Mercurial > repos > iuc > sra_tools
changeset 0:b723c120161a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
| author | iuc |
|---|---|
| date | Sun, 06 Dec 2015 09:04:37 -0500 |
| parents | |
| children | 462ee06c9358 |
| files | LICENSE README.rst fastq_dump.xml sam_dump.xml sra_macros.xml sra_pileup.xml test-data/bam_dump_result.bam test-data/fastq_dump_result.fastq test-data/sam_dump_result.sam test-data/sra_pileup_result.pileup tool_dependencies.xml |
| diffstat | 11 files changed, 610 insertions(+), 0 deletions(-) [+] |
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--- /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'.
--- /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 <http://www.gnu.org/licenses/>. + +# 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.
--- /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 @@ +<tool id="fastq_dump" name="Extract reads" version="1.2.5"> + <description>in FASTQ/A format from NCBI SRA.</description> + <macros> + <import>sra_macros.xml</import> + </macros> + <expand macro="requirements"/> + <stdio> + <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/> + </stdio> + <version_command>fastq-dump --version</version_command> + <command> + <![CDATA[ + ## Need to set the home directory to the current working directory, + ## else the tool tries to write to home/.ncbi and fails when used + ## with a cluster manager. + export HOME=\$PWD && + vdb-config --restore-defaults && + #if $input.input_select == "file": + fastq-dump --log-level fatal --accession '${input.file.name}' + #else: + vdb-config -s "/repository/user/main/public/root=\$PWD" && + ## Do not use prefetch if region is specified, to avoid downloading + ## the complete sra file. + #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ): + ASCP_PATH=`command -v ascp` && + ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true && + prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" $input.accession && + ## Duplicate vdb-config, in case settings changed between prefetch and + ## dump command. + vdb-config -s "/repository/user/main/public/root=\$PWD" && + #end if + fastq-dump --accession "$input.accession" + #end if + --defline-seq '@\$sn[_\$rn]/\$ri' + --stdout + $adv.split + #if str( $adv.alignments ) == "aligned": + --aligned + #end if + #if str( $adv.alignments ) == "unaligned": + --unaligned + #end if + #if str( $adv.minID ) != "": + --minSpotId "$adv.minID" + #end if + #if str( $adv.maxID ) != "": + --maxSpotId "$adv.maxID" + #end if + #if str( $adv.minlen ) != "": + --minReadLen "$adv.minlen" + #end if + #if str( $adv.readfilter ) != "": + --read-filter "$adv.readfilter" + #end if + #if str( $adv.region ) != "": + --aligned-region "$adv.region" + #end if + #if str( $adv.spotgroups ) != "": + --spot-groups "$adv.spotgroups" + #end if + #if str( $adv.matepairDist ) != "": + --matepair-distance "$adv.matepairDist" + #end if + $adv.clip + $adv.skip_technical + #if str( $outputformat ) == "fasta": + --fasta + #end if + #if $input.input_select=="file": + "$input.file" > "$output_file" + #else: + "$input.accession" > "$output_accession" + #end if + ]]> + </command> + <inputs> + <expand macro="input_conditional"/> + <param name="outputformat" type="select" label="select output format"> + <option value="fastqsanger">fastq</option> + <option value="fasta">fasta</option> + </param> + <section name="adv" title="Advanced Options" expanded="False"> + <param name="minID" type="integer" label="minimum spot ID" optional="true"/> + <param name="maxID" type="integer" label="maximum spot ID" optional="true"/> + <param name="minlen" type="integer" label="minimum read length" optional="true"/> + <param name="split" type="boolean" checked="true" truevalue="--split-spot" falsevalue=""> + <label>split spot by read pairs</label> + </param> + <expand macro="alignments"/> + <expand macro="region"/> + <expand macro="matepairDist"/> + <param name="readfilter" type="select" value=""> + <label>filter by value</label> + <option value="">None</option> + <option value="pass">pass</option> + <option value="reject">reject</option> + <option value="criteria">criteria</option> + <option value="redacted">redacted</option> + </param> + <param name="spotgroups" type="text" label="filter by spot-groups" optional="true"/> + <param name="clip" type="boolean" truevalue="--clip" falsevalue=""> + <label>apply left and right clips</label> + </param> + <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="" checked="False" label="Dump only biological reads"/> + </section> + </inputs> + <outputs> + <data format="fastq" name="output_accession" label="${input.accession}.${outputformat}"> + <filter>input['input_select'] == "accession_number"</filter> + <change_format> + <when input="outputformat" value="fasta" format="fasta"/> + </change_format> + </data> + <data format="fastq" name="output_file" label="${input.file.name}.${outputformat}"> + <filter>input['input_select'] == "file"</filter> + <change_format> + <when input="outputformat" value="fasta" format="fasta"/> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input_select" value="accession_number"/> + <param name="outputformat" value="fastqsanger"/> + <param name="accession" value="SRR044777"/> + <param name="skip_technical" value="True"/> + <output name="output_accession"> + <assert_contents> + <not_has_text text="rRNA_primer"/> + <has_text text="F47USSH02GNP1D" /> + </assert_contents> + </output> + </test> + <test> + <param name="input_select" value="accession_number"/> + <param name="outputformat" value="fastqsanger"/> + <param name="accession" value="SRR925743"/> + <param name="maxID" value="5"/> + <output name="output_accession" file="fastq_dump_result.fastq" ftype="fastq"/> + </test> + </tests> + <help> + 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@ + </help> + <expand macro="citation"/> +</tool>
--- /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 @@ +<tool id="sam_dump" name="Extract reads" version="1.2.5"> + <description>in SAM or BAM format from NCBI SRA.</description> + <macros> + <import>sra_macros.xml</import> + </macros> + <expand macro="requirements"/> + <version_command>sam-dump --version</version_command> + <command> + <![CDATA[ + ## Need to set the home directory to the current working directory, + ## else the tool tries to write to home/.ncbi and fails when used + ## with a cluster manager. + export HOME=\$PWD && + vdb-config --restore-defaults && + vdb-config -s "/repository/user/main/public/root=\$PWD" && + ## Do not use prefetch if region is specified, to avoid downloading + ## the complete sra file. + #if ( str( $adv.region ) == "" ): + ASCP_PATH=`command -v ascp` && + ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true && + prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession" && + ## Duplicate vdb-config, in case settings changed between prefetch and + ## dump command. + vdb-config -s "/repository/user/main/public/root=\$PWD" && + #end if + sam-dump --log-level fatal --disable-multithreading + #if str( $adv.region ) != "": + --aligned-region "$adv.region" + #end if + #if str( $adv.matepairDist ) != "": + --matepair-distance "$adv.matepairDist" + #end if + #if str( $adv.minMapq ) != "": + --min-mapq "$adv.minMapq" + #end if + #if str( $adv.header ) == "yes": + --header + #else: + --no-header + #end if + #if str( $adv.alignments ) == "both": + --unaligned + #end if + #if str( $adv.alignments ) == "unaligned": + --unaligned-spots-only + #end if + #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ): + --primary + #end if + #if $input.input_select == "file": + "$input.file" + #elif $input.input_select == "accession_number": + "$input.accession" + #end if + #if str( $outputformat ) == "bam": + | samtools view -Sb - 2> /dev/null + #end if + #if $input.input_select == "file": + > "$output_file" + #elif $input.input_select == "accession_number": + > "$output_accession" + #end if + ]]> + </command> + <inputs> + <expand macro="input_conditional"/> + <param name="outputformat" type="select" label="select output format"> + <option value="bam">bam</option> + <option value="sam">sam</option> + </param> + <section name="adv" title="Advanced Options" expanded="False"> + <param name="header" type="select" value="yes"> + <label>output header</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <expand macro="alignments"/> + <expand macro="region"/> + <expand macro="matepairDist"/> + <param name="primary" type="select" value="no"> + <label>only primary aligments</label> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <expand macro="minMapq"></expand> + </section> + </inputs> + <outputs> + <data name="output_accession" format="bam" label="${input.accession}.${outputformat}"> + <filter>input['input_select'] == "accession_number"</filter> + <change_format> + <when input="outputformat" value="sam" format="sam"/> + </change_format> + </data> + <data name="output_file" format="bam" label="${input.file.name}.${outputformat}"> + <filter>input['input_select'] == "file"</filter> + <change_format> + <when input="outputformat" value="sam" format="sam"/> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input_select" value="accession_number"/> + <param name="accession" value="SRR925743"/> + <param name="outputformat" value="sam"/> + <param name="region" value="17:41243452-41277500"/> + <output name="output_accession" file="sam_dump_result.sam" compare="contains" ftype="sam"/> + </test> + </tests> + <help> + 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@ + </help> + <expand macro="citation"/> +</tool>
--- /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 @@ +<macros> + <macro name="requirements"> + <requirements> + <requirement type="package" version="1.1.3">ngs_sdk</requirement> + <requirement type="package" version="2.5.2">ncbi_vdb</requirement> + <requirement type="package" version="2.5.2">sra_toolkit</requirement> + <requirement type="package" version="5.18.1">perl</requirement> + </requirements> + </macro> + <macro name="input_conditional"> + <conditional name="input"> + <param name="input_select" type="select" label="select input type"> + <option value="accession_number">SRR accession</option> + <option value="file">SRA archive in current history</option> + </param> + <when value="accession_number"> + <param name="accession" type="text" label="SRR accession" help="Must start with SRR, e.g. SRR925743"/> + </when> + <when value="file"> + <param format="sra" name="file" type="data" label="sra archive"/> + </when> + </conditional> + </macro> + <macro name="alignments"> + <param name="alignments" type="select" value="both"> + <label>aligned or unaligned reads</label> + <option value="both">both</option> + <option value="aligned">aligned only</option> + <option value="unaligned">unaligned only</option> + </param> + </macro> + <macro name="minMapq"> + <param name="minMapq" type="integer" min="0" max="42" label="minimum mapping quality" optional="true"/> + </macro> + <macro name="region"> + <param format="text" name="region" type="text" label="aligned region" optional="true" + help="Filter by position on genome. Can be either accession.version (ex: NC_000001.10), chromosome name (ex:chr1 or 1) or 1-based coordinates (ex: chr1:1-101)."/> + </macro> + <macro name="matepairDist"> + <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true" + help="Filter by distance between matepairs. Use unknown to find matepairs split between the references. Use from-to (inclusive) to limit matepair distance on the same reference"/> + </macro> + <macro name="citation"> + <citations> + <citation type="doi">10.1093/nar/gkq1019</citation> + </citations> + </macro> + <token name="@SRATOOLS_ATTRRIBUTION@">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.</token> +</macros>
--- /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 @@ +<tool id="sra_pileup" name="Generate pileup format" version="1.2.5"> + <description>from NCBI sra.</description> + <macros> + <import>sra_macros.xml</import> + </macros> + <expand macro="requirements"/> + <version_command>sra-pileup --version</version_command> + <command> + <![CDATA[ + ## Need to set the home directory to the current working directory, + ## else the tool tries to write to home/.ncbi and fails when used + ## with a cluster manager. + export HOME=\$PWD && + vdb-config --restore-defaults && + vdb-config -s "/repository/user/main/public/root=\$PWD" && + #if ( str( $adv.region ) == "" ): + ASCP_PATH=`command -v ascp` && + ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true && + prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession" && + ## Duplicate vdb-config, in case settings changed between prefetch and + ## sra-pileup command. + vdb-config -s "/repository/user/main/public/root=\$PWD" && + #end if + sra-pileup --log-level fatal + #if str( $adv.region ) != "": + --aligned-region "$adv.region" + #end if + #if str( $adv.minMapq ) != "": + --minmapq "$adv.minMapq" + #end if + #if $input.input_select == "file": + "$input.file" > "$output_file" + #elif $input.input_select == "accession_number": + "$input.accession" > "$output_accession" + #elif $input.input_select == "text": + `cat "$input.text"` > "$output_text" + #end if + ]]> + </command> + <inputs> + <conditional name="input"> + <param name="input_select" type="select" label="select input type"> + <option value="accession_number">SRR accession</option> + <option value="file">SRA archive in current history</option> + <option value="text">text file containing SRR accession</option> + </param> + <when value="file"> + <param format="sra" name="file" type="data" label="sra archive"/> + </when> + <when value="accession_number"> + <param format="text" name="accession" type="text" label="SRR accession" help="Must start with SRR, e.g. SRR925743"/> + </when> + <when value="text"> + <param format="txt" name="text" type="data" label="text file"/> + </when> + </conditional> + <section name="adv" title="Advanced Options" expanded="False"> + <expand macro="region"/> + <expand macro="minMapq"/> + </section> + </inputs> + <outputs> + <data format="pileup" name="output_accession" label="${input.accession}.pileup"> + <filter>input['input_select'] == "accession_number"</filter> + </data> + <data format="pileup" name="output_file" label="${input.file.name}.pileup"> + <filter>input['input_select'] == "file"</filter> + </data> + <data format="pileup" name="output_text" label="${input.text.name}.pileup"> + <filter>input['input_select'] == "text"</filter> + </data> + </outputs> + <tests> + <test> + <param name="input_select" value="accession_number"/> + <param name="accession" value="SRR925743"/> + <param name="region" value="17:41243452-41277500"/> + <output name="output_accession" file="sra_pileup_result.pileup" compare="contains" ftype="pileup"/> + </test> + </tests> + <help> + 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@ + </help> + <expand macro="citation"/> +</tool>
--- /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@CDD<EDDE?2@?AEEDEED=D+C?5@A=6:>BA8:>@: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<@.<==@?.@@<?##### +@3/2 +ATGGATGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGT ++SRR925743.3 3 length=100 +HHHHHHHHHFIEGFHFHDHHHHGFFHGEGDIGGEGGHHHAGEGGGDHHHHHHHHHHHFGDGGGEGDFFF>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<.>><:<A7BABBE8@=:<<:@BB?C75:2?;.5<<3FEFGEEC88FEDEE=AB><AA@B<ABDC8.27<9:58.58??6<:@>+?=9@########
--- /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 HHHHHHHHHHHHHHHHHGHDHHHHHHHHHHHHHEHHHHHHHGHHHGHHHHHHHHHHHHHHHHHHHGFHHFHHHHHFHEBGHHHHHD<EFGBBBCAGFGE; RG:Z:0 +44155516 165 * 0 0 * 17 41275988 0 CATTAATGCTATGCAGATAATCATAGGAATCCCAAATTAATACACTCTTGTGCTGACTTACCAGATGGGACACTCTAAGATTTTCTGCATAGCATTAATG HHHHHHHHHHHHHHHHFGHHHHHHGHHHHHHHHGHFHHHHHHHEHHHHHFHHHHHFHHHHHHHHHFCCDDHFFHGFHHHBBHFHHFFF@FEFCCBBEE=: RG:Z:0 +44155520 133 * 0 0 * 17 41276001 0 ATCCCAAATTAATACACTCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTATTAATTTGGGATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGG HHHHHHHHHHHHHHHHHHHHHGHFHDHFHFHHHHHHHFHBHEHHFHHHHHGGGBGEHGGIHHHHHDHEHHEHHHHBHHHHHFFFFFEHEECHEBDEFEF# RG:Z:0 +44155522 133 * 0 0 * 17 41276005 0 CAAATTAATACACTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTA HHHHHHHHHHHGHHHGHHHHGHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHFHEHGHHHHGHHHBHEHFHHHEF3FF###### RG:Z:0 +44155523 133 * 0 0 * 17 41276005 0 CAAATTAATACACTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGGTAAGTCAGCACAAGAGTGTA FGDBGEFFDGGDEFGFFGFG=EACE>CBDDFCFBBDBCCDEGGFEEEE=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<G@CEA? RG:Z:0 +44155536 165 * 0 0 * 17 41276063 0 AACAGAAAGAAATGGATTTTCTGCATAGCATTAATGACATTTTGTACTTCTTCAACGCGAAGAGCAGATAAATCCATTTCTTTCTGTTAGATCGGAAGAG HHHHHHHHHFHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHFHHHHEHEHHHEHGHHHFEHFHHHHHHHHHFHEHHGHFHHHHFBFHHHHHF RG:Z:0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sra_pileup_result.pileup Sun Dec 06 09:04:37 2015 -0500 @@ -0,0 +1,10 @@ +CM000679.1 41277491 A 8 ....,,,, E4BHHHHG +CM000679.1 41277492 T 8 ....,,,, G<FHCHEF +CM000679.1 41277493 C 8 ....,,,, H7HGHEE8 +CM000679.1 41277494 A 8 ....,,,, ECGFHHHG +CM000679.1 41277495 A 8 ....,,,, F@GGHHHE +CM000679.1 41277496 G 8 ....,,,, DAGFHHHG +CM000679.1 41277497 G 8 ....,,,, =AE@HHHF +CM000679.1 41277498 T 8 ....,,,, F.?GFGFG +CM000679.1 41277499 A 8 ....,,,, G:EGHGH= +CM000679.1 41277500 C 8 ....,,,, E:EGHGGE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Dec 06 09:04:37 2015 -0500 @@ -0,0 +1,15 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ncbi_vdb" version="2.5.2"> + <repository changeset_revision="b980182ad267" name="package_ncbi_vdb_2_5_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="ngs_sdk" version="1.1.3"> + <repository changeset_revision="1197d3c98375" name="package_ngs_sdk_1_1_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="sra_toolkit" version="2.5.2"> + <repository changeset_revision="ab06c0240705" name="package_sra_toolkit_2_5_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="perl" version="5.18.1"> + <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>