# HG changeset patch # User iuc # Date 1449410677 18000 # Node ID b723c120161a5e7ed20b2c79545e184ff0597e0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 diff -r 000000000000 -r b723c120161a LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Sun Dec 06 09:04:37 2015 -0500 @@ -0,0 +1,60 @@ +CONTENTS + + Public Domain Notice + Exceptions (for bundled 3rd-party code) + Copyright F.A.Q. + + +============================================================== + PUBLIC DOMAIN NOTICE + National Center for Biotechnology Information + +With the exception of certain third-party files summarized below, this +software is a "United States Government Work" under the terms of the +United States Copyright Act. It was written as part of the authors' +official duties as United States Government employees and thus cannot +be copyrighted. This software is freely available to the public for +use. The National Library of Medicine and the U.S. Government have not +placed any restriction on its use or reproduction. + +Although all reasonable efforts have been taken to ensure the accuracy +and reliability of the software and data, the NLM and the U.S. +Government do not and cannot warrant the performance or results that +may be obtained by using this software or data. The NLM and the U.S. +Government disclaim all warranties, express or implied, including +warranties of performance, merchantability or fitness for any +particular purpose. + +Please cite the authors in any work or product based on this material. + + +============================================================== +Copyright F.A.Q. + + +-------------------------------------------------------------- +Q. Our product makes use of the NCBI source code, and we made changes + and additions to that version of the NCBI code to better fit it to + our needs. Can we copyright the code, and how? + +A. You can copyright only the *changes* or the *additions* you made to the + NCBI source code. You should identify unambiguously those sections of + the code that were modified, e.g. by commenting any changes you made + in the code you distribute. Therefore, your license has to make clear + to users that your product is a combination of code that is public domain + within the U.S. (but may be subject to copyright by the U.S. in foreign + countries) and code that has been created or modified by you. + +-------------------------------------------------------------- +Q. Can we (re)license all or part of the NCBI source code? + +A. No, you cannot license or relicense the source code written by NCBI + since you cannot claim any copyright in the software that was developed + at NCBI as a 'government work' and consequently is in the public domain + within the U.S. + +-------------------------------------------------------------- +Q. What if these copyright guidelines are not clear enough or are not + applicable to my particular case? + +A. Contact us. Send your questions to 'sra-tools@ncbi.nlm.nih.gov'. diff -r 000000000000 -r b723c120161a README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Sun Dec 06 09:04:37 2015 -0500 @@ -0,0 +1,68 @@ +The Galaxy tool wrappers contained in this tool shed repository rely on software developed by +the NCBI: http://github.com/ncbi/sra-tools. + +NCBI Sequence Read Archive: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. +Use of SRA Toolkit software herein should comply with the GPL v2 or greater. + +Copyright (C) 2013 Matthew Shirley + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +# INSTALLATION + +This software release was designed to install using the Galaxy toolshed under Linux and MacOS operating systems on Intel x86-compatible 32/64 bit architectures. + +*Build Requirements* + +- bash +- make +- gcc +- g++ +- libxml2 + +On a Debian OS use: + + apt-get install build-essential libxml2-dev + +On a Mac with [command line tools](https://developer.apple.com/downloads/index.action) installed: + + brew install libxml2 + +# Installation of Aspera connect ascp binary + +The sra-tools suite is ready to benefit from increased transfer speed and reliability by using Aspera Connect ascp. +To benefit, download the ascp commandline client, and place ascp and the required ssh keys into a PATH accessible to galaxys job handler. + +A convenience package for linux and OS X is available at https://toolshed.g2.bx.psu.edu/view/mvdbeek/package_ascp_3/e109f0ec22c3 . +It suffices to copy the contents of the $INSTALL_DIR/bin into PATH. + +Alternatively go to http://downloads.asperasoft.com/connect2/ . + +Aspera connect is not provided by the IUC due to its closed-source nature. + +# Firewall settings for highspeed transfer + +To benefit from increased transfer speeds using ascp3 your local firewall must permit UDP data transfer in both +directions on ports 33001-33009 for the following IP ranges: + + 130.14.*.* + + 165.112.*.* + +The firewall must also allow ssh traffic outbound to NCBI. +The wrapper will fall back to http download if these requirements are not met. + +CONTROLLED-ACCESS DATA + +Encrypted, controlled-access data is not supported. diff -r 000000000000 -r b723c120161a fastq_dump.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_dump.xml Sun Dec 06 09:04:37 2015 -0500 @@ -0,0 +1,149 @@ + + in FASTQ/A format from NCBI SRA. + + sra_macros.xml + + + + + + fastq-dump --version + + "$output_file" + #else: + "$input.accession" > "$output_accession" + #end if + ]]> + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + +
+ + + + input['input_select'] == "accession_number" + + + + + + input['input_select'] == "file" + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool extracts reads from SRA archives using fastq-dump. + The fastq-dump program is developed at NCBI, and is available at + http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. + @SRATOOLS_ATTRRIBUTION@ + + + diff -r 000000000000 -r b723c120161a sam_dump.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam_dump.xml Sun Dec 06 09:04:37 2015 -0500 @@ -0,0 +1,118 @@ + + in SAM or BAM format from NCBI SRA. + + sra_macros.xml + + + sam-dump --version + + /dev/null + #end if + #if $input.input_select == "file": + > "$output_file" + #elif $input.input_select == "accession_number": + > "$output_accession" + #end if + ]]> + + + + + + + +
+ + + + + + + + + + + + + + +
+ + + + input['input_select'] == "accession_number" + + + + + + input['input_select'] == "file" + + + + + + + + + + + + + + + + This tool extracts reads from sra archives using sam-dump. + The sam-dump program is developed at NCBI, and is available at + http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. + @SRATOOLS_ATTRRIBUTION@ + + + diff -r 000000000000 -r b723c120161a sra_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sra_macros.xml Sun Dec 06 09:04:37 2015 -0500 @@ -0,0 +1,52 @@ + + + + ngs_sdk + ncbi_vdb + sra_toolkit + perl + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1093/nar/gkq1019 + + + Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. + Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com). + Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com). + For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/galaxyproject/tools-iuc. + diff -r 000000000000 -r b723c120161a sra_pileup.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sra_pileup.xml Sun Dec 06 09:04:37 2015 -0500 @@ -0,0 +1,88 @@ + + from NCBI sra. + + sra_macros.xml + + + sra-pileup --version + + "$output_file" + #elif $input.input_select == "accession_number": + "$input.accession" > "$output_accession" + #elif $input.input_select == "text": + `cat "$input.text"` > "$output_text" + #end if + ]]> + + + + + + + + + + + + + + + + + + +
+ + +
+ + + + input['input_select'] == "accession_number" + + + input['input_select'] == "file" + + + input['input_select'] == "text" + + + + + + + + + + + + This tool produces pileup format from sra archives using sra-pileup. + The sra-pileup program is developed at NCBI, and is available at + http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. + @SRATOOLS_ATTRRIBUTION@ + + + diff -r 000000000000 -r b723c120161a test-data/bam_dump_result.bam Binary file test-data/bam_dump_result.bam has changed diff -r 000000000000 -r b723c120161a test-data/fastq_dump_result.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dump_result.fastq Sun Dec 06 09:04:37 2015 -0500 @@ -0,0 +1,40 @@ +@1/1 +AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT ++SRR925743.1 1 length=100 +EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDDBA8:>@:4+36945&4354445>/B>@ +@1/2 +CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA ++SRR925743.1 1 length=100 +GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF?EHGGHHHGHFHEHDEHGHFFEEE9BDDBEBAD.AD:ACBBC=4@>?5>=+? +@2/1 +AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGT ++SRR925743.2 2 length=100 +HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFGGEEAEEEDD0ADDBD9BDBDDA@6?BA;?CD=:-7<<::)1;5,6-6A@?=9 +@2/2 +CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA ++SRR925743.2 2 length=100 +HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHHHHHHHHHHGHHHGHHBHGHHFDBDDED5FCFCEEGF<@>>>@,<5<@@?>;D +@3/1 +CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCA ++SRR925743.3 3 length=100 +HHHHFHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHGEFHGEGGFGGGGGGHHHHEFEIDDEEEEEDD4DD;??:6>6<@.<==@?.@@BEEEE3B;BB;>B7C@DA=DFBDD.BEE=9 +@4/1 +CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTAACCCTAACCCTAACCCTA ++SRR925743.4 4 length=100 +HHGBHHHHGFHHHHHFDHHFHGEHHHHHEFHHHHEGEGEFFFAFFFDCFGF?@GCDFGFEFHHEFDF*F6DC4DD:A8>@D@CD8->=>=<@CB@##### +@4/2 +ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT ++SRR925743.4 4 length=100 +GFFFHHFFHHHFHHFEFGGBGEEEE?<9?6=>>:=DDDD@DBGDB;DBDBA.ADD8<2<>6A@=A5>550=>>>>BE;EEEDEEE79+336<68=BCEB@ +@5/1 +CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTCACACTCACCCTA ++SRR925743.5 5 length=100 +GGGFGFFGGGFBGGEGGFFGGGCFFGGGGGEGFFFFFGFFGFFFDFFB+FGGFEE?FCF::7B5A?+BB############################### +@5/2 +ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTAGGGTTAGGGTTAGGGTTAGGGGTAGGGT ++SRR925743.5 5 length=100 +479<.>><:+?=9@######## diff -r 000000000000 -r b723c120161a test-data/sam_dump_result.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sam_dump_result.sam Sun Dec 06 09:04:37 2015 -0500 @@ -0,0 +1,10 @@ +44155511 165 * 0 0 * 17 41275978 0 CATTAATGCTATGCAGATAATCATAGGAATCCCAAATTAATACACTCTTGTGCTGACTTACCAGATGGGACACTCTAAGATTTTCTGCATAGCATTAATG HHHHHHHHHHHHHHHHHGHDHHHHHHHHHHHHHEHHHHHHHGHHHGHHHHHHHHHHHHHHHHHHHGFHHFHHHHHFHEBGHHHHHDCBDDFCFBBDBCCDEGGFEEEE=ECADDFFGD@BGFFEEC8EEE=EEGDBDDDEGBDFG7@B>BAGBADGDEEB RG:Z:0 +44155531 165 * 0 0 * 17 41276036 0 AAGTTCATTGGGACACTCTAAGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTGTTCCAAT HFHHEHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHACFIFGIGHHHFHFGHHHHHFHHFF5HH RG:Z:0 +44155532 165 * 0 0 * 17 41276056 0 AGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTAGATCGGAAGAGCGTCGT HHHHHHHHHHHHHHHHHGHHHHHHHHHHHFHHHHHHGHHHHFGHHGHHHHHHHHHHHHHHHEHHFGBGGGFHHHHHHDHHHHHHFGHHC:EA9BEEDDGB RG:Z:0 +44155533 165 * 0 0 * 17 41276058 0 AGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTAGATCGGAAGAGCGTCGT HHHHHHHHHHHHHHHHHHHHHHDEHEHHHHEHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHGHEHHEHHHHHHHHHHHHEHHHHHFHHFHHHEEHF9 RG:Z:0 +44155535 165 * 0 0 * 17 41276061 0 AGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTAGATCGGAAGAGCGTCGT HHHHHHFHHHHHHHHHHHHGHHHFHHHHHFHHHHHFHHHHHHHHHHFHHHGFHHFGHHHHHHHHHEFHHHHHGHHGGHHGHHHHEGH=CHG@E + + + + + + + + + + + + + +