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commit 6f648580f4531374c9ea9bf1255d8c4757f95630 Author: Andreas Tille <[email protected]> Date: Fri Nov 13 23:41:49 2015 +0000 vsearch data now comes in a separate, differently versioned tarball so we create an extra package containing the test data --- debian/README.source | 35 +++++++++++++++++++++++++++++ debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 38 +++++++++++++++++++++++++++++++ debian/copyright | 54 +++++++++++++++++++++++++++++++++++++++++++++ debian/rules | 7 ++++++ debian/source/format | 1 + debian/upstream/metadata | 12 ++++++++++ debian/vsearch-data.install | 1 + debian/watch | 3 +++ 10 files changed, 157 insertions(+) diff --git a/debian/README.source b/debian/README.source new file mode 100644 index 0000000..a25e763 --- /dev/null +++ b/debian/README.source @@ -0,0 +1,35 @@ +Explanation for binary files inside source package according to + http://lists.debian.org/debian-devel/2013/09/msg00332.html + +Files: AF091148.fsa + AF091148.fsa is a tiny dataset with 180,704 nt in 1,403 seqs, + from 103 to 137 nt (avg 129). + +Files: BioMarKs*.fsa* + BioMarKs.fsa is a larger dataset with 119,117,805 nt in 312,503 seqs, + from 2 to 532 nt (avg 381). It is compressed with gzip due to GitHub's + 100MB file size limit. + +Files: constaint.fsa.bz2 + fasta file for constraint checking, i.e. special cases such as + 2048-long reads that can break the code + +Files: PR2-18S-rRNA-V4.*fsa* + PR2-18S-rRNA-V4.fsa is the latest 18S rRNA V4 reference from PR2 + (http://ssu-rrna.org/). + +Files: Rfam_9_1.fasta + Rfam_9_1.fasta is a dataset with 33,931,362 nt in 192,445 seqs, + from 20 to 1,250 nt (avg 176). It is Rfam release v9.1 (Gardner + et al., 2009). It was used for USEARCH testing in Edgar's paper. + Source: ftp://ftp.ebi.ac.uk/pub/databases/Rfam/9.1/Rfam.fasta.gz + +Files: Rfam_11_0*.fasta + Rfam_11_0.fasta is a dataset with 52,588,875 nt in 380,919 seqs, + from 19 to 1,875 nt (avg 138). It is Rfam release v11.0 (Gardner + et al., 2009). It was used for USEARCH testing + (http://drive5.com/usearch/benchmark_rfam.html). + Source: ftp://ftp.ebi.ac.uk/pub/databases/Rfam/11.0/Rfam.fasta.gz + +Files: fastq-test-suite + diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..250400e --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +vsearch-data (1.0.0-1) UNRELEASED; urgency=low + + * Initial package + + -- Andreas Tille <[email protected]> Tue, 29 Sep 2015 21:35:36 +0200 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..ec63514 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +9 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..60951bb --- /dev/null +++ b/debian/control @@ -0,0 +1,38 @@ +Source: vsearch-data +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Tim Booth <[email protected]>, + Andreas Tille <[email protected]> +Section: science +Priority: optional +Build-Depends: debhelper (>= 9), + dh-autoreconf, + zlib1g-dev, + libbz2-dev, + libssl-dev, + python-markdown, + ghostscript, + time +Standards-Version: 3.9.6 +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/vsearch-data/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/vsearch-data/trunk/ +Homepage: https://github.com/torognes/vsearch-data + +Package: vsearch-data +Architecture: all +Depends: ${misc:Depends} +Description: example data for vsearch tool for processing metagenomic sequences + Open and free 64-bit multithreaded tool for processing metagenomic sequences, + including searching, clustering, chimera detection, dereplication, sorting, + masking and shuffling + . + The aim of this project is to create an alternative to the USEARCH tool + developed by Robert C. Edgar (2010). The new tool should: + . + - have open source code with an appropriate open source license + - be free of charge, gratis + - have a 64-bit design that handles very large databases and much more + than 4GB of memory + - be as accurate or more accurate than usearch + - be as fast or faster than usearch + . + This package only contains data to run the vsearch test suite. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..d030a5e --- /dev/null +++ b/debian/copyright @@ -0,0 +1,54 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: VSEARCH-data +Upstream-Contact: Torbjørn Rognes <[email protected]> +Source: https://github.com/torognes/vsearch-data/releases + +Files: * +Copyright: © 2014-2015 Torbjorn Rognes <[email protected]>, + Tomas Flouri, Frederic Mahe +License: BSD-2-clause + +Files: fastq-test-suite +Copyright: 2009 P.J.A. Cock, C.J. Fields, N. Goto, M.L. Heuer and P.M. Rice +License: free_test_data + These files are provided freely and we encourage anyone writing a FASTQ parser + to use them as part of your test suite. Permission is granted to freely + distribute and modify the files. We request (but do not insist) that this + README file is included, or at least a reference to the above paper. Please + cite the above paper if appropriate. We also request (but do not insist) that + the example files are not modified, in order that they may serve as a common + reference. +Comment: The citation is mentioned in debian/upstream/metadata + +Files: debian/* +Copyright: © 2014-2015 Tim Booth <[email protected]> + © 2015 Andreas Tille <[email protected]> +License: BSD-2-clause + +License: BSD-2-clause + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + . + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + . + 2. 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. +Comment: The source code is dual licensed GPL-3+ or BSD-2-clause. + For the packaging we pick BSD-2-clause since otherwise lintian throws + error possible-gpl-code-linked-with-openssl. diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..657234c --- /dev/null +++ b/debian/rules @@ -0,0 +1,7 @@ +#!/usr/bin/make -f + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +%: + dh $@ diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/upstream/metadata b/debian/upstream/metadata new file mode 100644 index 0000000..2b26bdf --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,12 @@ +Reference: + Author: Peter J. A. Cock and Christopher J. Fields and Naohisa Goto and Michael L. Heuer and Peter M. Rice + Title: "The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants" + Journal: Nucleic Acid Research + Year: 2010 + Volume: 38 + Number: 6 + Pages: 1767-1771 + DOI: 10.1093/nar/gkp1137 + PMID: 20015970 + URL: http://nar.oxfordjournals.org/content/38/6/1767 + eprint: http://nar.oxfordjournals.org/content/38/6/1767.full.pdf+html diff --git a/debian/vsearch-data.install b/debian/vsearch-data.install new file mode 100644 index 0000000..3db5b62 --- /dev/null +++ b/debian/vsearch-data.install @@ -0,0 +1 @@ +[A-Za-ce-z]* usr/share/vsearch/data diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..02e5c91 --- /dev/null +++ b/debian/watch @@ -0,0 +1,3 @@ +version=3 + +https://github.com/torognes/vsearch-data/releases .*/archive/v([0-9.rc-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/vsearch-data.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
