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 <[email protected]> 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 <[email protected]> Uploaders: Laszlo Kajan <[email protected]> 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"); _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
