Author: alteholz Date: 2013-04-07 14:33:19 +0000 (Sun, 07 Apr 2013) New Revision: 13269
Added: trunk/packages/uc-echo/ trunk/packages/uc-echo/trunk/ trunk/packages/uc-echo/trunk/debian/ trunk/packages/uc-echo/trunk/debian/changelog trunk/packages/uc-echo/trunk/debian/compat trunk/packages/uc-echo/trunk/debian/control trunk/packages/uc-echo/trunk/debian/copyright trunk/packages/uc-echo/trunk/debian/patches/ trunk/packages/uc-echo/trunk/debian/patches/hardening-flags.patch trunk/packages/uc-echo/trunk/debian/patches/include.patch trunk/packages/uc-echo/trunk/debian/patches/series trunk/packages/uc-echo/trunk/debian/rules trunk/packages/uc-echo/trunk/debian/script/ trunk/packages/uc-echo/trunk/debian/script/uc-echo trunk/packages/uc-echo/trunk/debian/source/ trunk/packages/uc-echo/trunk/debian/source/format trunk/packages/uc-echo/trunk/debian/uc-echo.1 trunk/packages/uc-echo/trunk/debian/uc-echo.install trunk/packages/uc-echo/trunk/debian/uc-echo.lintian-overrides trunk/packages/uc-echo/trunk/debian/uc-echo.manpages trunk/packages/uc-echo/trunk/debian/watch Log: initial version of uc-echo Property changes on: trunk/packages/uc-echo/trunk/debian ___________________________________________________________________ Added: mergeWithUpstream + 1 Added: trunk/packages/uc-echo/trunk/debian/changelog =================================================================== --- trunk/packages/uc-echo/trunk/debian/changelog (rev 0) +++ trunk/packages/uc-echo/trunk/debian/changelog 2013-04-07 14:33:19 UTC (rev 13269) @@ -0,0 +1,6 @@ +uc-echo (1.12-1) unstable; urgency=low + + * initial version (Closes: #704902) + + -- Thorsten Alteholz <deb...@alteholz.de> Tue, 12 Mar 2013 18:00:07 +0100 + Added: trunk/packages/uc-echo/trunk/debian/compat =================================================================== --- trunk/packages/uc-echo/trunk/debian/compat (rev 0) +++ trunk/packages/uc-echo/trunk/debian/compat 2013-04-07 14:33:19 UTC (rev 13269) @@ -0,0 +1 @@ +9 Added: trunk/packages/uc-echo/trunk/debian/control =================================================================== --- trunk/packages/uc-echo/trunk/debian/control (rev 0) +++ trunk/packages/uc-echo/trunk/debian/control 2013-04-07 14:33:19 UTC (rev 13269) @@ -0,0 +1,25 @@ +Source: uc-echo +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> +Uploaders: Thorsten Alteholz <deb...@alteholz.de> +Build-Depends: debhelper (>= 9), + python-all-dev (>=2.6), + python-scipy, + python-numpy, + g++-multilib +Standards-Version: 3.9.4 +Homepage: http://uc-echo.sourceforge.net/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/uc-echo/trunk/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/uc-echo/trunk/ + +Package: uc-echo +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends} +Description: error correction algorithm designed for short-reads from NGS + ECHO is an error correction algorithm designed for short-reads + from next-generation sequencing platforms such as Illumina's + Genome Analyzer II. The algorithm uses a Bayesian framework to + improve the quality of the reads in a given data set by employing + maximum a posteriori estimation. + Added: trunk/packages/uc-echo/trunk/debian/copyright =================================================================== --- trunk/packages/uc-echo/trunk/debian/copyright (rev 0) +++ trunk/packages/uc-echo/trunk/debian/copyright 2013-04-07 14:33:19 UTC (rev 13269) @@ -0,0 +1,32 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: uc-echo +Source: http://uc-echo.sourceforge.net/ + +Files: * +Copyright: 2011, Yun S. Song +License: BSD + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are met: + . + Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + . + Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + . + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE + FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL + DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR + SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER + CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +Files: debian/* +Copyright: 2013 Thorsten Alteholz <deb...@alteholz.de> +License: BSD + see above Added: trunk/packages/uc-echo/trunk/debian/patches/hardening-flags.patch =================================================================== --- trunk/packages/uc-echo/trunk/debian/patches/hardening-flags.patch (rev 0) +++ trunk/packages/uc-echo/trunk/debian/patches/hardening-flags.patch 2013-04-07 14:33:19 UTC (rev 13269) @@ -0,0 +1,22 @@ +Author: Thorsten Alteholz <deb...@alteholz.de> +Description: use hardening flags +Index: echo_v1_12/Makefile +=================================================================== +--- echo_v1_12.orig/Makefile 2013-04-07 12:49:41.000000000 +0200 ++++ echo_v1_12/Makefile 2013-04-07 12:50:19.000000000 +0200 +@@ -1,5 +1,5 @@ + CXX = g++ +-CXXFLAGS = -Wall -O3 -m64 ++CXXFLAGS += -Wall -O3 -m64 $(CLFAGS) $(CPPFLAGS) + HEADERS = *.hpp + LIB = DNASeq.o NeighborSet.o KmerHashMap.o + TARGETS = hashing NeighborJoin NeighborJoinParam NeighborMerge Voting HashMerge +@@ -8,7 +8,7 @@ + $(CXX) -c $(CXXFLAGS) $< -o $*.o + + %: %.cpp $(LIB) $(HEADERS) +- $(CXX) $(CXXFLAGS) -o $* $*.cpp $(LIB) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $* $*.cpp $(LIB) + + all: $(LIB) $(TARGETS) + Added: trunk/packages/uc-echo/trunk/debian/patches/include.patch =================================================================== --- trunk/packages/uc-echo/trunk/debian/patches/include.patch (rev 0) +++ trunk/packages/uc-echo/trunk/debian/patches/include.patch 2013-04-07 14:33:19 UTC (rev 13269) @@ -0,0 +1,14 @@ +Author: Thorsten Alteholz <deb...@alteholz.de> +Description: add #include <unistd.h> for definition of open() +Index: echo_v1_12/MMAP.hpp +=================================================================== +--- echo_v1_12.orig/MMAP.hpp 2013-04-02 17:40:01.000000000 +0200 ++++ echo_v1_12/MMAP.hpp 2013-04-02 17:40:01.000000000 +0200 +@@ -6,6 +6,7 @@ + #include <sys/stat.h> + #include <fcntl.h> + #include <stdexcept> ++#include <unistd.h> + + class MMAP { + int fdes; Added: trunk/packages/uc-echo/trunk/debian/patches/series =================================================================== --- trunk/packages/uc-echo/trunk/debian/patches/series (rev 0) +++ trunk/packages/uc-echo/trunk/debian/patches/series 2013-04-07 14:33:19 UTC (rev 13269) @@ -0,0 +1,2 @@ +hardening-flags.patch +include.patch Added: trunk/packages/uc-echo/trunk/debian/rules =================================================================== --- trunk/packages/uc-echo/trunk/debian/rules (rev 0) +++ trunk/packages/uc-echo/trunk/debian/rules 2013-04-07 14:33:19 UTC (rev 13269) @@ -0,0 +1,19 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +LIBRARY_PATH=/usr/lib/$(gcc -print-multiarch) +CPATH=/usr/include/$(gcc -print-multiarch) +export LIBRARY_PATH CPATH + +%: + dh $@ --with python2 + +override_dh_auto_install: + dh_auto_install + dh_installchangelogs README + +get-orig-source: + mkdir -p ../tarballs + uscan --verbose --force-download --destdir=../tarballs + Added: trunk/packages/uc-echo/trunk/debian/script/uc-echo =================================================================== --- trunk/packages/uc-echo/trunk/debian/script/uc-echo (rev 0) +++ trunk/packages/uc-echo/trunk/debian/script/uc-echo 2013-04-07 14:33:19 UTC (rev 13269) @@ -0,0 +1,3 @@ +#!/bin/bash + +python /usr/lib/uc-echo/ErrorCorrection.py $@ Added: trunk/packages/uc-echo/trunk/debian/source/format =================================================================== --- trunk/packages/uc-echo/trunk/debian/source/format (rev 0) +++ trunk/packages/uc-echo/trunk/debian/source/format 2013-04-07 14:33:19 UTC (rev 13269) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/uc-echo/trunk/debian/uc-echo.1 =================================================================== --- trunk/packages/uc-echo/trunk/debian/uc-echo.1 (rev 0) +++ trunk/packages/uc-echo/trunk/debian/uc-echo.1 2013-04-07 14:33:19 UTC (rev 13269) @@ -0,0 +1,112 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1. +.TH UC-ECHO "1" "April 2013" "uc-echo" "User Commands" +.SH NAME +uc-echo - Short-read Error Correction +.SH SYNOPSIS +.B uc-echo +[\fIoptions\fR] \fIread_file_name\fR +.SH OPTIONS +.TP +\fB\-h\fR, \fB\-\-help\fR +show this help message and exit +.TP +\fB\-o\fR OUTPUT_FILENAME, \fB\-\-output\fR=\fIOUTPUT_FILENAME\fR +Output file name +.TP +\fB\-l\fR LOG_FILENAME, \fB\-\-log\fR=\fILOG_FILENAME\fR +Log file name +.TP +\fB\-\-DD\fR=\fITMP_DIRECTORY\fR, \fB\-\-tmp_dir\fR=\fITMP_DIRECTORY\fR +Temporary data directory +.TP +\fB\-u\fR NCPU, \fB\-\-ncpu\fR=\fINCPU\fR +Number of processes used in training +.TP +\fB\-b\fR BSIZE, \fB\-\-block_size\fR=\fIBSIZE\fR +Split data into blocks of specified size +.TP +\fB\-\-nh\fR=\fINHASH\fR, \fB\-\-n_hash_block\fR=\fINHASH\fR +Split hash table into n tables +.TP +\fB\-\-rm\fR=\fIREAD_MERGE\fR, \fB\-\-read_merge_size\fR=\fIREAD_MERGE\fR +Merge n hash tables at a time +.TP +\fB\-\-hm\fR=\fIHASH_MERGE\fR, \fB\-\-hash_merge_batch_size\fR=\fIHASH_MERGE\fR +Merge n adjacency lists at a time +.TP +\fB\-k\fR K, \fB\-\-kmer\fR=\fIK\fR +k\-mer size used for hashing +.TP +\fB\-e\fR E, \fB\-\-min_error_tolerance\fR=\fIE\fR +Minimum error tolerance for parameter searching +.TP +\fB\-E\fR E, \fB\-\-max_error_tolerance\fR=\fIE\fR +Maximum error tolerance for parameter searching +.TP +\fB\-\-hh\fR=\fIH\fR, \fB\-\-min_minimum_overlap\fR=\fIH\fR +Minimum minimum overlap length for parameter searching +.TP +\fB\-\-hH\fR=\fIH\fR, \fB\-\-max_minimum_overlap\fR=\fIH\fR +Maximum minimum overlap length for parameter searching +.TP +\fB\-\-h_rate\fR=\fIH_RATE\fR, \fB\-\-heterozygous_rate\fR=\fIH_RATE\fR +Rate for heterozygous site +.TP +\fB\-\-model_selection_size\fR=\fIMSIZE\fR +Model selection data set size +.TP +\fB\-\-keep_all_files\fR +Keep all temporary files. By default, temporary files +are deleted automatically. +.TP +\fB\-h\fR, \fB\-\-help\fR +show this help message and exit +.TP +\fB\-o\fR OUTPUT_FILENAME, \fB\-\-output\fR=\fIOUTPUT_FILENAME\fR +Output file name +.TP +\fB\-l\fR LOG_FILENAME, \fB\-\-log\fR=\fILOG_FILENAME\fR +Log file name +.TP +\fB\-\-DD\fR=\fITMP_DIRECTORY\fR, \fB\-\-tmp_dir\fR=\fITMP_DIRECTORY\fR +Temporary data directory +.TP +\fB\-u\fR NCPU, \fB\-\-ncpu\fR=\fINCPU\fR +Number of processes used in training +.TP +\fB\-b\fR BSIZE, \fB\-\-block_size\fR=\fIBSIZE\fR +Split data into blocks of specified size +.TP +\fB\-\-nh\fR=\fINHASH\fR, \fB\-\-n_hash_block\fR=\fINHASH\fR +Split hash table into n tables +.TP +\fB\-\-rm\fR=\fIREAD_MERGE\fR, \fB\-\-read_merge_size\fR=\fIREAD_MERGE\fR +Merge n hash tables at a time +.TP +\fB\-\-hm\fR=\fIHASH_MERGE\fR, \fB\-\-hash_merge_batch_size\fR=\fIHASH_MERGE\fR +Merge n adjacency lists at a time +.TP +\fB\-k\fR K, \fB\-\-kmer\fR=\fIK\fR +k\-mer size used for hashing +.TP +\fB\-e\fR E, \fB\-\-min_error_tolerance\fR=\fIE\fR +Minimum error tolerance for parameter searching +.TP +\fB\-E\fR E, \fB\-\-max_error_tolerance\fR=\fIE\fR +Maximum error tolerance for parameter searching +.TP +\fB\-\-hh\fR=\fIH\fR, \fB\-\-min_minimum_overlap\fR=\fIH\fR +Minimum minimum overlap length for parameter searching +.TP +\fB\-\-hH\fR=\fIH\fR, \fB\-\-max_minimum_overlap\fR=\fIH\fR +Maximum minimum overlap length for parameter searching +.TP +\fB\-\-h_rate\fR=\fIH_RATE\fR, \fB\-\-heterozygous_rate\fR=\fIH_RATE\fR +Rate for heterozygous site +.TP +\fB\-\-model_selection_size\fR=\fIMSIZE\fR +Model selection data set size +.TP +\fB\-\-keep_all_files\fR +Keep all temporary files. By default, temporary files +are deleted automatically. Added: trunk/packages/uc-echo/trunk/debian/uc-echo.install =================================================================== --- trunk/packages/uc-echo/trunk/debian/uc-echo.install (rev 0) +++ trunk/packages/uc-echo/trunk/debian/uc-echo.install 2013-04-07 14:33:19 UTC (rev 13269) @@ -0,0 +1,8 @@ +hashing /usr/lib/uc-echo +NeighborJoin /usr/lib/uc-echo +NeighborJoinParam /usr/lib/uc-echo +NeighborMerge /usr/lib/uc-echo +Voting /usr/lib/uc-echo +HashMerge /usr/lib/uc-echo +ErrorCorrection.py /usr/lib/uc-echo +debian/script/uc-echo /usr/bin Added: trunk/packages/uc-echo/trunk/debian/uc-echo.lintian-overrides =================================================================== --- trunk/packages/uc-echo/trunk/debian/uc-echo.lintian-overrides (rev 0) +++ trunk/packages/uc-echo/trunk/debian/uc-echo.lintian-overrides 2013-04-07 14:33:19 UTC (rev 13269) @@ -0,0 +1,8 @@ +# these flags are really used +uc-echo: hardening-no-fortify-functions usr/lib/uc-echo/HashMerge +uc-echo: hardening-no-fortify-functions usr/lib/uc-echo/NeighborJoin +uc-echo: hardening-no-fortify-functions usr/lib/uc-echo/NeighborJoinParam +uc-echo: hardening-no-fortify-functions usr/lib/uc-echo/NeighborMerge +uc-echo: hardening-no-fortify-functions usr/lib/uc-echo/Voting +uc-echo: hardening-no-fortify-functions usr/lib/uc-echo/hashing + Added: trunk/packages/uc-echo/trunk/debian/uc-echo.manpages =================================================================== --- trunk/packages/uc-echo/trunk/debian/uc-echo.manpages (rev 0) +++ trunk/packages/uc-echo/trunk/debian/uc-echo.manpages 2013-04-07 14:33:19 UTC (rev 13269) @@ -0,0 +1 @@ +debian/uc-echo.1 Added: trunk/packages/uc-echo/trunk/debian/watch =================================================================== --- trunk/packages/uc-echo/trunk/debian/watch (rev 0) +++ trunk/packages/uc-echo/trunk/debian/watch 2013-04-07 14:33:19 UTC (rev 13269) @@ -0,0 +1,4 @@ +version=3 +opts="uversionmangle=s/_/./" \ + http://sf.net/uc-echo/echo_v([\d_]+)\.tgz + _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
