[med-svn] r9779 - in trunk/packages/hhsuite/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Fri Feb 24 16:45:09 UTC 2012
Author: lkajan-guest
Date: 2012-02-24 16:45:08 +0000 (Fri, 24 Feb 2012)
New Revision: 9779
Added:
trunk/packages/hhsuite/trunk/debian/hhsuite-data.install
trunk/packages/hhsuite/trunk/debian/hhsuite-data.links
trunk/packages/hhsuite/trunk/debian/hhsuite.examples
trunk/packages/hhsuite/trunk/debian/hhsuite.links
Removed:
trunk/packages/hhsuite/trunk/debian/ffindex.changelog
trunk/packages/hhsuite/trunk/debian/ffindex.docs
trunk/packages/hhsuite/trunk/debian/ffindex.install
trunk/packages/hhsuite/trunk/debian/ffindex.manpages
trunk/packages/hhsuite/trunk/debian/libffindex0-dbg.changelog
trunk/packages/hhsuite/trunk/debian/libffindex0-dev.changelog
trunk/packages/hhsuite/trunk/debian/libffindex0-dev.install
trunk/packages/hhsuite/trunk/debian/libffindex0.changelog
trunk/packages/hhsuite/trunk/debian/libffindex0.install
trunk/packages/hhsuite/trunk/debian/patches/default_path
Modified:
trunk/packages/hhsuite/trunk/debian/control
trunk/packages/hhsuite/trunk/debian/hhsuite.install
trunk/packages/hhsuite/trunk/debian/patches/Makefile
trunk/packages/hhsuite/trunk/debian/patches/series
trunk/packages/hhsuite/trunk/debian/rules
Log:
added hhsuite-data; added symlinks to make upstreams paths work on debian as well
Modified: trunk/packages/hhsuite/trunk/debian/control
===================================================================
--- trunk/packages/hhsuite/trunk/debian/control 2012-02-24 16:35:39 UTC (rev 9778)
+++ trunk/packages/hhsuite/trunk/debian/control 2012-02-24 16:45:08 UTC (rev 9779)
@@ -12,7 +12,7 @@
Package: hhsuite
Architecture: amd64
-Depends: ${shlibs:Depends}, ${misc:Depends}, ffindex
+Depends: ${shlibs:Depends}, ${misc:Depends}, ffindex, hhsuite-data
Description: sensitive protein sequence searching based on HMM-HMM alignment
HH-suite is an open-source software package for sensitive protein sequence
searching based on the pairwise alignment of hidden Markov models (HMMs).
@@ -32,6 +32,15 @@
HHblits is faster, up to twice as sensitive and produces more accurate
alignments.
+Package: hhsuite-data
+Architecture: all
+Depends: ${misc:Depends}
+Description: sensitive protein sequence searching based on HMM-HMM alignment
+ HH-suite is an open-source software package for sensitive protein sequence
+ searching based on the pairwise alignment of hidden Markov models (HMMs).
+ .
+ This package contains architecture independent scripts and data files.
+
Package: hhsuite-dbg
Architecture: amd64
Section: debug
@@ -41,56 +50,3 @@
searching based on the pairwise alignment of hidden Markov models (HMMs).
.
This package contains the debugging symbols.
-
-Package: ffindex
-Architecture: any
-Depends: libffindex0 (= ${binary:Version}), ${shlibs:Depends}, ${misc:Depends}
-Description: simple index/database for huge amounts of small files
- FFindex is a very simple index/database for huge amounts of small files. The
- files are stored concatenated in one big data file, separated by '\0'. A
- second file contains a plain text index, giving name, offset and length of
- the small files. The lookup is currently done with a binary search on an
- array made from the index file.
- .
- This package provides the executables.
-
-Package: libffindex0
-Architecture: any
-Section: libs
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: simple index/database for huge amounts of small files
- FFindex is a very simple index/database for huge amounts of small files. The
- files are stored concatenated in one big data file, separated by '\0'. A
- second file contains a plain text index, giving name, offset and length of
- the small files. The lookup is currently done with a binary search on an
- array made from the index file.
- .
- This package provides the shared library.
-
-Package: libffindex0-dev
-Architecture: any
-Section: libdevel
-Depends: libffindex0 (= ${binary:Version}), ${misc:Depends}
-Provides: libffindex-dev
-Description: simple index/database for huge amounts of small files
- FFindex is a very simple index/database for huge amounts of small files. The
- files are stored concatenated in one big data file, separated by '\0'. A
- second file contains a plain text index, giving name, offset and length of
- the small files. The lookup is currently done with a binary search on an
- array made from the index file.
- .
- This package contains the header files and documentation
- needed to develop applications with libffindex.
-
-Package: libffindex0-dbg
-Architecture: any
-Section: debug
-Depends: libffindex0 (= ${binary:Version}), ${misc:Depends}
-Description: simple index/database for huge amounts of small files
- FFindex is a very simple index/database for huge amounts of small files. The
- files are stored concatenated in one big data file, separated by '\0'. A
- second file contains a plain text index, giving name, offset and length of
- the small files. The lookup is currently done with a binary search on an
- array made from the index file.
- .
- This package provides the detached debug symbols for libffindex.
Deleted: trunk/packages/hhsuite/trunk/debian/ffindex.changelog
===================================================================
--- trunk/packages/hhsuite/trunk/debian/ffindex.changelog 2012-02-24 16:35:39 UTC (rev 9778)
+++ trunk/packages/hhsuite/trunk/debian/ffindex.changelog 2012-02-24 16:45:08 UTC (rev 9779)
@@ -1,6 +0,0 @@
-hhsuite (0.9.2-1) UNRELEASED; urgency=low
-
- * Initial release of ffindex and libffindex as part of hhsuite.
-
- -- Laszlo Kajan <lkajan at rostlab.org> Thu, 23 Feb 2012 10:42:07 +0100
-
Deleted: trunk/packages/hhsuite/trunk/debian/ffindex.docs
===================================================================
--- trunk/packages/hhsuite/trunk/debian/ffindex.docs 2012-02-24 16:35:39 UTC (rev 9778)
+++ trunk/packages/hhsuite/trunk/debian/ffindex.docs 2012-02-24 16:45:08 UTC (rev 9779)
@@ -1 +0,0 @@
-lib/ffindex/README
Deleted: trunk/packages/hhsuite/trunk/debian/ffindex.install
===================================================================
--- trunk/packages/hhsuite/trunk/debian/ffindex.install 2012-02-24 16:35:39 UTC (rev 9778)
+++ trunk/packages/hhsuite/trunk/debian/ffindex.install 2012-02-24 16:45:08 UTC (rev 9779)
@@ -1 +0,0 @@
-usr/bin/ff*
Deleted: trunk/packages/hhsuite/trunk/debian/ffindex.manpages
===================================================================
--- trunk/packages/hhsuite/trunk/debian/ffindex.manpages 2012-02-24 16:35:39 UTC (rev 9778)
+++ trunk/packages/hhsuite/trunk/debian/ffindex.manpages 2012-02-24 16:45:08 UTC (rev 9779)
@@ -1,3 +0,0 @@
-ffindex_build.1
-ffindex_get.1
-ffindex_modify.1
Added: trunk/packages/hhsuite/trunk/debian/hhsuite-data.install
===================================================================
--- trunk/packages/hhsuite/trunk/debian/hhsuite-data.install (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/hhsuite-data.install 2012-02-24 16:45:08 UTC (rev 9779)
@@ -0,0 +1,2 @@
+usr/share/hhsuite/data
+usr/share/hhsuite/scripts
Added: trunk/packages/hhsuite/trunk/debian/hhsuite-data.links
===================================================================
--- trunk/packages/hhsuite/trunk/debian/hhsuite-data.links (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/hhsuite-data.links 2012-02-24 16:45:08 UTC (rev 9779)
@@ -0,0 +1,3 @@
+usr/share/hhsuite/scripts usr/lib/hhsuite/scripts
+usr/share/hhsuite/data/context_data.lib usr/lib/hhsuite/data/context_data.lib
+usr/share/hhsuite/data/cs219.lib usr/lib/hhsuite/data/cs219.lib
Added: trunk/packages/hhsuite/trunk/debian/hhsuite.examples
===================================================================
--- trunk/packages/hhsuite/trunk/debian/hhsuite.examples (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/hhsuite.examples 2012-02-24 16:45:08 UTC (rev 9779)
@@ -0,0 +1 @@
+data/query.*
Modified: trunk/packages/hhsuite/trunk/debian/hhsuite.install
===================================================================
--- trunk/packages/hhsuite/trunk/debian/hhsuite.install 2012-02-24 16:35:39 UTC (rev 9778)
+++ trunk/packages/hhsuite/trunk/debian/hhsuite.install 2012-02-24 16:45:08 UTC (rev 9779)
@@ -1,4 +1,3 @@
usr/bin/hh*
usr/lib/hhsuite/bin
usr/lib/hhsuite/data
-usr/lib/hhsuite/scripts
Added: trunk/packages/hhsuite/trunk/debian/hhsuite.links
===================================================================
--- trunk/packages/hhsuite/trunk/debian/hhsuite.links (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/hhsuite.links 2012-02-24 16:45:08 UTC (rev 9779)
@@ -0,0 +1 @@
+/usr/lib/hhsuite usr/lib/hh
Deleted: trunk/packages/hhsuite/trunk/debian/libffindex0-dbg.changelog
===================================================================
--- trunk/packages/hhsuite/trunk/debian/libffindex0-dbg.changelog 2012-02-24 16:35:39 UTC (rev 9778)
+++ trunk/packages/hhsuite/trunk/debian/libffindex0-dbg.changelog 2012-02-24 16:45:08 UTC (rev 9779)
@@ -1 +0,0 @@
-link ffindex.changelog
\ No newline at end of file
Deleted: trunk/packages/hhsuite/trunk/debian/libffindex0-dev.changelog
===================================================================
--- trunk/packages/hhsuite/trunk/debian/libffindex0-dev.changelog 2012-02-24 16:35:39 UTC (rev 9778)
+++ trunk/packages/hhsuite/trunk/debian/libffindex0-dev.changelog 2012-02-24 16:45:08 UTC (rev 9779)
@@ -1 +0,0 @@
-link ffindex.changelog
\ No newline at end of file
Deleted: trunk/packages/hhsuite/trunk/debian/libffindex0-dev.install
===================================================================
--- trunk/packages/hhsuite/trunk/debian/libffindex0-dev.install 2012-02-24 16:35:39 UTC (rev 9778)
+++ trunk/packages/hhsuite/trunk/debian/libffindex0-dev.install 2012-02-24 16:45:08 UTC (rev 9779)
@@ -1,3 +0,0 @@
-usr/include/*
-usr/lib/libffindex.a
-usr/lib/libffindex.so
Deleted: trunk/packages/hhsuite/trunk/debian/libffindex0.changelog
===================================================================
--- trunk/packages/hhsuite/trunk/debian/libffindex0.changelog 2012-02-24 16:35:39 UTC (rev 9778)
+++ trunk/packages/hhsuite/trunk/debian/libffindex0.changelog 2012-02-24 16:45:08 UTC (rev 9779)
@@ -1 +0,0 @@
-link ffindex.changelog
\ No newline at end of file
Deleted: trunk/packages/hhsuite/trunk/debian/libffindex0.install
===================================================================
--- trunk/packages/hhsuite/trunk/debian/libffindex0.install 2012-02-24 16:35:39 UTC (rev 9778)
+++ trunk/packages/hhsuite/trunk/debian/libffindex0.install 2012-02-24 16:45:08 UTC (rev 9779)
@@ -1 +0,0 @@
-usr/lib/libffindex.so.*
Modified: trunk/packages/hhsuite/trunk/debian/patches/Makefile
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/Makefile 2012-02-24 16:35:39 UTC (rev 9778)
+++ trunk/packages/hhsuite/trunk/debian/patches/Makefile 2012-02-24 16:45:08 UTC (rev 9779)
@@ -2,38 +2,42 @@
* use $(MAKE) -C for making in subdirectories
* fix install mode of data files
* deinstall -> uninstall
-Index: hhsuite-2.0.12/Makefile
-===================================================================
---- hhsuite-2.0.12.orig/Makefile 2012-02-17 13:52:02.000000000 +0100
-+++ hhsuite-2.0.12/Makefile 2012-02-22 13:37:06.000000000 +0100
+* fix issues where the path in help pages is taken from the build-time location of the executables
+--- a/Makefile
++++ b/Makefile
@@ -1,5 +1,5 @@
- # This can be overridden e.g.: make install INSTALL_DIR=...
+-# This can be overridden e.g.: make install INSTALL_DIR=...
-INSTALL_DIR?=$(PWD)
-+INSTALL_DIR:=$(DESTDIR)/usr
++# This can be overridden e.g.: make install PREFIX=...
++PREFIX:=/usr
# Guess wether to use lib or lib64
#libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`
-@@ -8,36 +8,38 @@
+@@ -8,84 +8,83 @@
# Overriding this is currently not fully supported as the code won't know
# to what this is set then. You can try setting HHLIB.
-INSTALL_LIB_DIR?=$(INSTALL_DIR)/$(libdir)/hh
-+INSTALL_LIB_DIR?=$(INSTALL_DIR)/$(libdir)/hhsuite
- INSTALL_SCRIPTS_DIR?=$(INSTALL_LIB_DIR)/scripts
- INSTALL_DATA_DIR?=$(INSTALL_LIB_DIR)/data
+-INSTALL_SCRIPTS_DIR?=$(INSTALL_LIB_DIR)/scripts
+-INSTALL_DATA_DIR?=$(INSTALL_LIB_DIR)/data
++INSTALL_LIB_DIR?=$(PREFIX)/$(libdir)/hhsuite
++INSTALL_SCRIPTS_DIR?=$(PREFIX)/share/hhsuite/scripts
++INSTALL_DATA_DIR?=$(PREFIX)/share/hhsuite/data
++INSTALL_BDATA_DIR?=$(INSTALL_LIB_DIR)/data
INSTALL_LIB_BIN_DIR?=$(INSTALL_LIB_DIR)/bin
dist_name=hhsuite-2.0.12
-all_static: ffindex_static
- cd src && make all_static
--
+.PHONY: all
- all: ffindex
++all:
++ $(MAKE) -C data all
++ $(MAKE) -C src all
+
+-all: ffindex
- cd src && make all
-+ $(MAKE) -C src all
-+
-+all_static: ffindex_static
++all_static:
+ $(MAKE) -C src all_static
doc:
@@ -44,61 +48,96 @@
- cd src && make hhblits_static
+ $(MAKE) -C src hhblits_static
- hhblits: ffindex
+-hhblits: ffindex
- cd src && make all
++hhblits:
+ $(MAKE) -C src all
-+.PHONY: ffindex
- ffindex:
+-ffindex:
- cd lib/ffindex && make
-+ $(MAKE) -C lib/ffindex
-
- ffindex_static:
+-
+-ffindex_static:
- cd lib/ffindex && make FFINDEX_STATIC=1
-+ $(MAKE) -C lib/ffindex FFINDEX_STATIC=1
-
+-
install:
- cd lib/ffindex && make install INSTALL_DIR=$(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
-@@ -49,15 +51,15 @@
- mkdir -p $(INSTALL_LIB_BIN_DIR)
- install src/cstranslate $(INSTALL_LIB_BIN_DIR)/cstranslate
- mkdir -p $(INSTALL_DATA_DIR)
+- mkdir -p $(INSTALL_DIR)/bin
+- install src/hhblits $(INSTALL_DIR)/bin/hhblits
+- install src/hhalign $(INSTALL_DIR)/bin/hhalign
+- install src/hhconsensus $(INSTALL_DIR)/bin/hhconsensus
+- install src/hhfilter $(INSTALL_DIR)/bin/hhfilter
+- install src/hhmake $(INSTALL_DIR)/bin/hhmake
+- install src/hhsearch $(INSTALL_DIR)/bin/hhsearch
+- mkdir -p $(INSTALL_LIB_DIR)
+- 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 --mode=0644 data/context_data.lib $(INSTALL_DATA_DIR)/context_data.lib
-+ install --mode=0644 data/cs219.lib $(INSTALL_DATA_DIR)/cs219.lib
-+ install --mode=0644 data/do_not_delete $(INSTALL_DATA_DIR)/do_not_delete
-+ install --mode=0644 data/do_not_delete.phr $(INSTALL_DATA_DIR)/do_not_delete.phr
-+ install --mode=0644 data/do_not_delete.pin $(INSTALL_DATA_DIR)/do_not_delete.pin
-+ install --mode=0644 data/do_not_delete.psq $(INSTALL_DATA_DIR)/do_not_delete.psq
- mkdir -p $(INSTALL_SCRIPTS_DIR)
+- mkdir -p $(INSTALL_SCRIPTS_DIR)
- install scripts/Align.pm $(INSTALL_SCRIPTS_DIR)/Align.pm
- install scripts/HHPaths.pm $(INSTALL_SCRIPTS_DIR)/HHPaths.pm
-+ install --mode=0644 scripts/Align.pm $(INSTALL_SCRIPTS_DIR)/Align.pm
-+ install --mode=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
-@@ -66,8 +68,8 @@
- install scripts/multithread.pl $(INSTALL_SCRIPTS_DIR)/multithread.pl
- install scripts/hhblitsdb.pl $(INSTALL_SCRIPTS_DIR)/hhblitsdb.pl
-
+- 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/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
++ install src/hhconsensus $(DESTDIR)$(PREFIX)/bin/hhconsensus
++ install src/hhfilter $(DESTDIR)$(PREFIX)/bin/hhfilter
++ install src/hhmake $(DESTDIR)$(PREFIX)/bin/hhmake
++ install src/hhsearch $(DESTDIR)$(PREFIX)/bin/hhsearch
++ mkdir -p $(DESTDIR)$(INSTALL_LIB_DIR)
++ mkdir -p $(DESTDIR)$(INSTALL_LIB_BIN_DIR)
++ install src/cstranslate $(DESTDIR)$(INSTALL_LIB_BIN_DIR)/cstranslate
++ mkdir -p $(DESTDIR)$(INSTALL_DATA_DIR) $(DESTDIR)$(INSTALL_BDATA_DIR)
++ install --mode=0644 data/context_data.lib $(DESTDIR)$(INSTALL_DATA_DIR)/context_data.lib
++ install --mode=0644 data/cs219.lib $(DESTDIR)$(INSTALL_DATA_DIR)/cs219.lib
++ install --mode=0644 data/do_not_delete $(DESTDIR)$(INSTALL_BDATA_DIR)/do_not_delete
++ install --mode=0644 data/do_not_delete.phr $(DESTDIR)$(INSTALL_BDATA_DIR)/do_not_delete.phr
++ install --mode=0644 data/do_not_delete.pin $(DESTDIR)$(INSTALL_BDATA_DIR)/do_not_delete.pin
++ install --mode=0644 data/do_not_delete.psq $(DESTDIR)$(INSTALL_BDATA_DIR)/do_not_delete.psq
++ mkdir -p $(DESTDIR)$(INSTALL_SCRIPTS_DIR)
++ install --mode=0644 scripts/Align.pm $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/Align.pm
++ install --mode=0644 scripts/HHPaths.pm $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/HHPaths.pm
++ install scripts/addss.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/addss.pl
++ install scripts/create_profile_from_hhm.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/create_profile_from_hhm.pl
++ 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/multithread.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/multithread.pl
++ install scripts/hhblitsdb.pl $(DESTDIR)$(INSTALL_SCRIPTS_DIR)/hhblitsdb.pl
++
+uninstall:
-+ $(MAKE) -C lib/ffindex deinstall INSTALL_DIR=$(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 \
-@@ -83,9 +85,10 @@
++ 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
@@ -106,28 +145,44 @@
clean:
- cd lib/ffindex && make clean
- cd src && make clean
-+ $(MAKE) -C lib/ffindex clean
+ $(MAKE) -C src clean
++
++.PHONY: distclean
++distclean: clean
dist/$(dist_name).tar.gz:
make clean
-Index: hhsuite-2.0.12/scripts/HHPaths.pm
-===================================================================
---- hhsuite-2.0.12.orig/scripts/HHPaths.pm 2012-02-17 13:52:02.000000000 +0100
-+++ hhsuite-2.0.12/scripts/HHPaths.pm 2012-02-22 14:15:28.118982064 +0100
-@@ -38,7 +38,7 @@
+--- a/scripts/HHPaths.pm
++++ b/scripts/HHPaths.pm
+@@ -14,7 +14,7 @@
+ use Exporter;
+ our $VERSION = "version 2.0.12 (Feb 2012)";
+ our @ISA = qw(Exporter);
+-our @EXPORT = qw($VERSION $hhlib $hhdata $hhbin $hhscripts $execdir $datadir $ncbidir $dummydb $pdbdir $dsspdir $dssp $cs_lib $context_lib);
++our @EXPORT = qw($VERSION $hhlib $hhshare $hhdata $hhbdata $hhbin $hhscripts $execdir $datadir $ncbidir $dummydb $pdbdir $dsspdir $dssp $cs_lib $context_lib);
+
+ ##############################################################################################
+ # PLEASE COMPLETE THE PATHS ... TO PSIPRED AND OLD-STYLE BLAST (NOT BLAST+) (NEEDED FOR PSIPRED)
+@@ -38,11 +38,13 @@
# The lines below probably do not need to be changed
# Setting paths for hh-suite perl scripts
-our $hhlib = $ENV{"HHLIB"}; # main hh-suite directory
-+our $hhlib = "/usr/lib/hhsuite"; # main hh-suite directory
- our $hhdata = $hhlib."/data"; # path to data directory for hhblits, example files
+-our $hhdata = $hhlib."/data"; # path to data directory for hhblits, example files
++our $hhlib = $ENV{"HHLIB"} || "/usr/lib/hhsuite"; # main hh-suite directory
++our $hhshare = $ENV{"HHLIB"} || "/usr/share/hhsuite"; # main hh-suite directory
++our $hhdata = $hhshare."/data"; # path to arch indep data directory for hhblits, example files
++our $hhbdata = $hhlib."/data"; # path to arch dep data directory for hhblits, example files
our $hhbin = $hhlib."/bin"; # path to cstranslate (path to hhsearch, hhblits etc. should be in $PATH)
- our $hhscripts= $hhlib."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.)
-Index: hhsuite-2.0.12/src/hhdecl.C
-===================================================================
---- hhsuite-2.0.12.orig/src/hhdecl.C 2012-02-17 13:52:02.000000000 +0100
-+++ hhsuite-2.0.12/src/hhdecl.C 2012-02-22 13:37:06.000000000 +0100
+-our $hhscripts= $hhlib."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.)
+-our $dummydb = $hhdata."/do_not_delete"; # Name of dummy blast db for PSIPRED (single sequence formatted with NCBI formatdb)
++our $hhscripts= $hhshare."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.)
++our $dummydb = $hhbdata."/do_not_delete"; # Name of dummy blast db for PSIPRED (single sequence formatted with NCBI formatdb)
+
+ # HHblits data files
+ our $cs_lib = "$hhdata/cs219.lib";
+--- a/src/hhdecl.C
++++ b/src/hhdecl.C
@@ -278,7 +278,7 @@
if(getenv("HHLIB"))
strcpy(hhlib, getenv("HHLIB"));
@@ -155,93 +210,159 @@
exit(2);
}
-Index: hhsuite-2.0.12/lib/ffindex/Makefile
-===================================================================
---- hhsuite-2.0.12.orig/lib/ffindex/Makefile 2012-01-19 14:06:31.000000000 +0100
-+++ hhsuite-2.0.12/lib/ffindex/Makefile 2012-02-22 13:37:06.000000000 +0100
-@@ -7,13 +7,7 @@
- endif
+--- a/src/hhblits.C
++++ b/src/hhblits.C
+@@ -295,8 +295,8 @@
+ printf(" -M [0,100] use FASTA: columns with fewer than X%% gaps are match states \n");
+ if (all) {
+ printf("Directory paths \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");
+@@ -407,7 +407,12 @@
+ printf("An extended list of options can be obtained by using '-help all' as parameter \n");
+ }
+ printf("\n");
+- printf("Example: %s -i query.fas -oa3m query.a3m -n 2 \n",program_name);
++ printf("Examples:\n");
++ printf("%s -i query.fas -o query.hhr -d <database-basepath>\n",program_name);
++ printf("\n");
++ printf("%s -i query.fas -o query.hhr -oa3m query.a3m -n 2 -d <database-basepath>\n",program_name);
++ printf("\n");
++ printf("Download databases from ftp://toolkit.genzentrum.lmu.de/HH-suite/databases/hhblits/.\n");
+ cout<<endl;
+ }
- all:
-- cd src ; make -f $(MFILE)
-+ $(MAKE) -C src $@
+--- a/src/hhsearch.C
++++ b/src/hhsearch.C
+@@ -326,7 +326,7 @@
+ 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);
+ }
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -14,13 +14,13 @@
--install:
-- cd src ; make install
--
--deinstall:
-- cd src ; make deinstall
--
--clean:
-- cd src ; make clean
-+%:
-+ $(MAKE) -C src $@
-Index: hhsuite-2.0.12/lib/ffindex/src/Makefile
-===================================================================
---- hhsuite-2.0.12.orig/lib/ffindex/src/Makefile 2012-01-19 14:06:31.000000000 +0100
-+++ hhsuite-2.0.12/lib/ffindex/src/Makefile 2012-02-22 13:37:06.000000000 +0100
-@@ -1,12 +1,14 @@
- INSTALL_DIR?=..
--libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`
-+libdir=lib
- LANG=C
- CFLAGS+=-std=c99 -openmp -g -fPIC -Wall
-+SOCURRENT=0
-+SOVERSION=$(SOCURRENT).1.0
- ifdef FFINDEX_STATIC
- LDFLAGS+=-static
- FFINDEX_OBJECTS=libffindex.a
- else
-- FFINDEX_OBJECTS=libffindex.so libffindex.so.0.1
-+ FFINDEX_OBJECTS=libffindex.so libffindex.so.$(SOVERSION)
- endif
+ ifdef ICC
+ CXX = env LANG=C icc
+- CXXFLAGS = -fast -Wall -fno-strict-aliasing -finline-functions -funroll-loops -fp-model fast=2 -fast-transcendentals -wd981 -wd383 -wd2259 -wd1572 -D HH_SSE3 -I$(CS_DIR) -I$(FFINDEX_DIR)
++ CXXFLAGS = -fast -Wall -fno-strict-aliasing -finline-functions -funroll-loops -fp-model fast=2 -fast-transcendentals -wd981 -wd383 -wd2259 -wd1572 -D HH_SSE3 -I$(CS_DIR)
+ HHSEARCH_LIBS = -lpthread -lrt
+ HHBLITS_LIBS = -lpthread -lrt -openmp
+ OBJECT_LIBS = -openmp
+ else # ifndef ICC
+ CXX = g++
+- CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG) -I$(FFINDEX_DIR)
++ CXXFLAGS = -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -I$(CS_DIR) $(BITS_FLAG)
+ HHSEARCH_LIBS = -lpthread
+ HHBLITS_LIBS = -lpthread -fopenmp
+ HHALIGN_LIBS =
+@@ -92,7 +92,7 @@
+ $(CPP_VALGRIND) hhsearch.C -o hhsearch_valgrind $(CS_OBJECTS) $(HHSEARCH_LIBS)
- #-Wl,--version-script=libffindex.map
-@@ -24,11 +26,12 @@
- ffindex_modify: $(FFINDEX_OBJECTS) ffindex_modify.o ffindex.h
- $(CC) -o $@ ffindex_modify.o $(LDFLAGS) -L. -lffindex
+ hhblits: hhblits.C $(SOURCES) $(HEADERS) $(CS_OBJECTS)
+- $(CPP) hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a
++ $(CPP) hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) -lffindex
--libffindex.so.0.1: ffindex.o ffutil.o
-- $(CC) -Wl,-z,defs -shared -Wl,-soname,libffindex.so.0.1 -o libffindex.so.0.1 ffindex.o ffutil.o -lc
-+libffindex.so.$(SOVERSION): ffindex.o ffutil.o
-+ $(CC) -Wl,-z,defs,-z,noexecstack -shared -Wl,-soname,libffindex.so.$(SOCURRENT) -o libffindex.so.$(SOVERSION) ffindex.o ffutil.o -lc
+ hhblits_static: hhblits.C $(SOURCES) $(HEADERS)$(CS_OBJECTS)
+ $(CPP) -static hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a
+--- a/scripts/addss.pl
++++ b/scripts/addss.pl
+@@ -28,7 +28,7 @@
--libffindex.so: libffindex.so.0.1
-- ln -sf libffindex.so.0.1 libffindex.so
-+libffindex.so: libffindex.so.$(SOVERSION)
-+ ln -sf libffindex.so.$(SOVERSION) libffindex.so.$(SOCURRENT)
-+ ln -sf libffindex.so.$(SOVERSION) libffindex.so
+ # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
- libffindex.a: ffindex.o ffutil.o
- ar rcs libffindex.a ffutil.o ffindex.o
-@@ -53,7 +56,7 @@
- LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" zsh -c "time ./ffindex_get ../test_big/nr20_11Jan10_a3m_db ../test_big/nr20_11Jan10_a3m_db.ffindex BABBAMIBA.a3m KARDUZEBA.a3m HARPAQIBA.a3m WOQQATEBA.a3m BEBRAQIBA.a3m GIRSAKEBA.a3m NAQTIFIBA.a3m BIWCIQABA.a3m > /dev/null"
+-use lib $ENV{"HHLIB"}."/scripts";
++use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
+ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+ use Align; # Needleman-Wunsch and Smith-Waterman alignment functions
+ use File::Temp qw/ tempfile tempdir /;
+--- a/scripts/hhblitsdb.pl
++++ b/scripts/hhblitsdb.pl
+@@ -28,7 +28,7 @@
- clean:
-- rm -f ffindex.o ffutil.o ffindex_build ffindex_build.o ffindex_get ffindex_get.o libffindex.so libffindex.so.0.1 ffindex_modify ffindex_modify.o libffindex.a
-+ rm -f ffindex.o ffutil.o ffindex_build ffindex_build.o ffindex_get ffindex_get.o libffindex.so libffindex.so.$(SOCURRENT) libffindex.so.$(SOVERSION) ffindex_modify ffindex_modify.o libffindex.a
+ # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
- install:
- mkdir -p $(INSTALL_DIR)/bin
-@@ -62,16 +65,17 @@
- install ffindex_get $(INSTALL_DIR)/bin/ffindex_get
- install ffindex_build $(INSTALL_DIR)/bin/ffindex_build
- install ffindex_modify $(INSTALL_DIR)/bin/ffindex_modify
-- install libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.so.0.1
-+ install libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOVERSION)
- install libffindex.a $(INSTALL_DIR)/$(libdir)/libffindex.a
-- ln -sf libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.so
-+ ln -sf libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOCURRENT)
-+ ln -sf libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so
- install ffindex.h $(INSTALL_DIR)/include/ffindex.h
- install ffutil.h $(INSTALL_DIR)/include/ffutil.h
+-use lib $ENV{"HHLIB"}."/scripts";
++use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
+ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+ use strict;
- deinstall:
- rm -f $(INSTALL_DIR)/bin/ffindex_get $(INSTALL_DIR)/bin/ffindex_build $(INSTALL_DIR)/bin/ffindex_modify \
-- $(INSTALL_DIR)/$(libdir)/libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.a \
-- $(INSTALL_DIR)/$(libdir)/libffindex.so $(INSTALL_DIR)/include/ffindex.h $(INSTALL_DIR)/include/ffutil.h
-+ $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.a \
-+ $(INSTALL_DIR)/$(libdir)/libffindex.so $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOCURRENT) $(INSTALL_DIR)/include/ffindex.h $(INSTALL_DIR)/include/ffutil.h
- rmdir $(INSTALL_DIR)/bin || true
- rmdir $(INSTALL_DIR)/$(libdir) || true
- rmdir $(INSTALL_DIR)/include || true
+--- a/scripts/hhmakemodel.pl
++++ b/scripts/hhmakemodel.pl
+@@ -28,7 +28,7 @@
+
+ # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
+
+-use lib $ENV{"HHLIB"}."/scripts";
++use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
+ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+ use strict;
+ use Align;
+--- /dev/null
++++ b/data/Makefile
+@@ -0,0 +1,11 @@
++#!/usr/bin/make -f
++
++DUMMYDB:=do_not_delete.phr do_not_delete.pin do_not_delete.psq
++
++all: $(DUMMYDB)
++
++%.phr %.pin %.psq : %
++ formatdb -i '$<' && rm -f formatdb.log
++
++clean:
++ rm -f $(DUMMYDB) formatdb.log
+--- a/scripts/create_profile_from_hhm.pl
++++ b/scripts/create_profile_from_hhm.pl
+@@ -27,7 +27,7 @@
+
+ # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
+
+-use lib $ENV{"HHLIB"}."/scripts";
++use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
+ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+ use strict;
+
+--- a/scripts/create_profile_from_hmmer.pl
++++ b/scripts/create_profile_from_hmmer.pl
+@@ -27,7 +27,7 @@
+
+ # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
+
+-use lib $ENV{"HHLIB"}."/scripts";
++use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
+ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+ use strict;
+
+--- a/scripts/multithread.pl
++++ b/scripts/multithread.pl
+@@ -29,7 +29,7 @@
+
+ # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
+
+-use lib $ENV{"HHLIB"}."/scripts";
++use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
+ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+ use strict;
+ use POSIX;
+--- a/scripts/reformat.pl
++++ b/scripts/reformat.pl
+@@ -27,7 +27,7 @@
+
+ # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
+
+-use lib $ENV{"HHLIB"}."/scripts";
++use lib ( $ENV{"HHLIB"} || '/usr/share/hhsuite' )."/scripts";
+ use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
+ use strict;
+ use warnings;
Deleted: trunk/packages/hhsuite/trunk/debian/patches/default_path
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/default_path 2012-02-24 16:35:39 UTC (rev 9778)
+++ trunk/packages/hhsuite/trunk/debian/patches/default_path 2012-02-24 16:45:08 UTC (rev 9779)
@@ -1,168 +0,0 @@
-* fix issues where the path in help pages is taken from the build-time location of the executables
-Index: hhsuite-2.0.12/lib/ffindex/src/ffindex_build.c
-===================================================================
---- hhsuite-2.0.12.orig/lib/ffindex/src/ffindex_build.c 2012-02-22 14:15:27.966982036 +0100
-+++ hhsuite-2.0.12/lib/ffindex/src/ffindex_build.c 2012-02-22 14:15:57.550982145 +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"
-@@ -39,7 +39,7 @@
- "\t\t-f can be specified up to %d times\n"
- "\t-s\tsort index file\n"
- "\t-v\tprint version and other info then exit\n"
-- "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n", program_name, MAX_FILENAME_LIST_FILES);
-+ "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n", MAX_FILENAME_LIST_FILES);
- }
-
- int main(int argn, char **argv)
-Index: hhsuite-2.0.12/lib/ffindex/src/ffindex_get.c
-===================================================================
---- hhsuite-2.0.12.orig/lib/ffindex/src/ffindex_get.c 2012-02-22 14:15:27.990982045 +0100
-+++ hhsuite-2.0.12/lib/ffindex/src/ffindex_get.c 2012-02-22 14:15:57.554982179 +0100
-@@ -26,9 +26,8 @@
- {
- if(argn < 3)
- {
-- fprintf(stderr, "USAGE: %s data_filename index_filename filename(s)\n"
-- "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n",
-- argv[0]);
-+ 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");
- return -1;
- }
- char *data_filename = argv[1];
-Index: hhsuite-2.0.12/lib/ffindex/src/ffindex_modify.c
-===================================================================
---- hhsuite-2.0.12.orig/lib/ffindex/src/ffindex_modify.c 2012-02-22 14:15:28.022982106 +0100
-+++ hhsuite-2.0.12/lib/ffindex/src/ffindex_modify.c 2012-02-22 14:15:57.562982390 +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"
-@@ -38,7 +38,7 @@
- "\t-u\tunlink entry (remove from index only)\n"
- "\t-v\tprint version and other info then exit\n"
- "\nDesigned and implemented by Andreas W. Hauser <hauser at genzentrum.lmu.de>.\n",
-- program_name, MAX_FILENAME_LIST_FILES);
-+ MAX_FILENAME_LIST_FILES);
- }
-
- int main(int argn, char **argv)
-Index: hhsuite-2.0.12/src/hhblits.C
-===================================================================
---- hhsuite-2.0.12.orig/src/hhblits.C 2012-02-22 14:15:28.046982074 +0100
-+++ hhsuite-2.0.12/src/hhblits.C 2012-02-22 14:15:57.578982148 +0100
-@@ -295,8 +295,8 @@
- printf(" -M [0,100] use FASTA: columns with fewer than X%% gaps are match states \n");
- if (all) {
- printf("Directory paths \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");
-@@ -407,7 +407,12 @@
- printf("An extended list of options can be obtained by using '-help all' as parameter \n");
- }
- printf("\n");
-- printf("Example: %s -i query.fas -oa3m query.a3m -n 2 \n",program_name);
-+ printf("Examples:\n");
-+ printf("%s -i query.fas -o query.hhr -d <database-basepath>\n",program_name);
-+ printf("\n");
-+ printf("%s -i query.fas -o query.hhr -oa3m query.a3m -n 2 -d <database-basepath>\n",program_name);
-+ printf("\n");
-+ printf("Download databases from ftp://toolkit.genzentrum.lmu.de/HH-suite/databases/hhblits/.\n");
- cout<<endl;
- }
-
-Index: hhsuite-2.0.12/src/hhsearch.C
-===================================================================
---- hhsuite-2.0.12.orig/src/hhsearch.C 2012-02-22 14:15:28.066982015 +0100
-+++ hhsuite-2.0.12/src/hhsearch.C 2012-02-22 14:15:57.586982154 +0100
-@@ -326,7 +326,7 @@
- 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);
- }
-Index: hhsuite-2.0.12/scripts/HHPaths.pm
-===================================================================
---- hhsuite-2.0.12.orig/scripts/HHPaths.pm 2012-02-22 14:15:28.118982064 +0100
-+++ hhsuite-2.0.12/scripts/HHPaths.pm 2012-02-22 14:15:57.590982410 +0100
-@@ -38,7 +38,7 @@
- # The lines below probably do not need to be changed
-
- # Setting paths for hh-suite perl scripts
--our $hhlib = "/usr/lib/hhsuite"; # main hh-suite directory
-+our $hhlib = $ENV{"HHLIB"} || "/usr/lib/hhsuite"; # main hh-suite directory
- our $hhdata = $hhlib."/data"; # path to data directory for hhblits, example files
- our $hhbin = $hhlib."/bin"; # path to cstranslate (path to hhsearch, hhblits etc. should be in $PATH)
- our $hhscripts= $hhlib."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.)
-Index: hhsuite-2.0.12/src/Makefile
-===================================================================
---- hhsuite-2.0.12.orig/src/Makefile 2012-02-22 14:15:50.830982145 +0100
-+++ hhsuite-2.0.12/src/Makefile 2012-02-22 14:15:57.602982363 +0100
-@@ -92,7 +92,7 @@
- $(CPP_VALGRIND) hhsearch.C -o hhsearch_valgrind $(CS_OBJECTS) $(HHSEARCH_LIBS)
-
- hhblits: hhblits.C $(SOURCES) $(HEADERS) $(CS_OBJECTS)
-- $(CPP) hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a
-+ $(CPP) hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) -lffindex -L$(FFINDEX_DIR)
-
- hhblits_static: hhblits.C $(SOURCES) $(HEADERS)$(CS_OBJECTS)
- $(CPP) -static hhblits.C -o hhblits $(CS_OBJECTS) $(HHBLITS_LIBS) $(FFINDEX_DIR)/libffindex.a
-Index: hhsuite-2.0.12/scripts/addss.pl
-===================================================================
---- hhsuite-2.0.12.orig/scripts/addss.pl 2012-02-22 14:15:28.138982026 +0100
-+++ hhsuite-2.0.12/scripts/addss.pl 2012-02-22 14:15:57.606982395 +0100
-@@ -28,7 +28,7 @@
-
- # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
-
--use lib $ENV{"HHLIB"}."/scripts";
-+use lib ( $ENV{"HHLIB"} || '/usr/lib/hhsuite' )."/scripts";
- use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
- use Align; # Needleman-Wunsch and Smith-Waterman alignment functions
- use File::Temp qw/ tempfile tempdir /;
-Index: hhsuite-2.0.12/scripts/hhblitsdb.pl
-===================================================================
---- hhsuite-2.0.12.orig/scripts/hhblitsdb.pl 2012-02-22 14:15:28.162982056 +0100
-+++ hhsuite-2.0.12/scripts/hhblitsdb.pl 2012-02-22 14:15:57.618982227 +0100
-@@ -28,7 +28,7 @@
-
- # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
-
--use lib $ENV{"HHLIB"}."/scripts";
-+use lib ( $ENV{"HHLIB"} || '/usr/lib/hhsuite' )."/scripts";
- use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
- use strict;
-
-Index: hhsuite-2.0.12/scripts/hhmakemodel.pl
-===================================================================
---- hhsuite-2.0.12.orig/scripts/hhmakemodel.pl 2012-02-22 14:15:28.190982103 +0100
-+++ hhsuite-2.0.12/scripts/hhmakemodel.pl 2012-02-22 14:15:57.626982140 +0100
-@@ -28,7 +28,7 @@
-
- # We are very grateful for bug reports! Please contact us at soeding at genzentrum.lmu.de
-
--use lib $ENV{"HHLIB"}."/scripts";
-+use lib ( $ENV{"HHLIB"} || '/usr/lib/hhsuite' )."/scripts";
- use HHPaths; # config file with path variables for nr, blast, psipred, pdb, dssp etc.
- use strict;
- use Align;
Modified: trunk/packages/hhsuite/trunk/debian/patches/series
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/series 2012-02-24 16:35:39 UTC (rev 9778)
+++ trunk/packages/hhsuite/trunk/debian/patches/series 2012-02-24 16:45:08 UTC (rev 9779)
@@ -1,2 +1 @@
Makefile
-default_path
Modified: trunk/packages/hhsuite/trunk/debian/rules
===================================================================
--- trunk/packages/hhsuite/trunk/debian/rules 2012-02-24 16:35:39 UTC (rev 9778)
+++ trunk/packages/hhsuite/trunk/debian/rules 2012-02-24 16:45:08 UTC (rev 9779)
@@ -3,42 +3,37 @@
# Uncomment this to turn on verbose mode.
export DH_VERBOSE=1
-VERSION=2.0.5
-
%:
dh $@ --parallel
+VERSION=$(shell awk '/VERSION_AND_DATE/{ match($$0, "version ([0-9][0-9.]*)", a); print a[1]; }' ./src/hhdecl.C)
+
.PHONY: override_dh_strip
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: hhmanpages
+hhmanpages: $(HHMANPAGES)
+
+export n_hhalign=align a query alignment/HMM to a template alignment/HMM
+export n_hhblits=fast homology detection method to iteratively search a HMM database
+export n_hhconsensus=calculate the consensus sequence for an A3M/FASTA input file
+export n_hhfilter=filter an alignment by maximum sequence identity of match states and minimum coverage
+export n_hhmake=build an HMM from an input alignment or convert between HMMER format and HHsearch format
+export n_hhsearch=search a database of HMMs with a query alignment or query HMM
+
.PHONY: override_dh_installman
-override_dh_installman: $(FFMANPAGES) $(HHMANPAGES)
+override_dh_installman: $(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 '$@'
-
$(HHMANPAGES): %.1 : debian/tmp/usr/bin/%
- unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=debian/tmp/usr/lib/hhsuite && eval '$(BINNAMES)' && help2man --no-info '--help-option=-h all' -n "$$$*" --version-string=$(VERSION) '$<' -o '$@'
+ unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=debian/tmp/usr/share/hhsuite && help2man --no-info --help-option '-h all' --version-string $(VERSION) -n "$$n_$*" '$<' -o '$@'
.PHONY: override_dh_clean
override_dh_clean:
- rm -f $(FFMANPAGES) $(HHMANPAGES)
+ rm -f $(HHMANPAGES)
dh_clean
get-orig-source:
More information about the debian-med-commit
mailing list