlo Kajan <lkajan at rostlab.org>
Build-Depends: debhelper (>= 8.0.0), libffindex0-dev, help2man, libpng12-dev
-Standards-Version: 3.9.2
+Standards-Version: 3.9.3
Homepage: http://toolkit.genzentrum.lmu.de/sections/search
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/hhsuite/trunk/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/hhsuite/trunk/
Modified: trunk/packages/hhsuite/trunk/debian/patches/Makefile
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/Makefile 2012-03-07 08:53:07 UTC (rev 9915)
+++ trunk/packages/hhsuite/trunk/debian/patches/Makefile 2012-03-07 09:28:06 UTC (rev 9916)
@@ -13,7 +13,7 @@
# Guess wether to use lib or lib64
#libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`
-@@ -8,84 +8,83 @@
+@@ -8,19 +8,17 @@
# Overriding this is currently not fully supported as the code won't know
# to what this is set then. You can try setting HHLIB.
@@ -26,41 +26,24 @@
+INSTALL_BDATA_DIR?=$(INSTALL_LIB_DIR)/data
INSTALL_LIB_BIN_DIR?=$(INSTALL_LIB_DIR)/bin
- dist_name=hhsuite-2.0.12
+ dist_name=hhsuite-2.0.13
+-.PHONY: all_static
-all_static: ffindex_static
-- cd src && make all_static
-+.PHONY: all
+- $(MAKE) -C src all_static
+-
+ .PHONY: all
+-all: ffindex
+all:
+ $(MAKE) -C data all
-+ $(MAKE) -C src all
+ $(MAKE) -C src all
--all: ffindex
-- cd src && make all
-+all_static:
-+ $(MAKE) -C src all_static
-
doc:
-- cd src && make hhsuite-userguide.pdf
-+ $(MAKE) -C src hhsuite-userguide.pdf
-
- hhblits_static: hhblits_static
-- cd src && make hhblits_static
-+ $(MAKE) -C src hhblits_static
-
--hhblits: ffindex
-- cd src && make all
-+hhblits:
-+ $(MAKE) -C src all
-
--ffindex:
-- cd lib/ffindex && make
--
--ffindex_static:
-- cd lib/ffindex && make FFINDEX_STATIC=1
--
+@@ -40,35 +38,34 @@
+ $(MAKE) -C lib/ffindex FFINDEX_STATIC=1
+
install:
-- cd lib/ffindex && make install INSTALL_DIR=$(INSTALL_DIR)
+- $(MAKE) -C lib/ffindex install INSTALL_DIR=$(INSTALL_DIR)
- mkdir -p $(INSTALL_DIR)/bin
- install src/hhblits $(INSTALL_DIR)/bin/hhblits
- install src/hhalign $(INSTALL_DIR)/bin/hhalign
@@ -72,29 +55,23 @@
- mkdir -p $(INSTALL_LIB_BIN_DIR)
- install src/cstranslate $(INSTALL_LIB_BIN_DIR)/cstranslate
- mkdir -p $(INSTALL_DATA_DIR)
-- install data/context_data.lib $(INSTALL_DATA_DIR)/context_data.lib
-- install data/cs219.lib $(INSTALL_DATA_DIR)/cs219.lib
-- install data/do_not_delete $(INSTALL_DATA_DIR)/do_not_delete
-- install data/do_not_delete.phr $(INSTALL_DATA_DIR)/do_not_delete.phr
-- install data/do_not_delete.pin $(INSTALL_DATA_DIR)/do_not_delete.pin
-- install data/do_not_delete.psq $(INSTALL_DATA_DIR)/do_not_delete.psq
+- install -m 0644 data/context_data.lib $(INSTALL_DATA_DIR)/context_data.lib
+- install -m 0644 data/cs219.lib $(INSTALL_DATA_DIR)/cs219.lib
+- install -m 0644 data/do_not_delete $(INSTALL_DATA_DIR)/do_not_delete
+- install -m 0644 data/do_not_delete.phr $(INSTALL_DATA_DIR)/do_not_delete.phr
+- install -m 0644 data/do_not_delete.pin $(INSTALL_DATA_DIR)/do_not_delete.pin
+- install -m 0644 data/do_not_delete.psq $(INSTALL_DATA_DIR)/do_not_delete.psq
- mkdir -p $(INSTALL_SCRIPTS_DIR)
-- install scripts/Align.pm $(INSTALL_SCRIPTS_DIR)/Align.pm
-- install scripts/HHPaths.pm $(INSTALL_SCRIPTS_DIR)/HHPaths.pm
+- install -m 0644 scripts/Align.pm $(INSTALL_SCRIPTS_DIR)/Align.pm
+- install -m 0644 scripts/HHPaths.pm $(INSTALL_SCRIPTS_DIR)/HHPaths.pm
- install scripts/addss.pl $(INSTALL_SCRIPTS_DIR)/addss.pl
- install scripts/create_profile_from_hhm.pl $(INSTALL_SCRIPTS_DIR)/create_profile_from_hhm.pl
- install scripts/create_profile_from_hmmer.pl $(INSTALL_SCRIPTS_DIR)/create_profile_from_hmmer.pl
- install scripts/hhmakemodel.pl $(INSTALL_SCRIPTS_DIR)/hhmakemodel.pl
- install scripts/reformat.pl $(INSTALL_SCRIPTS_DIR)/reformat.pl
+- install scripts/splitfasta.pl $(INSTALL_SCRIPTS_DIR)/splitfasta.pl
- install scripts/multithread.pl $(INSTALL_SCRIPTS_DIR)/multithread.pl
- install scripts/hhblitsdb.pl $(INSTALL_SCRIPTS_DIR)/hhblitsdb.pl
--
--deinstall:
-- cd lib/ffindex && make deinstall INSTALL_DIR=$(INSTALL_DIR)
-- rm -f $(INSTALL_DIR)/bin/hhblits $(INSTALL_DIR)/bin/hhalign \
-- $(INSTALL_DIR)/bin/hhconsensus $(INSTALL_DIR)/bin/hhfilter $(INSTALL_DIR)/bin/hhmake $(INSTALL_DIR)/bin/hhsearch
-- rm -f $(INSTALL_DATA_DIR)/context_data.lib $(INSTALL_DATA_DIR)/cs219.lib $(INSTALL_DATA_DIR)/do_not_delete \
-- $(INSTALL_DATA_DIR)/do_not_delete.phr $(INSTALL_DATA_DIR)/do_not_delete.pin $(INSTALL_DATA_DIR)/do_not_delete.psq
+ mkdir -p $(DESTDIR)$(PREFIX)/bin
+ install src/hhblits $(DESTDIR)$(PREFIX)/bin/hhblits
+ install src/hhalign $(DESTDIR)$(PREFIX)/bin/hhalign
@@ -120,38 +97,25 @@
+ install scripts/create_profile_from_hmmer.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/create_profile_from_hmmer.pl
+ install scripts/hhmakemodel.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/hhmakemodel.pl
+ install scripts/reformat.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/reformat.pl
++ install scripts/splitfasta.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/splitfasta.pl
+ install scripts/multithread.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/multithread.pl
+ install scripts/hhblitsdb.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/hhblitsdb.pl
-+
-+uninstall:
-+ rm -f $(PREFIX)/bin/hhblits $(PREFIX)/bin/hhalign \
-+ $(PREFIX)/bin/hhconsensus $(PREFIX)/bin/hhfilter $(PREFIX)/bin/hhmake $(PREFIX)/bin/hhsearch
-+ rm -f $(INSTALL_DATA_DIR)/context_data.lib $(INSTALL_DATA_DIR)/cs219.lib $(INSTALL_BDATA_DIR)/do_not_delete \
-+ $(INSTALL_BDATA_DIR)/do_not_delete.phr $(INSTALL_BDATA_DIR)/do_not_delete.pin $(INSTALL_BDATA_DIR)/do_not_delete.psq
- rm -f $(INSTALL_SCRIPTS_DIR)/Align.pm $(INSTALL_SCRIPTS_DIR)/HHPaths.pm \
- $(INSTALL_SCRIPTS_DIR)/addss.pl $(INSTALL_SCRIPTS_DIR)/create_profile_from_hhm.pl \
- $(INSTALL_SCRIPTS_DIR)/create_profile_from_hmmer.pl $(INSTALL_SCRIPTS_DIR)/hhmakemodel.pl \
- $(INSTALL_SCRIPTS_DIR)/reformat.pl $(INSTALL_SCRIPTS_DIR)/multithread.pl $(INSTALL_SCRIPTS_DIR)/hhblitsdb.pl
- rm -f $(INSTALL_LIB_BIN_DIR)/cstranslate
- rmdir $(INSTALL_LIB_BIN_DIR) || true
-- rmdir $(INSTALL_DIR)/bin || true
-+ rmdir $(PREFIX)/bin || true
- rmdir $(INSTALL_DATA_DIR) || true
-+ rmdir $(INSTALL_BDATA_DIR) || true
- rmdir $(INSTALL_SCRIPTS_DIR) || true
- rmdir $(INSTALL_LIB_DIR) || true
-+.PHONY: clean
+ deinstall:
+ $(MAKE) -C lib/ffindex deinstall INSTALL_DIR=$(INSTALL_DIR)
+@@ -89,9 +86,11 @@
+
+ .PHONY: clean
clean:
-- cd lib/ffindex && make clean
-- cd src && make clean
-+ $(MAKE) -C src clean
-+
+- cd lib/ffindex && $(MAKE) clean
+ $(MAKE) -C src clean
+
+.PHONY: distclean
+distclean: clean
-
++
dist/$(dist_name).tar.gz:
make clean
+ mkdir -p dist
--- a/scripts/HHPaths.pm
+++ b/scripts/HHPaths.pm
@@ -14,7 +14,7 @@
@@ -183,7 +147,7 @@
our $cs_lib = "$hhdata/cs219.lib";
--- a/src/hhdecl.C
+++ b/src/hhdecl.C
-@@ -278,7 +278,7 @@
+@@ -279,7 +279,7 @@
if(getenv("HHLIB"))
strcpy(hhlib, getenv("HHLIB"));
else
@@ -192,7 +156,7 @@
strcat(strcpy(hhdata, hhlib), "/data");
strcat(strcpy(clusterfile, hhdata), "/context_data.lib");
-@@ -290,7 +290,7 @@
+@@ -291,7 +291,7 @@
/* we did not find HHLIB, if called with full path or in dist dir, we can try relative to program path */
if(program_path != NULL)
{
@@ -201,15 +165,6 @@
strcat(strcpy(hhdata, hhlib), "/data");
strcat(strcpy(clusterfile, hhdata), "/context_data.lib");
strcat(strcpy(cs_library, hhdata), "/cs219.lib");
-@@ -305,7 +305,7 @@
- if (testf) { fclose(testf); return;}
- }
-
-- cerr<<endl<<"Error in "<<argv[0]<<": could not find context_data.lib and cs219.lib.\nPlease set the HHLIB environment variable to the HH-suite directory (Linux bash: export HHLIB=<hh_dir>, csh/tcsh: setenv HHLIB=<hh_dir>).\nThe missing files should be in $HHLIB/data/.\n ";
-+ cerr<<endl<<"Error in "<<argv[0]<<": could not find context_data.lib and cs219.lib in '" << hhlib << "'.\nPlease set the HHLIB environment variable to the HH-suite directory (Linux bash: export HHLIB=<hh_dir>, csh/tcsh: setenv HHLIB=<hh_dir>).\nThe missing files should be in $HHLIB/data/.\n ";
- exit(2);
- }
-
--- a/src/hhblits.C
+++ b/src/hhblits.C
@@ -295,8 +295,8 @@
@@ -223,7 +178,7 @@
printf(" -psipred <dir> directory with PSIPRED executables (default=%s) \n",par.psipred);
printf(" -psipred_data <dir> directory with PSIPRED data (default=%s) \n",par.psipred_data);
printf("\n");
-@@ -407,7 +407,12 @@
+@@ -408,7 +408,12 @@
printf("An extended list of options can be obtained by using '-help all' as parameter \n");
}
printf("\n");
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