Author: tbooth-guest Date: 2015-06-23 16:40:40 +0000 (Tue, 23 Jun 2015) New Revision: 19359
Added: packages/sickle/trunk/debian/changelog packages/sickle/trunk/debian/compat packages/sickle/trunk/debian/control packages/sickle/trunk/debian/copyright packages/sickle/trunk/debian/docs packages/sickle/trunk/debian/install packages/sickle/trunk/debian/manpages packages/sickle/trunk/debian/patches/ packages/sickle/trunk/debian/patches/makefile_ldflags packages/sickle/trunk/debian/patches/series packages/sickle/trunk/debian/rules packages/sickle/trunk/debian/source/ packages/sickle/trunk/debian/source/format Log: As requested by Andreas Added: packages/sickle/trunk/debian/changelog =================================================================== --- packages/sickle/trunk/debian/changelog (rev 0) +++ packages/sickle/trunk/debian/changelog 2015-06-23 16:40:40 UTC (rev 19359) @@ -0,0 +1,18 @@ +sickle (0.94-1biolinux1.1) trusty; urgency=low + + * Rebuild for Trusty + * Pass standard CFLAGS to build + + -- Tim Booth <[email protected]> Wed, 07 May 2014 16:43:48 +0100 + +sickle (0.94-0precise2) precise; urgency=low + + * Fix manpage to have more useful info + + -- Tim Booth <[email protected]> Mon, 29 Apr 2013 12:47:44 +0100 + +sickle (0.94-0precise1) precise; urgency=low + + * Initial build for PPA. + + -- Tim Booth <[email protected]> Mon, 29 Apr 2013 12:00:14 +0100 Added: packages/sickle/trunk/debian/compat =================================================================== --- packages/sickle/trunk/debian/compat (rev 0) +++ packages/sickle/trunk/debian/compat 2015-06-23 16:40:40 UTC (rev 19359) @@ -0,0 +1 @@ +9 Added: packages/sickle/trunk/debian/control =================================================================== --- packages/sickle/trunk/debian/control (rev 0) +++ packages/sickle/trunk/debian/control 2015-06-23 16:40:40 UTC (rev 19359) @@ -0,0 +1,33 @@ +Source: sickle +Section: science +Priority: optional +Maintainer: Tim Booth <[email protected]> +Build-Depends: zlib1g-dev, help2man (>= 1.40.4), debhelper (>= 9) +Standards-Version: 3.9.3 +Homepage: https://github.com/vsbuffalo/sickle + +Package: sickle +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: windowed adaptive trimming tool for FASTQ files using quality + Most modern sequencing technologies produce reads that have deteriorating + quality towards the 3'-end. Incorrectly called bases here negatively impact + assembles, mapping, and downstream bioinformatics analyses. + . + Sickle is a tool that uses sliding windows along with quality and length + thresholds to determine when quality is sufficiently low to trim the 3'-end + of reads. It will also discard reads based upon the length threshold. It takes + the quality values and slides a window across them whose length is 0.1 times + the length of the read. If this length is less than 1, then the window is set + to be equal to the length of the read. Otherwise, the window slides along the + quality values until the average quality in the window drops below the + threshold. At that point the algorithm determines where in the window the drop + occurs and cuts both the read and quality strings there. However, if the cut + point is less than the minimum length threshold, then the read is discarded + entirely. + . + Sickle supports four types of quality values: Illumina, Solexa, Phred, and + Sanger. Note that the Solexa quality setting is an approximation (the actual + conversion is a non-linear transformation). The end approximation is close. + . + Sickle also supports gzipped file inputs. Added: packages/sickle/trunk/debian/copyright =================================================================== --- packages/sickle/trunk/debian/copyright (rev 0) +++ packages/sickle/trunk/debian/copyright 2015-06-23 16:40:40 UTC (rev 19359) @@ -0,0 +1,27 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Source: https://github.com/vsbuffalo/sickle/archive/master.zip +License: MIT + +Files: * +Copyright: © 2008 Genome Research Ltd (GRL)., + © 2012 - Vince Buffalo +License: MIT + Permission is hereby granted, free of charge, to any person + obtaining a copy of this software and associated documentation + files (the "Software"), to deal in the Software without + restriction, including without limitation the rights to use, copy, + modify, merge, publish, distribute, sublicense, and/or sell copies + of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be + included in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, + EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF + MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND + NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS + BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN + ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN + CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. Added: packages/sickle/trunk/debian/docs =================================================================== --- packages/sickle/trunk/debian/docs (rev 0) +++ packages/sickle/trunk/debian/docs 2015-06-23 16:40:40 UTC (rev 19359) @@ -0,0 +1 @@ +README.md Added: packages/sickle/trunk/debian/install =================================================================== --- packages/sickle/trunk/debian/install (rev 0) +++ packages/sickle/trunk/debian/install 2015-06-23 16:40:40 UTC (rev 19359) @@ -0,0 +1 @@ +sickle usr/bin Added: packages/sickle/trunk/debian/manpages =================================================================== --- packages/sickle/trunk/debian/manpages (rev 0) +++ packages/sickle/trunk/debian/manpages 2015-06-23 16:40:40 UTC (rev 19359) @@ -0,0 +1 @@ +sickle.1 Added: packages/sickle/trunk/debian/patches/makefile_ldflags =================================================================== --- packages/sickle/trunk/debian/patches/makefile_ldflags (rev 0) +++ packages/sickle/trunk/debian/patches/makefile_ldflags 2015-06-23 16:40:40 UTC (rev 19359) @@ -0,0 +1,20 @@ +--- a/Makefile ++++ b/Makefile +@@ -1,7 +1,7 @@ + PROGRAM_NAME = sickle + VERSION = 0.94 + CC = gcc +-CFLAGS = -Wall -pedantic -DVERSION=$(VERSION) ++CFLAGS += -Wall -pedantic -DVERSION=$(VERSION) + DEBUG = -g + OPT = -O3 + ARCHIVE = $(PROGRAM_NAME)_$(VERSION) +@@ -34,7 +34,7 @@ + tar -zcf $(ARCHIVE).tar.gz src Makefile + + build: sliding.o trim_single.o trim_paired.o sickle.o +- $(CC) $(CFLAGS) $(LDFLAGS) $(OPT) $? -o sickle ++ $(CC) $(CFLAGS) $(OPT) $? -o sickle $(LDFLAGS) + + debug: + $(MAKE) build "CFLAGS=-Wall -pedantic -g -DDEBUG" Added: packages/sickle/trunk/debian/patches/series =================================================================== --- packages/sickle/trunk/debian/patches/series (rev 0) +++ packages/sickle/trunk/debian/patches/series 2015-06-23 16:40:40 UTC (rev 19359) @@ -0,0 +1 @@ +makefile_ldflags Added: packages/sickle/trunk/debian/rules =================================================================== --- packages/sickle/trunk/debian/rules (rev 0) +++ packages/sickle/trunk/debian/rules 2015-06-23 16:40:40 UTC (rev 19359) @@ -0,0 +1,21 @@ +#!/usr/bin/make -f + +%: + dh $@ + +# export DH_VERBOSE=1 + +override_dh_clean: + dh_clean + rm -f README.help2man sickle.1 + +override_dh_auto_build: + dh_auto_build + echo '[DESCRIPTION]' > README.help2man + grep -A200 '^## Usage' README.md >> README.help2man + help2man --no-discard-stderr -i README.help2man \ + -n "windowed adaptive trimming tool for FASTQ files using quality" \ + ./sickle > sickle.1 + +get-orig-source: + echo Source was donloaded from GitHub. There is no script to fetch it (yet) Property changes on: packages/sickle/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: packages/sickle/trunk/debian/source/format =================================================================== --- packages/sickle/trunk/debian/source/format (rev 0) +++ packages/sickle/trunk/debian/source/format 2015-06-23 16:40:40 UTC (rev 19359) @@ -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
