Author: moeller Date: 2013-07-26 01:28:39 +0000 (Fri, 26 Jul 2013) New Revision: 14244
Added: trunk/packages/kclust/trunk/debian/ trunk/packages/kclust/trunk/debian/README.Debian trunk/packages/kclust/trunk/debian/compat trunk/packages/kclust/trunk/debian/control trunk/packages/kclust/trunk/debian/copyright trunk/packages/kclust/trunk/debian/docs trunk/packages/kclust/trunk/debian/kClust.1 trunk/packages/kclust/trunk/debian/kDP.1 trunk/packages/kclust/trunk/debian/kclust.install trunk/packages/kclust/trunk/debian/manpages trunk/packages/kclust/trunk/debian/patches/ trunk/packages/kclust/trunk/debian/patches/accept_dash_dash_help.patch trunk/packages/kclust/trunk/debian/patches/no_intel_compiler_by_default.patch trunk/packages/kclust/trunk/debian/patches/series trunk/packages/kclust/trunk/debian/patches/test_seeks_custom.h trunk/packages/kclust/trunk/debian/patches/variable_visibility.patch trunk/packages/kclust/trunk/debian/rules trunk/packages/kclust/trunk/debian/source/ trunk/packages/kclust/trunk/debian/source/format Log: Interim upload of packaging instructions for kclust. manpages, copyright, ... much left to do. Added: trunk/packages/kclust/trunk/debian/README.Debian =================================================================== --- trunk/packages/kclust/trunk/debian/README.Debian (rev 0) +++ trunk/packages/kclust/trunk/debian/README.Debian 2013-07-26 01:28:39 UTC (rev 14244) @@ -0,0 +1,6 @@ +kclust for Debian +----------------- + +<possible notes regarding this package - if none, delete this file> + + -- Steffen Moeller <[email protected]> Thu, 25 Jul 2013 16:47:34 +0200 Added: trunk/packages/kclust/trunk/debian/compat =================================================================== --- trunk/packages/kclust/trunk/debian/compat (rev 0) +++ trunk/packages/kclust/trunk/debian/compat 2013-07-26 01:28:39 UTC (rev 14244) @@ -0,0 +1 @@ +8 Added: trunk/packages/kclust/trunk/debian/control =================================================================== --- trunk/packages/kclust/trunk/debian/control (rev 0) +++ trunk/packages/kclust/trunk/debian/control 2013-07-26 01:28:39 UTC (rev 14244) @@ -0,0 +1,24 @@ +Source: kclust +Section: unknown +Priority: extra +Maintainer: Steffen Moeller <[email protected]> +Build-Depends: debhelper (>= 8.0.0), libboost-regex-dev +Standards-Version: 3.9.4 +Homepage: ftp://toolkit.genzentrum.lmu.de/pub/kClust/ +#Vcs-Git: git://git.debian.org/collab-maint/kclust.git +#Vcs-Browser: http://git.debian.org/?p=collab-maint/kclust.git;a=summary + +Package: kclust +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: clustering of protein sequences + kClust is a fast and sensitive clustering method for the clustering of + protein sequences. It is able to cluster large protein databases down + to 20-30% sequence identity. IT came to fame for its contribution to + HHpred and the HH-suite for HMM-HMM similarities for predicting protein + structures. + . + kClust generates a clustering where each cluster is represented by its + longest sequence (representative sequence). This may be taken as a seed + to construct HMMs for each cluster. + Added: trunk/packages/kclust/trunk/debian/copyright =================================================================== --- trunk/packages/kclust/trunk/debian/copyright (rev 0) +++ trunk/packages/kclust/trunk/debian/copyright 2013-07-26 01:28:39 UTC (rev 14244) @@ -0,0 +1,38 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: kclust +Source: <url://example.com> + +Files: * +Copyright: <years> <put author's name and email here> + <years> <likewise for another author> +License: <special license> + <Put the license of the package here indented by 1 space> + <This follows the format of Description: lines in control file> + . + <Including paragraphs> + +# If you want to use GPL v2 or later for the /debian/* files use +# the following clauses, or change it to suit. Delete these two lines +Files: debian/* +Copyright: 2013 Steffen Moeller <[email protected]> +License: GPL-2+ + This package is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + . + This package is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/> + . + On Debian systems, the complete text of the GNU General + Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". + +# Please also look if there are files or directories which have a +# different copyright/license attached and list them here. +# Please avoid to pick license terms that are more restrictive than the +# packaged work, as it may make Debian's contributions unacceptable upstream. Added: trunk/packages/kclust/trunk/debian/docs =================================================================== --- trunk/packages/kclust/trunk/debian/docs (rev 0) +++ trunk/packages/kclust/trunk/debian/docs 2013-07-26 01:28:39 UTC (rev 14244) @@ -0,0 +1 @@ +README Added: trunk/packages/kclust/trunk/debian/kClust.1 =================================================================== --- trunk/packages/kclust/trunk/debian/kClust.1 (rev 0) +++ trunk/packages/kclust/trunk/debian/kClust.1 2013-07-26 01:28:39 UTC (rev 14244) @@ -0,0 +1,83 @@ +.TH kClust: "1" "July 2013" +.SH NAME +kClust \- manual page for Usage: ./kClust -i [fasta-db-file] -d [directory] [options] +.SH SYNOPSIS +.B kClust +\fI-i \fR[\fIfasta-db-file\fR] \fI-d \fR[\fIdirectory\fR] [\fIoptions\fR] +.SH DESCRIPTION +Version 1.0 +.PP +kClust is a clustering program for protein sequences. +.SH OPTIONS +.SS "Required arguments:" +.TP +\fB\-i\fR +[fasta\-db\-file] : Sequence database in fasta format or directory with the output of the previous kClust run if \fB\-P\fR option is set. +.TP +\fB\-d\fR +[directory] : Directory for temporary and result files. +.SS "Optional arguments:" +.TP +\fB\-M\fR +[megabytes] : Memory limit for clustering (default=3500MB). +.TP +\fB\-P\fR +: Cluster profiles computed from existing alignment files (default=false). +.TP +\fB\-sc\fR +: Use sequence background frequency score correction for the k\-mer scores (default=false). +.TP +\fB\-td\fR +[directory] : Directory for temporary files (default=WORKING_DIR/tmp) +.TP +\fB\-s\fR +[float] : Clustering threshold (score per column) (default=1.12 half bits ~ 30% sequence identity). Set to zero for the clustering based only on the e\-value of the hit. +.TP +\fB\-e\fR +[float] : Clustering E\-value threshold (default=1.0e\-4). +.TP +\fB\-c\fR +[float] : Alignment coverage of the longer sequence (default=0.8). +.TP +\fB\-\-merge\-ncbi\-headers\fR +: Compress NCBI headers in representatives database, creating a merged header instead of the representative sequence header. +.TP +\fB\-\-merge\-uniprot\-headers\fR +: Compress Uniprot headers in representatives database, creating a merged header instead of the representative sequence header. +.TP +\fB\-\-write\-time\-benchmark\fR +: Write time benchmark files, containing sequences which consume the most computation time (default=false). +.SS "Expert arguments:" +.TP +\fB\-\-filter\-k\fR +[integer] : Length of k\-mers for similarity scoring filter (default=6). +.TP +\fB\-\-filter\-T\fR +[float] : Similarity threshold for filter k\-mer generation (default=4.3 half bits). +.TP +\fB\-\-filter\-t\fR +[float] : k\-mer score threshold for prefiltering (default=0.55 half bits). +.TP +\fB\-\-kdp\-k\fR +[integer] : Length of k\-mers for kDP alignments (default=4). +.TP +\fB\-\-kdp\-T\fR +[float] : Similarity threshold for kDP k\-mer generation (default=2.9 half bits). +.TP +\fB\-\-kdp\-G\fR +[float] : Gap open penalty (default=12.0 half bits). +.TP +\fB\-\-kdp\-E\fR +[float] : Gap extension penalty (default=2.0 half bits). +.TP +\fB\-\-kdp\-F\fR +[float] : Intra\-diagonal gap penalty (default=0.27 half bits). +.TP +\fB\-\-kdp\-delta\fR +[integer] : Width of delta window (default=50). +.PP +Sequence identity ~ score per column (see \fB\-s\fR option): +20% 30% 40% 50% 60% 70% 80% 90% 99% +0.52 1.12 1.73 2.33 2.93 3.53 4.14 4.74 5.28 +.SH AUTHOR +Written by Christian Mayer ([email protected]) and Maria Hauser ([email protected]) Added: trunk/packages/kclust/trunk/debian/kDP.1 =================================================================== --- trunk/packages/kclust/trunk/debian/kDP.1 (rev 0) +++ trunk/packages/kclust/trunk/debian/kDP.1 2013-07-26 01:28:39 UTC (rev 14244) @@ -0,0 +1,44 @@ +.TH kDP "1" "July 2013" +.SH NAME +kDP \- all\-against\-all protein sequence comparison +.SH SYNOPSIS +.B kDP +[\fIfasta-file-1\fR] [[\fIfasta-file-2\fR] [\fIoptions\fR]] +.SH DESCRIPTION +Version 1.0 +.PP +kDP is a program for all\-against\-all protein sequence comparison. +Optional arguments: +.TP +[fasta\-file\-2] +: Compare all sequences of [fasta\-file\-1] to all sequences of [fasta\-file\-2] +.TP +\fB\-T\fR +[float] : Threshold for similar k\-mers (default=2.9 half bits). +.TP +\fB\-c\fR +[float] : Coverage (default=disabled). +.TP +\fB\-D\fR +[int] : Width of delta\-window (default=50). +.TP +\fB\-p\fR +[float] : Probability for chance match (default=1e\-3). +.TP +\fB\-G\fR +[float] : Gap open penalty (default=12.0 half bits). +.TP +\fB\-E\fR +[float] : Gap extension penalty (default=2.0 half bits). +.TP +\fB\-F\fR +[float] : Gap penalty for intra\-diagonal distance (default=0.27 half bits). +.TP +\fB\-\-round\fR +: Round BLOSUM substitution scores to integers. +.TP +\fB\-\-scores\fR +: Print scores only. +.TP +\fB\-\-spaced\fR +: Use spaced k\-mers (XX0XX). Added: trunk/packages/kclust/trunk/debian/kclust.install =================================================================== --- trunk/packages/kclust/trunk/debian/kclust.install (rev 0) +++ trunk/packages/kclust/trunk/debian/kclust.install 2013-07-26 01:28:39 UTC (rev 14244) @@ -0,0 +1,4 @@ +kClust +kClust_benchmark +kClust_mkAln +kDP Added: trunk/packages/kclust/trunk/debian/manpages =================================================================== --- trunk/packages/kclust/trunk/debian/manpages (rev 0) +++ trunk/packages/kclust/trunk/debian/manpages 2013-07-26 01:28:39 UTC (rev 14244) @@ -0,0 +1,2 @@ +debian/kClust.1 +debian/kDP.1 Added: trunk/packages/kclust/trunk/debian/patches/accept_dash_dash_help.patch =================================================================== --- trunk/packages/kclust/trunk/debian/patches/accept_dash_dash_help.patch (rev 0) +++ trunk/packages/kclust/trunk/debian/patches/accept_dash_dash_help.patch 2013-07-26 01:28:39 UTC (rev 14244) @@ -0,0 +1,13 @@ +Index: kclust-0~20120309/kDP.cpp +=================================================================== +--- kclust-0~20120309.orig/kDP.cpp ++++ kclust-0~20120309/kDP.cpp +@@ -35,7 +35,7 @@ + + int main(int argc, const char **argv){ + +- if( argc<2 ){ ++ if( argc<3 ){ + usage(std::cerr); + return 1; + } Added: trunk/packages/kclust/trunk/debian/patches/no_intel_compiler_by_default.patch =================================================================== --- trunk/packages/kclust/trunk/debian/patches/no_intel_compiler_by_default.patch (rev 0) +++ trunk/packages/kclust/trunk/debian/patches/no_intel_compiler_by_default.patch 2013-07-26 01:28:39 UTC (rev 14244) @@ -0,0 +1,39 @@ +Index: kclust-0~20120309/Makefile +=================================================================== +--- kclust-0~20120309.orig/Makefile ++++ kclust-0~20120309/Makefile +@@ -4,16 +4,19 @@ + + MYSQLPPLIB = -lmysqlpp -I/usr/include/mysql++/ + +-CXX = icpc +-CXXFLAGS = -w0 -fast +-#CXX = g++ +-#CXXFLAGS = -O3 ++#CXX = icpc ++CXX = g++ ++ifeq (icpc,$(CXX)) ++CXXFLAGS += -w0 -fast ++else ++CXXFLAGS += -O3 ++endif + + ifdef OPENMP + CXXFLAGS += -DOPENMP=1 -openmp + endif + +-CPP = $(CXX) $(CXXFLAGS) ++CPP = $(CXX) $(CPPFLAGS) $(CXXFLAGS) + RANLIB = ranlib + OBJEXT = o + AR = ar +@@ -64,6 +67,9 @@ + + all: $(TARGETS) + ++.c.o: $< ++ $(CPP) -c $< ++ + libwnlib.a: $(WNLIB_OBJECTS) + -rm -f libwnlib.a + $(WNLIB_AR) libwnlib.a $(WNLIB_OBJECTS) Added: trunk/packages/kclust/trunk/debian/patches/series =================================================================== --- trunk/packages/kclust/trunk/debian/patches/series (rev 0) +++ trunk/packages/kclust/trunk/debian/patches/series 2013-07-26 01:28:39 UTC (rev 14244) @@ -0,0 +1,4 @@ +no_intel_compiler_by_default.patch +variable_visibility.patch +test_seeks_custom.h +accept_dash_dash_help.patch Added: trunk/packages/kclust/trunk/debian/patches/test_seeks_custom.h =================================================================== --- trunk/packages/kclust/trunk/debian/patches/test_seeks_custom.h (rev 0) +++ trunk/packages/kclust/trunk/debian/patches/test_seeks_custom.h 2013-07-26 01:28:39 UTC (rev 14244) @@ -0,0 +1,41 @@ +Index: kclust-0~20120309/test.cpp +=================================================================== +--- kclust-0~20120309.orig/test.cpp ++++ kclust-0~20120309/test.cpp +@@ -19,7 +19,7 @@ + ***************************************************************************/ + + #include <mysql++.h> +-#include "custom.h" ++//#include "custom.h" + + + #include "mysql_spec_structures.h" +@@ -45,7 +45,7 @@ + #include "packed_sequence.h" + #include "simple_hash.h" + +-#include "ident_clust.h" ++//#include "ident_clust.h" + #include "params.h" + //requires -msse + //#include <emmintrin.h> +Index: kclust-0~20120309/Makefile +=================================================================== +--- kclust-0~20120309.orig/Makefile ++++ kclust-0~20120309/Makefile +@@ -67,6 +67,9 @@ + + all: $(TARGETS) + ++test: ++ echo "Nothing to do!!!!" ++ + .c.o: $< + $(CPP) -c $< + +@@ -103,3 +106,4 @@ + clean: clean-wnlib + -rm -f *.o + -rm -f $(TARGETS) ++ Added: trunk/packages/kclust/trunk/debian/patches/variable_visibility.patch =================================================================== --- trunk/packages/kclust/trunk/debian/patches/variable_visibility.patch (rev 0) +++ trunk/packages/kclust/trunk/debian/patches/variable_visibility.patch 2013-07-26 01:28:39 UTC (rev 14244) @@ -0,0 +1,20 @@ +Index: kclust-0~20120309/mkaln.cpp +=================================================================== +--- kclust-0~20120309.orig/mkaln.cpp ++++ kclust-0~20120309/mkaln.cpp +@@ -82,7 +82,6 @@ + } + + ++it; +- int i = 1; + while( it!=end ){ + Sequence *s = dbr->get( (*it).idx, true, false); + +@@ -292,7 +291,6 @@ + + // add other sequences in the cluster + ++it; +- int i = 1; + while( it!=end ){ + Sequence *s = dbr->get( (*it).idx, true, false); + Added: trunk/packages/kclust/trunk/debian/rules =================================================================== --- trunk/packages/kclust/trunk/debian/rules (rev 0) +++ trunk/packages/kclust/trunk/debian/rules 2013-07-26 01:28:39 UTC (rev 14244) @@ -0,0 +1,16 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# Sample debian/rules that uses debhelper. +# This file was originally written by Joey Hess and Craig Small. +# As a special exception, when this file is copied by dh-make into a +# dh-make output file, you may use that output file without restriction. +# This special exception was added by Craig Small in version 0.37 of dh-make. + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +export CPPFLAGS = -I/usr/include/mysql -I/usr/include/mysql++ + + +%: + dh $@ Property changes on: trunk/packages/kclust/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/kclust/trunk/debian/source/format =================================================================== --- trunk/packages/kclust/trunk/debian/source/format (rev 0) +++ trunk/packages/kclust/trunk/debian/source/format 2013-07-26 01:28:39 UTC (rev 14244) @@ -0,0 +1 @@ +3.0 (quilt) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
