[med-svn] r13269 - in trunk/packages: . uc-echo uc-echo/trunk uc-echo/trunk/debian uc-echo/trunk/debian/patches uc-echo/trunk/debian/script uc-echo/trunk/debian/source
Thorsten Alteholz
alteholz at alioth.debian.org
Sun Apr 7 14:33:19 UTC 2013
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 <debian at 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-packaging at lists.alioth.debian.org>
+Uploaders: Thorsten Alteholz <debian at 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 <debian at 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 <debian at 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) $(TARGETS)
+
Added: trunk/packages/uc-echo/trunk/debian/patches/include.patch
===================================================================
--- trunk/packages/uc-echo/trunk/debian/patches/include.patch (rev 0)
+++ trunk/packages/uc-echo/trunk/debian/patches/include.patch 2013-04-07 14:33:19 UTC (rev 13269)
@@ -0,0 +1,14 @@
+Author: Thorsten Alteholz <debian at alteholz.de>
+Description: add #include <unistd.h> for definition of open()
+Index: echo_v1_12/MMAP.hpp
+===================================================================
+--- echo_v1_12.orig/MMAP.hpp 2013-04-02 17:40:01.000000000 +0200
++++ echo_v1_12/MMAP.hpp 2013-04-02 17:40:01.000000000 +0200
+@@ -6,6 +6,7 @@
+ #include <sys/stat.h>
+ #include <fcntl.h>
+ #include <stdexcept>
++#include <unistd.h>
+
+ class MMAP {
+ int fdes;
Added: trunk/packages/uc-echo/trunk/debian/patches/series
===================================================================
--- trunk/packages/uc-echo/trunk/debian/patches/series (rev 0)
+++ trunk/packages/uc-echo/trunk/debian/patches/series 2013-04-07 14:33:19 UTC (rev 13269)
@@ -0,0 +1,2 @@
+hardening-flags.patch
+include.patch
Added: trunk/packages/uc-echo/trunk/debian/rules
===================================================================
--- trunk/packages/uc-echo/trunk/debian/rules (rev 0)
+++ trunk/packages/uc-echo/trunk/debian/rules 2013-04-07 14:33:19 UTC (rev 13269)
@@ -0,0 +1,19 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+LIBRARY_PATH=/usr/lib/$(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
+
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