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commit 4da904535e2af8ca8ca034e50270735499ccca50 Author: Andreas Tille <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> +License: MIT + +Files: debian/* +Copyright: 2016 Andreas Tille <[email protected]> +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 <[email protected]> +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) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cutadapt.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
