Author: lkajan Date: 2013-05-28 10:51:59 +0000 (Tue, 28 May 2013) New Revision: 13727
Modified: trunk/packages/hhsuite/trunk/debian/patches/help trunk/packages/hhsuite/trunk/debian/rules Log: HHLIB=/usr/share/hhsuite is used to generate man pages - no need to patch paths for par.cs_library and par.clusterfile Modified: trunk/packages/hhsuite/trunk/debian/patches/help =================================================================== --- trunk/packages/hhsuite/trunk/debian/patches/help 2013-05-28 10:40:13 UTC (rev 13726) +++ trunk/packages/hhsuite/trunk/debian/patches/help 2013-05-28 10:51:59 UTC (rev 13727) @@ -4,26 +4,15 @@ Author: Laszlo Kajan <[email protected]> --- a/src/hhblits.C +++ b/src/hhblits.C -@@ -381,8 +381,8 @@ - printf("\n"); - printf("Context-specific pseudo-counts: \n"); - printf(" -nocontxt use substitution-matrix instead of context-specific pseudocounts \n"); -- printf(" -contxt <file> context file for computing context-specific pseudocounts (default=%s)\n",par.clusterfile); -- printf(" -cslib <file> column state file for fast database prefiltering (default=%s)\n",par.cs_library); -+ printf(" -contxt <file> context file for computing context-specific pseudocounts (default=/usr/lib/hhsuite/data/context_data.lib)\n"); -+ printf(" -cslib <file> column state file for fast database prefiltering (default=/usr/lib/hhsuite/data/cs219.lib)\n"); - printf("\n"); - printf("Predict secondary structure\n"); - printf(" -addss add 2ndary structure predicted with PSIPRED to result MSA \n"); @@ -411,7 +411,12 @@ printf("An extended list of options can be obtained by calling 'hhblits -help'\n"); } printf("\n"); - printf("Example: %s -i query.fas -oa3m query.a3m -n 1 \n",program_name); + printf("Examples:\n"); -+ printf("%s -i query.fas -o query.hhr -d <database-basepath>\n",program_name); ++ printf("%s -i query.fas -o query.hhr -d ./uniprot20\n",program_name); + printf("\n"); -+ printf("%s -i query.fas -o query.hhr -oa3m query.a3m -n 1 -d <database-basepath>\n",program_name); ++ printf("%s -i query.fas -o query.hhr -oa3m query.a3m -n 1 -d ./uniprot20\n",program_name); + printf("\n"); + printf("Download databases from <ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/databases/>.\n"); cout<<endl; @@ -39,14 +28,3 @@ #include <errno.h> // perror() #include <cassert> #include <stdexcept> -@@ -308,8 +309,8 @@ - printf("\n"); - printf("Context-specific pseudo-counts: \n"); - printf(" -nocontxt use substitution-matrix instead of context-specific pseudocounts \n"); -- printf(" -contxt <file> context file for computing context-specific pseudocounts (default=%s)\n",par.clusterfile); -- printf(" -cslib <file> column state file for fast database prefiltering (default=%s)\n",par.cs_library); -+ printf(" -contxt <file> context file for computing context-specific pseudocounts (default=/usr/lib/hhsuite/data/context_data.lib)\n"); -+ printf(" -cslib <file> column state file for fast database prefiltering (default=/usr/lib/hhsuite/data/cs219.lib)\n"); - if (all) { - printf(" -csw [0,inf] weight of central position in cs pseudocount mode (def=%.1f)\n", par.csw); - printf(" -csb [0,1] weight decay parameter for positions in cs pc mode (def=%.1f)\n", par.csb); Modified: trunk/packages/hhsuite/trunk/debian/rules =================================================================== --- trunk/packages/hhsuite/trunk/debian/rules 2013-05-28 10:40:13 UTC (rev 13726) +++ trunk/packages/hhsuite/trunk/debian/rules 2013-05-28 10:51:59 UTC (rev 13727) @@ -31,7 +31,7 @@ dh_installman $(HHMANPAGES): %.1 : debian/tmp/usr/bin/% - unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=debian/tmp/usr/share/hhsuite && help2man --no-info --help-option '-h all' --version-string $(VERSION) -n "$$n_$*" '$<' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > '$@' + unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=/usr/share/hhsuite && help2man --no-info --help-option '-h all' --version-string $(VERSION) -n "$$n_$*" '$<' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > '$@' .PHONY: override_dh_clean override_dh_clean: _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
