[med-svn] r13727 - in trunk/packages/hhsuite/trunk/debian: . patches

[Laszlo Kajan]

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 <lkajan at rostlab.org>
 --- 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: