[med-svn] [cutadapt] 02/02: Initial packaging
Andreas Tille
tille at debian.org
Mon Jun 20 13:12:14 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository cutadapt.
commit 4da904535e2af8ca8ca034e50270735499ccca50
Author: Andreas Tille <tille at debian.org>
Date: Mon Jun 20 15:11:42 2016 +0200
Initial packaging
---
debian/changelog | 5 +
debian/compat | 1 +
debian/control | 38 +++++
debian/copyright | 30 ++++
debian/cutadapt.1 | 301 ++++++++++++++++++++++++++++++++++++
debian/manpages | 1 +
debian/patches/cython_version.patch | 16 ++
debian/patches/series | 1 +
debian/rules | 8 +
debian/source/format | 1 +
debian/upstream/metadata | 11 ++
debian/watch | 3 +
12 files changed, 416 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..933ec96
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+cutadapt (1.10-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Mon, 20 Jun 2016 14:38:23 +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..7f6368f
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,38 @@
+Source: cutadapt
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ cython,
+ dh-python,
+ python-dev,
+ python-setuptools,
+ python-nose
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/cutadapt.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/cutadapt.git
+Homepage: http://cutadapt.readthedocs.io/en/stable/
+
+Package: cutadapt
+Architecture: any
+Depends: ${python:Depends},
+ ${shlibs:Depends},
+ ${misc:Depends}
+Description: finds and removes adapter sequences, primers, poly-A tails in gene sequences
+ Cutadapt finds and removes adapter sequences, primers, poly-A tails
+ and other types of unwanted sequence from your high-throughput
+ sequencing reads.
+ .
+ Cleaning your data in this way is often required: Reads from small-RNA
+ sequencing contain the 3’ sequencing adapter because the read is longer
+ than the molecule that is sequenced. Amplicon reads start with a primer
+ sequence. Poly-A tails are useful for pulling out RNA from your sample,
+ but often you don’t want them to be in your reads.
+ .
+ Cutadapt helps with these trimming tasks by finding the adapter or
+ primer sequences in an error-tolerant way. It can also modify and filter
+ reads in various ways. Adapter sequences can contain IUPAC wildcard
+ characters. Also, paired-end reads and even colorspace data is
+ supported. If you want, you can also just demultiplex your input data,
+ without removing adapter sequences at all.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..6e35f27
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,30 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: cutadapt
+Source: https://github.com/marcelm/cutadapt/releases
+
+Files: *
+Copyright: 2010-2016 Marcel Martin <marcel.martin at scilifelab.se>
+License: MIT
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: MIT
+
+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.
diff --git a/debian/cutadapt.1 b/debian/cutadapt.1
new file mode 100644
index 0000000..6bce735
--- /dev/null
+++ b/debian/cutadapt.1
@@ -0,0 +1,301 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH CUTADAPT "1" "June 2016" "cutadapt 1.10" "User Commands"
+.SH NAME
+cutadapt \- remove adapter sequences from high-throughput sequencing reads
+.SH SYNOPSIS
+.IP
+.B cutadapt
+\fB\-a\fR ADAPTER [options] [\-o output.fastq] input.fastq
+.P
+For paired-end reads:
+.IP
+.B cutadapt
+\fB\-a\fR ADAPT1 \fB\-A\fR ADAPT2 [options] \fB\-o\fR out1.fastq \fB\-p\fR out2.fastq in1.fastq in2.fastq
+.SH DESCRIPTION
+Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC wildcard
+characters are supported. The reverse complement is *not* automatically
+searched. All reads from input.fastq will be written to output.fastq with the
+adapter sequence removed. Adapter matching is error\-tolerant. Multiple adapter
+sequences can be given (use further \fB\-a\fR options), but only the best\-matching
+adapter will be removed.
+.PP
+Input may also be in FASTA format. Compressed input and output is supported and
+auto\-detected from the file name (.gz, .xz, .bz2). Use the file name '\-' for
+standard input/output. Without the \fB\-o\fR option, output is sent to standard output.
+.SH OPTIONS
+.TP
+\fB\-\-help\fR
+show all command\-line options
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-debug\fR
+Print debugging information.
+.TP
+\fB\-f\fR FORMAT, \fB\-\-format\fR=\fI\,FORMAT\/\fR
+Input file format; can be either 'fasta', 'fastq' or
+\&'sra\-fastq'. Ignored when reading csfasta/qual files.
+Default: auto\-detect from file name extension.
+.IP
+Finding adapters::
+.IP
+Parameters \fB\-a\fR, \fB\-g\fR, \fB\-b\fR specify adapters to be removed from each read
+(or from the first read in a pair if data is paired). If specified
+multiple times, only the best matching adapter is trimmed (but see the
+\fB\-\-times\fR option). When the special notation 'file:FILE' is used,
+adapter sequences are read from the given FASTA file.
+.TP
+\fB\-a\fR ADAPTER, \fB\-\-adapter\fR=\fI\,ADAPTER\/\fR
+Sequence of an adapter ligated to the 3' end (paired
+data: of the first read). The adapter and subsequent
+bases are trimmed. If a '$' character is appended
+('anchoring'), the adapter is only found if it is a
+suffix of the read.
+.TP
+\fB\-g\fR ADAPTER, \fB\-\-front\fR=\fI\,ADAPTER\/\fR
+Sequence of an adapter ligated to the 5' end (paired
+data: of the first read). The adapter and any
+preceding bases are trimmed. Partial matches at the 5'
+end are allowed. If a '^' character is prepended
+('anchoring'), the adapter is only found if it is a
+prefix of the read.
+.TP
+\fB\-b\fR ADAPTER, \fB\-\-anywhere\fR=\fI\,ADAPTER\/\fR
+Sequence of an adapter that may be ligated to the 5'
+or 3' end (paired data: of the first read). Both types
+of matches as described under \fB\-a\fR und \fB\-g\fR are allowed.
+If the first base of the read is part of the match,
+the behavior is as with \fB\-g\fR, otherwise as with \fB\-a\fR. This
+option is mostly for rescuing failed library
+preparations \- do not use if you know which end your
+adapter was ligated to!
+.TP
+\fB\-e\fR ERROR_RATE, \fB\-\-error\-rate\fR=\fI\,ERROR_RATE\/\fR
+Maximum allowed error rate (no. of errors divided by
+the length of the matching region). Default: 0.1
+.TP
+\fB\-\-no\-indels\fR
+Allow only mismatches in alignments. Default: allow
+both mismatches and indels
+.TP
+\fB\-n\fR COUNT, \fB\-\-times\fR=\fI\,COUNT\/\fR
+Remove up to COUNT adapters from each read. Default: 1
+.TP
+\fB\-O\fR MINLENGTH, \fB\-\-overlap\fR=\fI\,MINLENGTH\/\fR
+If the overlap between the read and the adapter is
+shorter than MINLENGTH, the read is not modified.
+Reduces the no. of bases trimmed due to random adapter
+matches. Default: 3
+.TP
+\fB\-\-match\-read\-wildcards\fR
+Interpret IUPAC wildcards in reads. Default: False
+.TP
+\fB\-N\fR, \fB\-\-no\-match\-adapter\-wildcards\fR
+Do not interpret IUPAC wildcards in adapters.
+.TP
+\fB\-\-no\-trim\fR
+Match and redirect reads to output/untrimmed\-output as
+usual, but do not remove adapters.
+.TP
+\fB\-\-mask\-adapter\fR
+Mask adapters with 'N' characters instead of trimming
+them.
+.IP
+Additional read modifications:
+.TP
+\fB\-u\fR LENGTH, \fB\-\-cut\fR=\fI\,LENGTH\/\fR
+Remove bases from each read (first read only if
+paired). If LENGTH is positive, remove bases from the
+beginning. If LENGTH is negative, remove bases from
+the end. Can be used twice if LENGTHs have different
+signs.
+.TP
+\fB\-q\fR [5'CUTOFF,]3'CUTOFF, \fB\-\-quality\-cutoff\fR=\fI\,[5\/\fR'CUTOFF,]3'CUTOFF
+Trim low\-quality bases from 5' and/or 3' ends of each
+read before adapter removal. Applied to both reads if
+data is paired. If one value is given, only the 3' end
+is trimmed. If two comma\-separated cutoffs are given,
+the 5' end is trimmed with the first cutoff, the 3'
+end with the second.
+.TP
+\fB\-\-nextseq\-trim\fR=\fI\,3\/\fR'CUTOFF
+NextSeq\-specific quality trimming (each read). Trims
+also dark cycles appearing as high\-quality G bases
+(EXPERIMENTAL).
+.TP
+\fB\-\-quality\-base\fR=\fI\,QUALITY_BASE\/\fR
+Assume that quality values in FASTQ are encoded as
+ascii(quality + QUALITY_BASE). This needs to be set to
+64 for some old Illumina FASTQ files. Default: 33
+.TP
+\fB\-\-trim\-n\fR
+Trim N's on ends of reads.
+.TP
+\fB\-x\fR PREFIX, \fB\-\-prefix\fR=\fI\,PREFIX\/\fR
+Add this prefix to read names. Use {name} to insert
+the name of the matching adapter.
+.TP
+\fB\-y\fR SUFFIX, \fB\-\-suffix\fR=\fI\,SUFFIX\/\fR
+Add this suffix to read names; can also include {name}
+.TP
+\fB\-\-strip\-suffix\fR=\fI\,STRIP_SUFFIX\/\fR
+Remove this suffix from read names if present. Can be
+given multiple times.
+.TP
+\fB\-\-length\-tag\fR=\fI\,TAG\/\fR
+Search for TAG followed by a decimal number in the
+description field of the read. Replace the decimal
+number with the correct length of the trimmed read.
+For example, use \fB\-\-length\-tag\fR 'length=' to correct
+fields like 'length=123'.
+.IP
+Filtering of processed reads:
+.TP
+\fB\-\-discard\-trimmed\fR, \fB\-\-discard\fR
+Discard reads that contain an adapter. Also use \fB\-O\fR to
+avoid discarding too many randomly matching reads!
+.TP
+\fB\-\-discard\-untrimmed\fR, \fB\-\-trimmed\-only\fR
+Discard reads that do not contain the adapter.
+.TP
+\fB\-m\fR LENGTH, \fB\-\-minimum\-length\fR=\fI\,LENGTH\/\fR
+Discard trimmed reads that are shorter than LENGTH.
+Reads that are too short even before adapter removal
+are also discarded. In colorspace, an initial primer
+is not counted. Default: 0
+.TP
+\fB\-M\fR LENGTH, \fB\-\-maximum\-length\fR=\fI\,LENGTH\/\fR
+Discard trimmed reads that are longer than LENGTH.
+Reads that are too long even before adapter removal
+are also discarded. In colorspace, an initial primer
+is not counted. Default: no limit
+.TP
+\fB\-\-max\-n\fR=\fI\,COUNT\/\fR
+Discard reads with too many N bases. If COUNT is an
+integer, it is treated as the absolute number of N
+bases. If it is between 0 and 1, it is treated as the
+proportion of N's allowed in a read.
+.IP
+Output:
+.TP
+\fB\-\-quiet\fR
+Print only error messages.
+.TP
+\fB\-o\fR FILE, \fB\-\-output\fR=\fI\,FILE\/\fR
+Write trimmed reads to FILE. FASTQ or FASTA format is
+chosen depending on input. The summary report is sent
+to standard output. Use '{name}' in FILE to
+demultiplex reads into multiple files. Default: write
+to standard output
+.TP
+\fB\-\-info\-file\fR=\fI\,FILE\/\fR
+Write information about each read and its adapter
+matches into FILE. See the documentation for the file
+format.
+.TP
+\fB\-r\fR FILE, \fB\-\-rest\-file\fR=\fI\,FILE\/\fR
+When the adapter matches in the middle of a read,
+write the rest (after the adapter) into FILE.
+.TP
+\fB\-\-wildcard\-file\fR=\fI\,FILE\/\fR
+When the adapter has N bases (wildcards), write
+adapter bases matching wildcard positions to FILE.
+When there are indels in the alignment, this will
+often not be accurate.
+.TP
+\fB\-\-too\-short\-output\fR=\fI\,FILE\/\fR
+Write reads that are too short (according to length
+specified by \fB\-m\fR) to FILE. Default: discard reads
+.TP
+\fB\-\-too\-long\-output\fR=\fI\,FILE\/\fR
+Write reads that are too long (according to length
+specified by \fB\-M\fR) to FILE. Default: discard reads
+.TP
+\fB\-\-untrimmed\-output\fR=\fI\,FILE\/\fR
+Write reads that do not contain the adapter to FILE.
+Default: output to same file as trimmed reads
+.IP
+Colorspace options:
+.TP
+\fB\-c\fR, \fB\-\-colorspace\fR
+Enable colorspace mode: Also trim the color that is
+adjacent to the found adapter.
+.TP
+\fB\-d\fR, \fB\-\-double\-encode\fR
+Double\-encode colors (map 0,1,2,3,4 to A,C,G,T,N).
+.TP
+\fB\-t\fR, \fB\-\-trim\-primer\fR
+Trim primer base and the first color (which is the
+transition to the first nucleotide)
+.TP
+\fB\-\-strip\-f3\fR
+Strip the _F3 suffix of read names
+.TP
+\fB\-\-maq\fR, \fB\-\-bwa\fR
+MAQ\- and BWA\-compatible colorspace output. This
+enables \fB\-c\fR, \fB\-d\fR, \fB\-t\fR, \fB\-\-strip\-f3\fR and \fB\-y\fR '/1'.
+.TP
+\fB\-\-no\-zero\-cap\fR
+Do not change negative quality values to zero in
+colorspace data. By default, they are since many tools
+have problems with negative qualities.
+.TP
+\fB\-z\fR, \fB\-\-zero\-cap\fR
+Change negative quality values to zero. This is
+enabled by default when \fB\-c\fR/\-\-colorspace is also
+enabled. Use the above option to disable it.
+.IP
+Paired\-end options:
+.IP
+The \fB\-A\fR/\-G/\-B/\-U options work like their \fB\-a\fR/\-b/\-g/\-u counterparts, but
+are applied to the second read in each pair.
+.TP
+\fB\-A\fR ADAPTER
+3' adapter to be removed from second read in a pair.
+.TP
+\fB\-G\fR ADAPTER
+5' adapter to be removed from second read in a pair.
+.TP
+\fB\-B\fR ADAPTER
+5'/3 adapter to be removed from second read in a pair.
+.TP
+\fB\-U\fR LENGTH
+Remove LENGTH bases from second read in a pair (see
+\fB\-\-cut\fR).
+.TP
+\fB\-p\fR FILE, \fB\-\-paired\-output\fR=\fI\,FILE\/\fR
+Write second read in a pair to FILE.
+.TP
+\fB\-\-pair\-filter=\fR(any|both)
+Which of the reads in a paired\-end read have to match
+the filtering criterion in order for it to be
+filtered. Default: any
+.TP
+\fB\-\-interleaved\fR
+Read and write interleaved paired\-end reads.
+.TP
+\fB\-\-untrimmed\-paired\-output\fR=\fI\,FILE\/\fR
+Write second read in a pair to this FILE when no
+adapter was found in the first read. Use this option
+together with \fB\-\-untrimmed\-output\fR when trimming pairedend reads. Default: output to same file as trimmed
+reads
+.TP
+\fB\-\-too\-short\-paired\-output\fR=\fI\,FILE\/\fR
+Write second read in a pair to this file if pair is
+too short. Use together with \fB\-\-too\-short\-output\fR.
+.TP
+\fB\-\-too\-long\-paired\-output\fR=\fI\,FILE\/\fR
+Write second read in a pair to this file if pair is
+too long. Use together with \fB\-\-too\-long\-output\fR.
+.SH SEE ALSO
+See http://cutadapt.readthedocs.org/ for full documentation.
+.SS Citation
+Marcel Martin. Cutadapt removes adapter sequences from high\-throughput
+sequencing reads. EMBnet.Journal, 17(1):10\-12, May 2011.
+http://dx.doi.org/10.14806/ej.17.1.200
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/patches/cython_version.patch b/debian/patches/cython_version.patch
new file mode 100644
index 0000000..3a43387
--- /dev/null
+++ b/debian/patches/cython_version.patch
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 20 Jun 2016 14:38:23 +0200
+Description: Lets hope that the available cython (even in Jessie backports)
+ version is sufficient ...
+
+--- a/setup.py
++++ b/setup.py
+@@ -14,7 +14,7 @@ from distutils.version import LooseVersi
+ from distutils.command.sdist import sdist as _sdist
+ from distutils.command.build_ext import build_ext as _build_ext
+
+-MIN_CYTHON_VERSION = '0.24'
++MIN_CYTHON_VERSION = '0.23.2'
+
+ if sys.version_info < (2, 6):
+ sys.stdout.write("At least Python 2.6 is required.\n")
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..80f9065
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+cython_version.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..eef8cce
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,8 @@
+#!/usr/bin/make -f
+
+# Fails to build when set to +all
+# export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
+
+%:
+ dh $@ --with python2 --buildsystem=pybuild
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..750f74f
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Marcel Martin
+ Title: Cutadapt removes adapter sequences from high-throughput sequencing reads
+ Journal: EMBnet.journal
+ Year: 2012
+ Volume: 17
+ Number: 1
+ Pages: 10-12
+ DOI: 10.14806/ej.17.1.200
+ URL: http://journal.embnet.org/index.php/embnetjournal/article/view/200
+ eprint: http://journal.embnet.org/index.php/embnetjournal/article/view/200/458
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..8d62bc2
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+https://github.com/marcelm/cutadapt/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
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