[med-svn] r14244 - in trunk/packages/kclust/trunk: . debian debian/patches debian/source
Steffen Möller
moeller at alioth.debian.org
Fri Jul 26 01:28:39 UTC 2013
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 <moeller at debian.org> 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 <moeller at debian.org>
+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 <moeller at debian.org>
+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 (christian.eberhard.mayer at googlemail.com) and Maria Hauser (mhauser at genzentrum.lmu.de)
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)
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