[med-svn] [vsearch-data] 01/06: vsearch data now comes in a separate, differently versioned tarball so we create an extra package containing the test data
Andreas Tille
tille at debian.org
Sat Dec 30 17:31:27 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository vsearch-data.
commit 6f648580f4531374c9ea9bf1255d8c4757f95630
Author: Andreas Tille <tille at debian.org>
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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
+ Andreas Tille <tille at debian.org>
+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 <torognes at ifi.uio.no>
+Source: https://github.com/torognes/vsearch-data/releases
+
+Files: *
+Copyright: © 2014-2015 Torbjorn Rognes <torognes at ifi.uio.no>,
+ 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 <tbooth at ceh.ac.uk>
+ © 2015 Andreas Tille <tille at debian.org>
+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)
--
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