debian/0000755000000000000000000000000012153630703007166 5ustar debian/control0000644000000000000000000000252412153630703010574 0ustar Source: jellyfish Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Shaun Jackman , Andreas Tille Build-Depends: debhelper (>= 9), autotools-dev Standards-Version: 3.9.4 Homepage: http://www.cbcb.umd.edu/software/jellyfish/ Vcs-Git: git://anonscm.debian.org/debian-med/jellyfish.git Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/jellyfish.git Package: jellyfish Architecture: any-amd64 Depends: ${shlibs:Depends}, ${misc:Depends} Description: count k-mers in DNA sequences JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. debian/install0000644000000000000000000000002012153630703010547 0ustar usr/bin usr/lib debian/rules0000755000000000000000000000033512153630703010247 0ustar #!/usr/bin/make -f export DH_OPTIONS %: dh $@ override_dh_auto_configure: dh_auto_configure override_dh_auto_install: dh_auto_install --destdir=debian/tmp override_dh_install: dh_install -X*.a -X*.la -Xpkgconfig debian/manpages0000644000000000000000000000002212153630703010676 0ustar doc/jellyfish.man debian/watch0000644000000000000000000000011612153630703010215 0ustar version=3 http://www.cbcb.umd.edu/software/jellyfish/ jellyfish-(.+)\.tar\.gz debian/upstream0000644000000000000000000000041512153630703010751 0ustar Reference: Author: Guillaume Marcais and Carl Kingsford Title: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers Journal: Bioinformatics Year: 2011 Volume: 27 Number: 6 Pages: 764-770 DOI: 10.1093/bioinformatics/btr011 debian/lintian-overrides0000644000000000000000000000037012153630703012547 0ustar # Upstream decided to use a dynamic library without really intending to make this a development package jellyfish: package-name-doesnt-match-sonames libjellyfish-.* jellyfish: non-dev-pkg-with-shlib-symlink .* jellyfish: no-symbols-control-file .* debian/copyright0000644000000000000000000000370112153630703011122 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: JELLYFISH Upstream-Contact: Guillaume Marçais Source: http://www.cbcb.umd.edu/software/jellyfish/ Files: * Copyright: Copyright 2011 Guillaume Marçais1, Carl Kingsford License: GPL-3+ See `/usr/share/common-licenses/GPL'. Files: randomc.h Copyright: Copyright 2008 Agner Fog License: GPL See `/usr/share/common-licenses/GPL'. Files: half.h Copyright: Copyright 2002, Industrial Light & Magic License: other 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. * Neither the name of Industrial Light & Magic nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . 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 OWNER 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. debian/source/0000755000000000000000000000000012153630703010466 5ustar debian/source/format0000644000000000000000000000001412153630703011674 0ustar 3.0 (quilt) debian/changelog0000644000000000000000000000362612153630703011047 0ustar jellyfish (1.1.10-1) unstable; urgency=low * New upstream version Closes: #701423 * debian/{rules,install}: Make sure dynamic library will be installed * debian/control: - Removed DM-Upload-Allowed - Standards-Version: 3.9.4 (no changes needed) - Build-Depends autotools-dev - canonical VCS URLs * debian/lintian-overrides: Upstream decided to use a dynamic library without really intending to make this a development package * debian/doc-base: docbase control file * debian/patches/man: refreshed + DEP3 description -- Andreas Tille Wed, 05 Jun 2013 11:58:53 +0200 jellyfish (1.1.5-1) unstable; urgency=low * New upstream version fixing the FTBFS with gcc-4.7 bug Closes: #667214 * debian/patches/fix-unused-but-set-variable.patch: Removed because applied upstream -- Andreas Tille Mon, 21 May 2012 21:56:38 +0200 jellyfish (1.1.4-1) unstable; urgency=low * New upstream version * debian/patches/ptrdiff_t: Removed because applied upstream * debian/patches/cmdline: Removed because upstream code was changed in a way that it becomes superfluous * debian/patches/fix-unused-but-set-variable.patch: Due to the use of hardening flags warnings about unused-but-set-variable becomes an error - start working on a patch * debian/source/local-options: Add dpkg-source local-options hints * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Move citation from long desciption to debian/upstream - debhelper (>= 9) * debian/upstream: Use the agreed way to specify citations * debian/copyright: DEP5 verified using cme fix dpkg-copyright * debian/compat: 9 -- Andreas Tille Sat, 31 Mar 2012 08:50:25 +0200 jellyfish (1.1.2-1) unstable; urgency=low * Initial release. Closes: #644925. -- Shaun Jackman Mon, 10 Oct 2011 11:49:11 -0700 debian/patches/0000755000000000000000000000000012153630703010615 5ustar debian/patches/man0000644000000000000000000000055512153630703011320 0ustar Author: Andreas Tille Description: Fix NAME section in manpage --- a/doc/jellyfish.man +++ b/doc/jellyfish.man @@ -12,11 +12,7 @@ .. .TH "JELLYFISH" "1" "2010/10/1" "k\-mer counter " "k\-mer counter " .SH NAME - -.PP -Jellyfish -is a software to count k\-mers in DNA sequences. -.PP +jellyfish - count k\-mers in DNA sequences .SH SYNOPSIS jellyfish count debian/patches/series0000644000000000000000000000000412153630703012024 0ustar man debian/doc-base0000644000000000000000000000173312153630703010572 0ustar Document: jellyfish Title: Jellyfish: A fast k-mer counter Author: G. Marcais and C. Kingsford Abstract: Jellyfish is a software to count k-mers in DNA sequences. JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. Section: Science/Biology Format: pdf Files: /usr/share/doc/jellyfish/jellyfish.pdf.gz debian/compat0000644000000000000000000000000212153630703010364 0ustar 9 debian/docs0000644000000000000000000000003112153630703010033 0ustar README doc/jellyfish.pdf