[med-svn] r9393 - in trunk/packages/hhsuite/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Mon Jan 23 17:09:56 UTC 2012
Author: lkajan-guest
Date: 2012-01-23 17:09:56 +0000 (Mon, 23 Jan 2012)
New Revision: 9393
Added:
trunk/packages/hhsuite/trunk/debian/ffindex.manpages
trunk/packages/hhsuite/trunk/debian/hhsuite.manpages
trunk/packages/hhsuite/trunk/debian/patches/default_path
Modified:
trunk/packages/hhsuite/trunk/debian/docs
trunk/packages/hhsuite/trunk/debian/patches/Makefile
trunk/packages/hhsuite/trunk/debian/patches/series
trunk/packages/hhsuite/trunk/debian/rules
Log:
added man pages
Modified: trunk/packages/hhsuite/trunk/debian/docs
===================================================================
--- trunk/packages/hhsuite/trunk/debian/docs 2012-01-23 15:54:07 UTC (rev 9392)
+++ trunk/packages/hhsuite/trunk/debian/docs 2012-01-23 17:09:56 UTC (rev 9393)
@@ -1 +1,2 @@
README
+hhsuite-userguide.pdf
Added: trunk/packages/hhsuite/trunk/debian/ffindex.manpages
===================================================================
--- trunk/packages/hhsuite/trunk/debian/ffindex.manpages (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/ffindex.manpages 2012-01-23 17:09:56 UTC (rev 9393)
@@ -0,0 +1,3 @@
+ffindex_build.1
+ffindex_get.1
+ffindex_modify.1
Added: trunk/packages/hhsuite/trunk/debian/hhsuite.manpages
===================================================================
--- trunk/packages/hhsuite/trunk/debian/hhsuite.manpages (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/hhsuite.manpages 2012-01-23 17:09:56 UTC (rev 9393)
@@ -0,0 +1,6 @@
+hhalign.1
+hhblits.1
+hhconsensus.1
+hhfilter.1
+hhmake.1
+hhsearch.1
Modified: trunk/packages/hhsuite/trunk/debian/patches/Makefile
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/Makefile 2012-01-23 15:54:07 UTC (rev 9392)
+++ trunk/packages/hhsuite/trunk/debian/patches/Makefile 2012-01-23 17:09:56 UTC (rev 9393)
@@ -1,7 +1,7 @@
Index: hhsuite-2.0.4/Makefile
===================================================================
---- hhsuite-2.0.4.orig/Makefile 2012-01-20 20:17:19.000000000 +0100
-+++ hhsuite-2.0.4/Makefile 2012-01-20 20:18:42.504242187 +0100
+--- hhsuite-2.0.4.orig/Makefile 2012-01-20 10:54:23.000000000 +0100
++++ hhsuite-2.0.4/Makefile 2012-01-23 15:39:20.036242021 +0100
@@ -1,5 +1,5 @@
# This can be overridden e.g.: make install INSTALL_DIR=...
-INSTALL_DIR?=$(PWD)
@@ -108,8 +108,8 @@
make clean
Index: hhsuite-2.0.4/scripts/HHPaths.pm
===================================================================
---- hhsuite-2.0.4.orig/scripts/HHPaths.pm 2012-01-20 20:17:19.000000000 +0100
-+++ hhsuite-2.0.4/scripts/HHPaths.pm 2012-01-20 20:18:42.512254195 +0100
+--- hhsuite-2.0.4.orig/scripts/HHPaths.pm 2012-01-20 10:54:23.000000000 +0100
++++ hhsuite-2.0.4/scripts/HHPaths.pm 2012-01-23 11:31:41.000000000 +0100
@@ -39,7 +39,7 @@
# The lines below probably do not need to be changed
@@ -121,19 +121,13 @@
our $hhscripts= $hhlib."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.)
Index: hhsuite-2.0.4/src/hhdecl.C
===================================================================
---- hhsuite-2.0.4.orig/src/hhdecl.C 2012-01-20 20:17:19.000000000 +0100
-+++ hhsuite-2.0.4/src/hhdecl.C 2012-01-20 20:18:42.528243118 +0100
-@@ -286,10 +286,10 @@
- {
- // set hhlib
- FILE* testf = NULL;
-- if(getenv("HHLIB"))
-- strcpy(hhlib, getenv("HHLIB"));
-- else
+--- hhsuite-2.0.4.orig/src/hhdecl.C 2012-01-20 10:54:23.000000000 +0100
++++ hhsuite-2.0.4/src/hhdecl.C 2012-01-23 16:22:16.328242836 +0100
+@@ -289,7 +289,7 @@
+ if(getenv("HHLIB"))
+ strcpy(hhlib, getenv("HHLIB"));
+ else
- strcpy(hhlib, "/usr/lib/hh");
-+// if(getenv("HHLIB"))
-+// strcpy(hhlib, getenv("HHLIB"));
-+// else
+ strcpy(hhlib, "/usr/lib/hhsuite");
strcat(strcpy(hhdata, hhlib), "/data");
@@ -147,10 +141,19 @@
strcat(strcpy(hhdata, hhlib), "/data");
strcat(strcpy(clusterfile, hhdata), "/context_data.lib");
strcat(strcpy(cs_library, hhdata), "/cs219.lib");
+@@ -316,7 +316,7 @@
+ 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 (under Linux: export 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 (under Linux: export HHLIB=<hh_dir>).\nThe missing files should be in $HHLIB/data/.\n ";
+ exit(2);
+ }
+
Index: hhsuite-2.0.4/lib/ffindex/Makefile
===================================================================
---- hhsuite-2.0.4.orig/lib/ffindex/Makefile 2012-01-20 20:17:19.000000000 +0100
-+++ hhsuite-2.0.4/lib/ffindex/Makefile 2012-01-20 20:18:42.540241867 +0100
+--- hhsuite-2.0.4.orig/lib/ffindex/Makefile 2012-01-19 14:06:31.000000000 +0100
++++ hhsuite-2.0.4/lib/ffindex/Makefile 2012-01-23 11:31:41.000000000 +0100
@@ -7,13 +7,7 @@
endif
@@ -170,8 +173,8 @@
+ $(MAKE) -C src $@
Index: hhsuite-2.0.4/lib/ffindex/src/Makefile
===================================================================
---- hhsuite-2.0.4.orig/lib/ffindex/src/Makefile 2012-01-20 20:17:19.000000000 +0100
-+++ hhsuite-2.0.4/lib/ffindex/src/Makefile 2012-01-20 21:33:12.932241991 +0100
+--- hhsuite-2.0.4.orig/lib/ffindex/src/Makefile 2012-01-19 14:06:31.000000000 +0100
++++ hhsuite-2.0.4/lib/ffindex/src/Makefile 2012-01-23 11:31:41.000000000 +0100
@@ -1,12 +1,14 @@
INSTALL_DIR?=..
-libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`
@@ -239,8 +242,8 @@
rmdir $(INSTALL_DIR)/include || true
Index: hhsuite-2.0.4/src/Makefile
===================================================================
---- hhsuite-2.0.4.orig/src/Makefile 2012-01-20 20:43:18.024242503 +0100
-+++ hhsuite-2.0.4/src/Makefile 2012-01-20 20:43:41.984242663 +0100
+--- hhsuite-2.0.4.orig/src/Makefile 2012-01-20 10:54:23.000000000 +0100
++++ hhsuite-2.0.4/src/Makefile 2012-01-23 11:31:41.000000000 +0100
@@ -31,7 +31,7 @@
ifeq ($(OS), Linux)
HHSEARCH_LIBS = -lpthread -lrt
Added: trunk/packages/hhsuite/trunk/debian/patches/default_path
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/default_path (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/patches/default_path 2012-01-23 17:09:56 UTC (rev 9393)
@@ -0,0 +1,67 @@
+Index: hhsuite-2.0.4/lib/ffindex/src/ffindex_build.c
+===================================================================
+--- hhsuite-2.0.4.orig/lib/ffindex/src/ffindex_build.c 2012-01-23 18:03:01.532243170 +0100
++++ hhsuite-2.0.4/lib/ffindex/src/ffindex_build.c 2012-01-23 18:05:51.100242425 +0100
+@@ -31,7 +31,7 @@
+
+ void usage(char *program_name)
+ {
+- fprintf(stderr, "USAGE: %s [-a|-v] [-s] [-f file]* data_filename index_filename [dir_to_index|file]*\n"
++ fprintf(stderr, "USAGE: ffindex_build [-a|-v] [-s] [-f file]* data_filename index_filename [dir_to_index|file]*\n"
+ "\t-a\tappend\n"
+ "\t-d a second ffindex data file for inserting/appending\n"
+ "\t-i a second ffindex index file for insterting/appending\n"
+Index: hhsuite-2.0.4/lib/ffindex/src/ffindex_get.c
+===================================================================
+--- hhsuite-2.0.4.orig/lib/ffindex/src/ffindex_get.c 2012-01-23 18:03:01.616245335 +0100
++++ hhsuite-2.0.4/lib/ffindex/src/ffindex_get.c 2012-01-23 18:06:33.956242514 +0100
+@@ -26,7 +26,7 @@
+ {
+ if(argn < 3)
+ {
+- fprintf(stderr, "USAGE: %s data_filename index_filename filename(s)\n"
++ fprintf(stderr, "USAGE: ffindex_get data_filename index_filename filename(s)\n"
+ "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n",
+ argv[0]);
+ return -1;
+Index: hhsuite-2.0.4/lib/ffindex/src/ffindex_modify.c
+===================================================================
+--- hhsuite-2.0.4.orig/lib/ffindex/src/ffindex_modify.c 2012-01-23 18:03:01.576242602 +0100
++++ hhsuite-2.0.4/lib/ffindex/src/ffindex_modify.c 2012-01-23 18:06:10.340241903 +0100
+@@ -30,7 +30,7 @@
+
+ void usage(char *program_name)
+ {
+- fprintf(stderr, "USAGE: %s [-s|-u|-v] [-t] [-f file]* index_filename [filename]*\n"
++ fprintf(stderr, "USAGE: ffindex_modify [-s|-u|-v] [-t] [-f file]* index_filename [filename]*\n"
+ "\t-f file\tfile each line containing a filename\n"
+ "\t\t-f can be specified up to %d times\n"
+ "\t-s\tsort index file\n"
+Index: hhsuite-2.0.4/src/hhblits.C
+===================================================================
+--- hhsuite-2.0.4.orig/src/hhblits.C 2012-01-23 17:50:34.640245145 +0100
++++ hhsuite-2.0.4/src/hhblits.C 2012-01-23 18:01:36.584242765 +0100
+@@ -410,8 +410,8 @@
+ printf("\n");
+ printf("Directory paths \n");
+ //printf(" -cs <file> compute context-specific pseudocounts with context library (def=off)\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(" -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");
+Index: hhsuite-2.0.4/src/hhsearch.C
+===================================================================
+--- hhsuite-2.0.4.orig/src/hhsearch.C 2012-01-23 17:50:34.684242434 +0100
++++ hhsuite-2.0.4/src/hhsearch.C 2012-01-23 18:02:22.412243167 +0100
+@@ -321,7 +321,7 @@
+ printf(" -pcc [0,3] extinction exponent for tau(Neff) (def=%-.1f) \n",par.pcc);
+ printf(" -pcw [0,3] weight of pos-specificity for pcs (def=%-.1f) \n",par.pcw);
+ // HHsearch option should be the same as HHblits option!!
+- printf(" -contxt <file> context file for computing context-specific pseudocounts (default=%s)\n",par.clusterfile);
++ printf(" -contxt <file> context file for computing context-specific pseudocounts (default=/usr/lib/hhsuite/data/context_data.lib)\n");
+ 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/patches/series
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/series 2012-01-23 15:54:07 UTC (rev 9392)
+++ trunk/packages/hhsuite/trunk/debian/patches/series 2012-01-23 17:09:56 UTC (rev 9393)
@@ -1 +1,2 @@
Makefile
+default_path
Modified: trunk/packages/hhsuite/trunk/debian/rules
===================================================================
--- trunk/packages/hhsuite/trunk/debian/rules 2012-01-23 15:54:07 UTC (rev 9392)
+++ trunk/packages/hhsuite/trunk/debian/rules 2012-01-23 17:09:56 UTC (rev 9393)
@@ -3,6 +3,8 @@
# Uncomment this to turn on verbose mode.
export DH_VERBOSE=1
+VERSION=2.0.4
+
%:
dh $@
@@ -16,3 +18,31 @@
override_dh_strip:
dh_strip --dbg-package=libffindex0-dbg -Xffindex_build -Xffindex_get -Xffindex_modify -Xhhalign -Xhhblits -Xhhconsensus -Xhhfilter -Xhhmake -Xhhsearch -Xcstranslate
dh_strip --dbg-package=hhsuite-dbg -Xlibffindex.a -Xlibffindex.so
+
+FFMANPAGES = ffindex_build.1 ffindex_get.1 ffindex_modify.1
+HHMANPAGES = hhalign.1 hhblits.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1
+BINNAMES = ffindex_build="build file index from files in directories";\
+ ffindex_get="retrieve entries from file index";\
+ ffindex_modify="modify file index entries";\
+ \
+ hhalign="align a query alignment/HMM to a template alignment/HMM";\
+ hhblits="fast homology detection method to iteratively search a HMM database";\
+ hhconsensus="calculate the consensus sequence for an A3M/FASTA input file";\
+ hhfilter="filter an alignment by maximum sequence identity of match states and minimum coverage";\
+ hhmake="build an HMM from an input alignment or convert between HMMER format and HHsearch format";\
+ hhsearch="search a database of HMMs with a query alignment or query HMM";
+
+.PHONY: override_dh_installman
+override_dh_installman: $(FFMANPAGES) $(HHMANPAGES)
+ dh_installman
+
+$(FFMANPAGES): %.1 : debian/tmp/usr/bin/%
+ unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && eval '$(BINNAMES)' && help2man --no-info --no-discard-stderr '--help-option= ' -n "$$$*" --version-string=$(VERSION) '$<' -o '$@'
+
+$(HHMANPAGES): %.1 : debian/tmp/usr/bin/%
+ export HHLIB=debian/tmp/usr/lib/hhsuite && eval '$(BINNAMES)' && help2man --no-info '--help-option=-h all' -n "$$$*" --version-string=$(VERSION) '$<' -o '$@'
+
+.PHONY: override_dh_clean
+override_dh_clean:
+ rm -f $(FFMANPAGES) $(HHMANPAGES)
+ dh_clean
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