# HG changeset patch # User crs4 # Date 1395143362 14400 # Node ID 6820983ba5d5218f8df18105c1c9c78b44c98bb5 Uploaded diff -r 000000000000 -r 6820983ba5d5 COPYING --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Tue Mar 18 07:49:22 2014 -0400 @@ -0,0 +1,182 @@ +Copyright (c) 2009-2013 Pennsylvania State University +Copyright © 2013 Yufei Luo +Copyright © 2014 CRS4 Srl. http://www.crs4.it/ +Created by: +Kelly Vincent +Daniel Blankenberg +Yufei Luo +Nicola Soranzo + +Licensed under the Academic Free License version 3.0 + + 1) Grant of Copyright License. Licensor grants You a worldwide, royalty-free, + non-exclusive, sublicensable license, for the duration of the copyright, to + do the following: + + a) to reproduce the Original Work in copies, either alone or as part of a + collective work; + + b) to translate, adapt, alter, transform, modify, or arrange the Original + Work, thereby creating derivative works ("Derivative Works") based upon + the Original Work; + + c) to distribute or communicate copies of the Original Work and Derivative + Works to the public, under any license of your choice that does not + contradict the terms and conditions, including Licensor's reserved + rights and remedies, in this Academic Free License; + + d) to perform the Original Work publicly; and + + e) to display the Original Work publicly. + + 2) Grant of Patent License. Licensor grants You a worldwide, royalty-free, + non-exclusive, sublicensable license, under patent claims owned or + controlled by the Licensor that are embodied in the Original Work as + furnished by the Licensor, for the duration of the patents, to make, use, + sell, offer for sale, have made, and import the Original Work and + Derivative Works. + + 3) Grant of Source Code License. The term "Source Code" means the preferred + form of the Original Work for making modifications to it and all available + documentation describing how to modify the Original Work. Licensor agrees + to provide a machine-readable copy of the Source Code of the Original Work + along with each copy of the Original Work that Licensor distributes. + Licensor reserves the right to satisfy this obligation by placing a + machine-readable copy of the Source Code in an information repository + reasonably calculated to permit inexpensive and convenient access by You + for as long as Licensor continues to distribute the Original Work. + + 4) Exclusions From License Grant. Neither the names of Licensor, nor the + names of any contributors to the Original Work, nor any of their + trademarks or service marks, may be used to endorse or promote products + derived from this Original Work without express prior permission of the + Licensor. Except as expressly stated herein, nothing in this License + grants any license to Licensor's trademarks, copyrights, patents, trade + secrets or any other intellectual property. No patent license is granted + to make, use, sell, offer for sale, have made, or import embodiments of + any patent claims other than the licensed claims defined in Section 2. + No license is granted to the trademarks of Licensor even if such marks + are included in the Original Work. Nothing in this License shall be + interpreted to prohibit Licensor from licensing under terms different + from this License any Original Work that Licensor otherwise would have a + right to license. + + 5) External Deployment. The term "External Deployment" means the use, + distribution, or communication of the Original Work or Derivative Works + in any way such that the Original Work or Derivative Works may be used by + anyone other than You, whether those works are distributed or + communicated to those persons or made available as an application + intended for use over a network. As an express condition for the grants + of license hereunder, You must treat any External Deployment by You of + the Original Work or a Derivative Work as a distribution under + section 1(c). + + 6) Attribution Rights. You must retain, in the Source Code of any Derivative + Works that You create, all copyright, patent, or trademark notices from + the Source Code of the Original Work, as well as any notices of licensing + and any descriptive text identified therein as an "Attribution Notice." + You must cause the Source Code for any Derivative Works that You create + to carry a prominent Attribution Notice reasonably calculated to inform + recipients that You have modified the Original Work. + + 7) Warranty of Provenance and Disclaimer of Warranty. Licensor warrants that + the copyright in and to the Original Work and the patent rights granted + herein by Licensor are owned by the Licensor or are sublicensed to You + under the terms of this License with the permission of the contributor(s) + of those copyrights and patent rights. Except as expressly stated in the + immediately preceding sentence, the Original Work is provided under this + License on an "AS IS" BASIS and WITHOUT WARRANTY, either express or + implied, including, without limitation, the warranties of + non-infringement, merchantability or fitness for a particular purpose. + THE ENTIRE RISK AS TO THE QUALITY OF THE ORIGINAL WORK IS WITH YOU. This + DISCLAIMER OF WARRANTY constitutes an essential part of this License. + No license to the Original Work is granted by this License except under + this disclaimer. + + 8) Limitation of Liability. Under no circumstances and under no legal + theory, whether in tort (including negligence), contract, or otherwise, + shall the Licensor be liable to anyone for any indirect, special, + incidental, or consequential damages of any character arising as a result + of this License or the use of the Original Work including, without + limitation, damages for loss of goodwill, work stoppage, computer failure + or malfunction, or any and all other commercial damages or losses. This + limitation of liability shall not apply to the extent applicable law + prohibits such limitation. + + 9) Acceptance and Termination. If, at any time, You expressly assented to + this License, that assent indicates your clear and irrevocable acceptance + of this License and all of its terms and conditions. If You distribute or + communicate copies of the Original Work or a Derivative Work, You must + make a reasonable effort under the circumstances to obtain the express + assent of recipients to the terms of this License. This License + conditions your rights to undertake the activities listed in Section 1, + including your right to create Derivative Works based upon the Original + Work, and doing so without honoring these terms and conditions is + prohibited by copyright law and international treaty. Nothing in this + License is intended to affect copyright exceptions and limitations + (including "fair use" or "fair dealing"). This License shall terminate + immediately and You may no longer exercise any of the rights granted to + You by this License upon your failure to honor the conditions in + Section 1(c). + +10) Termination for Patent Action. This License shall terminate + automatically and You may no longer exercise any of the rights granted + to You by this License as of the date You commence an action, including + a cross-claim or counterclaim, against Licensor or any licensee alleging + that the Original Work infringes a patent. This termination provision + shall not apply for an action alleging patent infringement by + combinations of the Original Work with other software or hardware. + +11) Jurisdiction, Venue and Governing Law. Any action or suit relating to + this License may be brought only in the courts of a jurisdiction wherein + the Licensor resides or in which Licensor conducts its primary business, + and under the laws of that jurisdiction excluding its conflict-of-law + provisions. The application of the United Nations Convention on + Contracts for the International Sale of Goods is expressly excluded. Any + use of the Original Work outside the scope of this License or after its + termination shall be subject to the requirements and penalties of + copyright or patent law in the appropriate jurisdiction. This section + shall survive the termination of this License. + +12) Attorneys' Fees. In any action to enforce the terms of this License or + seeking damages relating thereto, the prevailing party shall be entitled + to recover its costs and expenses, including, without limitation, + reasonable attorneys' fees and costs incurred in connection with such + action, including any appeal of such action. This section shall survive + the termination of this License. + +13) Miscellaneous. If any provision of this License is held to be + unenforceable, such provision shall be reformed only to the extent + necessary to make it enforceable. + +14) Definition of "You" in This License. "You" throughout this License, + whether in upper or lower case, means an individual or a legal entity + exercising rights under, and complying with all of the terms of, this + License. For legal entities, "You" includes any entity that controls, is + controlled by, or is under common control with you. For purposes of this + definition, "control" means (i) the power, direct or indirect, to cause + the direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + +15) Right to Use. You may use the Original Work in all ways not otherwise + restricted or conditioned by this License or by law, and Licensor + promises not to interfere with or be responsible for such uses by You. + +16) Modification of This License. This License is Copyright © 2005 Lawrence + Rosen. Permission is granted to copy, distribute, or communicate this + License without modification. Nothing in this License permits You to + modify this License as applied to the Original Work or to Derivative + Works. However, You may modify the text of this License and copy, + distribute or communicate your modified version (the "Modified + License") and apply it to other original works of authorship subject to + the following conditions: (i) You may not indicate in any way that your + Modified License is the "Academic Free License" or "AFL" and you may not + use those names in the name of your Modified License; (ii) You must + replace the notice specified in the first paragraph above with the + notice "Licensed under " or with a notice + of your own that is not confusingly similar to the notice in this + License; and (iii) You may not claim that your original works are open + source software unless your Modified License has been approved by Open + Source Initiative (OSI) and You comply with its license review and + certification process. diff -r 000000000000 -r 6820983ba5d5 bwa_mem.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwa_mem.py Tue Mar 18 07:49:22 2014 -0400 @@ -0,0 +1,273 @@ +# -*- coding: utf-8 -*- +#!/usr/bin/env python +## yufei.luo@gustave.roussy 22/07/2013 +## Copyright © 2014 CRS4 Srl. http://www.crs4.it/ +## Modified by: +## Nicola Soranzo + +""" +Runs BWA on single-end or paired-end data. +Produces a SAM file containing the mappings. +Works with BWA version >= 0.7.5. +NOTICE: In this wrapper, we only use 'mem' for mapping step. + +usage: bwa_mem.py [options] + +See below for options +""" + +import optparse, os, shutil, subprocess, sys, tempfile + +def stop_err( msg ): + sys.stderr.write( '%s\n' % msg ) + sys.exit() + +def check_is_double_encoded( fastq ): + # check that first read is bases, not one base followed by numbers + bases = [ 'A', 'C', 'G', 'T', 'a', 'c', 'g', 't', 'N' ] + nums = [ '0', '1', '2', '3' ] + for line in file( fastq, 'rb'): + if not line.strip() or line.startswith( '@' ): + continue + if len( [ b for b in line.strip() if b in nums ] ) > 0: + return False + elif line.strip()[0] in bases and len( [ b for b in line.strip() if b in bases ] ) == len( line.strip() ): + return True + else: + raise Exception, 'First line in first read does not appear to be a valid FASTQ read in either base-space or color-space' + raise Exception, 'There is no non-comment and non-blank line in your FASTQ file' + +def __main__(): + descr = "bwa_mem.py: Map (long length) reads against a reference genome with BWA-MEM." + parser = optparse.OptionParser(description=descr) + parser.add_option( '-t', '--threads', default=1, help='The number of threads to use [1]' ) + parser.add_option( '--ref', help='The reference genome to use or index' ) + parser.add_option( '-f', '--fastq', help='The (forward) fastq file to use for the mapping' ) + parser.add_option( '-F', '--rfastq', help='The reverse fastq file to use for mapping if paired-end data' ) + parser.add_option( '-u', '--output', help='The file to save the output (SAM format)' ) + parser.add_option( '-g', '--genAlignType', help='The type of pairing (single or paired)' ) + parser.add_option( '--params', help='Parameter setting to use (pre_set or full)' ) + parser.add_option( '-s', '--fileSource', help='Whether to use a previously indexed reference sequence or one form history (indexed or history)' ) + parser.add_option( '-D', '--dbkey', help='Dbkey for reference genome' ) + + parser.add_option( '-k', '--minEditDistSeed', default=19, type=int, help='Minimum edit distance to the seed [19]' ) + parser.add_option( '-w', '--bandWidth', default=100, type=int, help='Band width for banded alignment [100]' ) + parser.add_option( '-d', '--offDiagonal', default=100, type=int, help='off-diagonal X-dropoff [100]' ) + parser.add_option( '-r', '--internalSeeds', default=1.5, type=float, help='look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]' ) + parser.add_option( '-c', '--seedsOccurrence', default=10000, type=int, help='skip seeds with more than INT occurrences [10000]' ) + parser.add_option( '-S', '--mateRescue', default=False, help='skip mate rescue' ) + parser.add_option( '-P', '--skipPairing', default=False, help='skpe pairing, mate rescue performed unless -S also in use' ) + parser.add_option( '-A', '--seqMatch', default=1, type=int, help='score of a sequence match' ) + parser.add_option( '-B', '--mismatch', default=4, type=int, help='penalty for a mismatch' ) + parser.add_option( '-O', '--gapOpen', default=6, type=int, help='gap open penalty' ) + parser.add_option( '-E', '--gapExtension', default=None, help='gap extension penalty; a gap of size k cost {-O} + {-E}*k [1]' ) + parser.add_option( '-L', '--clipping', default=5, type=int, help='penalty for clipping [5]' ) + parser.add_option( '-U', '--unpairedReadpair', default=17, type=int, help='penalty for an unpaired read pair [17]' ) + parser.add_option( '-p', '--interPairEnd', default=False, help='first query file consists of interleaved paired-end sequences' ) + parser.add_option( '--rgid', help='Read group identifier' ) + parser.add_option( '--rgsm', help='Sample' ) + parser.add_option( '--rgpl', choices=[ 'CAPILLARY', 'LS454', 'ILLUMINA', 'SOLID', 'HELICOS', 'IONTORRENT', 'PACBIO' ], help='Platform/technology used to produce the reads' ) + parser.add_option( '--rglb', help='Library name' ) + parser.add_option( '--rgpu', help='Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)' ) + parser.add_option( '--rgcn', help='Sequencing center that produced the read' ) + parser.add_option( '--rgds', help='Description' ) + parser.add_option( '--rgdt', help='Date that run was produced (ISO8601 format date or date/time, like YYYY-MM-DD)' ) + parser.add_option( '--rgfo', help='Flow order' ) + parser.add_option( '--rgks', help='The array of nucleotide bases that correspond to the key sequence of each read' ) + parser.add_option( '--rgpg', help='Programs used for processing the read group' ) + parser.add_option( '--rgpi', help='Predicted median insert size' ) + parser.add_option( '-T', '--minScore', default=30, type=int, help='minimum score to output [30]' ) + parser.add_option( '-M', '--mark', default=False, help='mark shorter split hits as secondary (for Picard/GATK compatibility)' ) + parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' ) + (options, args) = parser.parse_args() + if len(args) > 0: + parser.error('Wrong number of arguments') + + # output version # of tool + try: + tmp = tempfile.NamedTemporaryFile().name + tmp_stdout = open( tmp, 'wb' ) + proc = subprocess.Popen( args='bwa 2>&1', shell=True, stdout=tmp_stdout ) + tmp_stdout.close() + returncode = proc.wait() + stdout = None + for line in open( tmp_stdout.name, 'rb' ): + if line.lower().find( 'version' ) >= 0: + stdout = line.strip() + break + if stdout: + sys.stdout.write( 'BWA %s\n' % stdout ) + else: + raise Exception + except: + sys.stdout.write( 'Could not determine BWA version\n' ) + + fastq = options.fastq + if options.rfastq: + rfastq = options.rfastq + + # make temp directory for placement of indices + tmp_index_dir = tempfile.mkdtemp() + tmp_dir = tempfile.mkdtemp() + # index if necessary + if options.fileSource == 'history': + ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir ) + ref_file_name = ref_file.name + ref_file.close() + os.symlink( options.ref, ref_file_name ) + # determine which indexing algorithm to use, based on size + try: + size = os.stat( options.ref ).st_size + if size <= 2**30: + indexingAlg = 'is' + else: + indexingAlg = 'bwtsw' + except: + indexingAlg = 'is' + indexing_cmds = '-a %s' % indexingAlg + cmd1 = 'bwa index %s %s' % ( indexing_cmds, ref_file_name ) + try: + tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + if returncode != 0: + raise Exception, stderr + except Exception, e: + # clean up temp dirs + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + if os.path.exists( tmp_dir ): + shutil.rmtree( tmp_dir ) + stop_err( 'Error indexing reference sequence. ' + str( e ) ) + else: + ref_file_name = options.ref + # if options.illumina13qual: + # illumina_quals = "-I" + # else: + # illumina_quals = "" + + # set up aligning and generate aligning command args + start_cmds = '-t %s ' % options.threads + if options.params == 'pre_set': + # aligning_cmds = '-t %s %s' % ( options.threads, illumina_quals ) + #start_cmds = '-t %s ' % options.threads + end_cmds = ' ' + print start_cmds, end_cmds + + else: + end_cmds = '-k %s -w %s -d %s -r %s -c %s -A %s -B %s -O %s -L %s -U %s -T %s ' % (options.minEditDistSeed, options.bandWidth, options.offDiagonal, options.internalSeeds, options.seedsOccurrence, options.seqMatch, options.mismatch, options.gapOpen, options.clipping, options.unpairedReadpair, options.minScore) + if options.mateRescue: + end_cmds += '-S ' + if options.skipPairing: + end_cmds += '-P ' + else: + if options.skipPairing: + print "Option Error and will not be considered, you should also choose 'skip mate rescue -S' option! " + if options.gapExtension != None: + end_cmds += '-E %s ' % options.gapExtension + + if options.rgid: + if not options.rglb or not options.rgpl or not options.rgsm or not options.rglb: + stop_err( 'If you want to specify read groups, you must include the ID, LB, PL, and SM tags.' ) + # readGroup = '@RG\tID:%s\tLB:%s\tPL:%s\tSM:%s' % ( options.rgid, options.rglb, options.rgpl, options.rgsm ) + readGroup = '@RG\tID:%s\tLB:%s\tPL:%s\tSM:%s' % ( options.rgid, options.rglb, options.rgpl, options.rgsm ) + if options.rgpu: + readGroup += '\tPU:%s' % options.rgpu + if options.rgcn: + readGroup += '\tCN:%s' % options.rgcn + if options.rgds: + readGroup += '\tDS:%s' % options.rgds + if options.rgdt: + readGroup += '\tDT:%s' % options.rgdt + if options.rgfo: + readGroup += '\tFO:%s' % options.rgfo + if options.rgks: + readGroup += '\tKS:%s' % options.rgks + if options.rgpg: + readGroup += '\tPG:%s' % options.rgpg + if options.rgpi: + readGroup += '\tPI:%s' % options.rgpi + end_cmds += ' -R "%s" ' % readGroup + + if options.interPairEnd: + end_cmds += '-p %s ' % options.interPairEnd + if options.mark: + end_cmds += '-M ' + + + if options.genAlignType == 'paired': + cmd = 'bwa mem %s %s %s %s %s > %s' % ( start_cmds, ref_file_name, fastq, rfastq, end_cmds, options.output ) + else: + cmd = 'bwa mem %s %s %s %s > %s' % ( start_cmds, ref_file_name, fastq, end_cmds, options.output ) + + # perform alignments + buffsize = 1048576 + try: + # need to nest try-except in try-finally to handle 2.4 + try: + try: + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + print "The cmd is %s" % cmd + proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) + stderr = '' + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + if returncode != 0: + raise Exception, stderr + except Exception, e: + raise Exception, 'Error generating alignments. ' + str( e ) + # remove header if necessary + if options.suppressHeader == 'true': + tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir) + tmp_out_name = tmp_out.name + tmp_out.close() + try: + shutil.move( options.output, tmp_out_name ) + except Exception, e: + raise Exception, 'Error moving output file before removing headers. ' + str( e ) + fout = file( options.output, 'w' ) + for line in file( tmp_out.name, 'r' ): + if not ( line.startswith( '@HD' ) or line.startswith( '@SQ' ) or line.startswith( '@RG' ) or line.startswith( '@PG' ) or line.startswith( '@CO' ) ): + fout.write( line ) + fout.close() + # check that there are results in the output file + if os.path.getsize( options.output ) > 0: + sys.stdout.write( 'BWA run on %s-end data' % options.genAlignType ) + else: + raise Exception, 'The output file is empty. You may simply have no matches, or there may be an error with your input file or settings.' + except Exception, e: + stop_err( 'The alignment failed.\n' + str( e ) ) + finally: + # clean up temp dir + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + if os.path.exists( tmp_dir ): + shutil.rmtree( tmp_dir ) + +if __name__ == "__main__": + __main__() diff -r 000000000000 -r 6820983ba5d5 bwa_mem.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwa_mem.xml Tue Mar 18 07:49:22 2014 -0400 @@ -0,0 +1,208 @@ + + + bwa + + + + bwa 2>&1 | grep "Version: " | sed -e 's/Version: //' + + bwa_mem.py + --threads="\${GALAXY_SLOTS:-1}" + --fileSource="${genomeSource.refGenomeSource}" + #if $genomeSource.refGenomeSource == "history": + ##build index on the fly + --ref="${genomeSource.ownFile}" + --dbkey="${dbkey}" + #else: + ##use precomputed indexes + --ref="${genomeSource.indices.fields.path}" + #end if + + ## input file(s) + --fastq="${paired.fastq}" + #if $paired.sPaired == "paired": + --rfastq="${paired.rfastq}" + #end if + + ## output file + --output="${output}" + + ## run parameters + --genAlignType="${paired.sPaired}" + --params="${params.source_select}" + #if $params.source_select != "pre_set": + --minEditDistSeed="${params.minEditDistSeed}" + --bandWidth="${params.bandWidth}" + --offDiagonal="${params.offDiagonal}" + --internalSeeds="${params.internalSeeds}" + --seedsOccurrence="${params.seedsOccurrence}" + --mateRescue="${params.mateRescue}" + --skipPairing="${params.skipPairing}" + --seqMatch="${params.seqMatch}" + --mismatch="${params.mismatch}" + --gapOpen="${params.gapOpen}" + --gapExtension="${params.gapExtension}" + --clipping="${params.clipping}" + --unpairedReadpair="${params.unpairedReadpair}" + --interPairEnd="${params.interPairEnd}" + --minScore="${params.minScore}" + --mark="${params.mark}" + + #if $params.readGroup.specReadGroup == "yes" + --rgid="${params.readGroup.rgid}" + --rgsm="${params.readGroup.rgsm}" + --rgpl="${params.readGroup.rgpl}" + --rglb="${params.readGroup.rglb}" + --rgpu="${params.readGroup.rgpu}" + --rgcn="${params.readGroup.rgcn}" + --rgds="${params.readGroup.rgds}" + --rgdt="${params.readGroup.rgdt}" + --rgfo="${params.readGroup.rgfo}" + --rgks="${params.readGroup.rgks}" + --rgpg="${params.readGroup.rgpg}" + --rgpi="${params.readGroup.rgpi}" + #end if + #end if + + ## suppress output SAM header + --suppressHeader="${suppressHeader}" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. BWA-MEM, which is the latest algorithm, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads. + +------ + +**Input formats** + +BWA accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*) or Illumina FASTQ format (galaxy type *fastqillumina*). Use the FASTQ Groomer to prepare your files. + +------ + +**License and citation** + +This tool uses `BWA`_, which is licensed separately. Please cite |Li2013|_. + +.. _BWA: http://bio-bwa.sourceforge.net/ +.. |Li2013| replace:: Li, H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997 [q-bio.GN] +.. _Li2013: http://arxiv.org/abs/1303.3997 + + diff -r 000000000000 -r 6820983ba5d5 readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Tue Mar 18 07:49:22 2014 -0400 @@ -0,0 +1,33 @@ +BWA-MEM wrapper +=============== + +This is a wrapper for BWA_, a software package for mapping low-divergent sequences against a large reference genome. This wrapper supports only the latest algorithm, BWA-MEM, which is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads. + +.. _BWA: http://bio-bwa.sourceforge.net/ + +If you need a wrapper for the old BWA-backtrack algorithm, you may install http://toolshed.g2.bx.psu.edu/view/devteam/bwa_wrappers repository. + +Configuration +------------- + +bwa_mem tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see https://wiki.galaxyproject.org/Admin/Config/Jobs and https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ). + +If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of CPU cores allocated by the job runner according to the configuration of the destination selected for this tool. + +If instead you are using an older Galaxy release, you should also add a line + + GALAXY_SLOTS=N; export GALAXY_SLOTS + +(where N is the number of CPU cores allocated by the job runner for this tool) to the file + + /bwa/0.7.7/crs4/bwa_mem//env.sh + +Version history +--------------- + +- Release 0: Initial release in the Tool Shed. This is a fork of http://toolshed.g2.bx.psu.edu/view/yufei-luo/bwa_0_7_5 repository with the following changes: Remove .loc file, only .loc.sample should be included. Fix bwa_index.loc.sample file to contain only comments. Add suppressHeader param as in bwa_wrappers. Use $GALAXY_SLOTS environment variable when available. Add and . Remove unused import. Fix spacing and typos. Use new recommended citation. Add tool_dependencies.xml . Rename to bwa_mem. Remove definitively colorspace support. Use optparse instead of argparse since Galaxy still supports Python 2.6 . + +Development +----------- + +Development is hosted at https://bitbucket.org/nsoranzo/bwa_mem . Contributions and bug reports are very welcome! diff -r 000000000000 -r 6820983ba5d5 tool-data/bwa_index.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bwa_index.loc.sample Tue Mar 18 07:49:22 2014 -0400 @@ -0,0 +1,38 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of BWA indexed sequences data files. You will need +#to create these data files and then create a bwa_index.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bwa_index.loc +#file has this format (longer white space characters are TAB characters): +# +# +# +#So, for example, if you had phiX indexed stored in +#/depot/data2/galaxy/phiX/base/, +#then the bwa_index.loc entry would look like this: +# +#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa +# +#and your /depot/data2/galaxy/phiX/base/ directory +#would contain phiX.fa.* files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt +#...etc... +# +#Your bwa_index.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# diff -r 000000000000 -r 6820983ba5d5 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Mar 18 07:49:22 2014 -0400 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+ diff -r 000000000000 -r 6820983ba5d5 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Mar 18 07:49:22 2014 -0400 @@ -0,0 +1,6 @@ + + + + + +