Mercurial > repos > iuc > package_art_2014_11_03

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
author iuc
date Thu, 11 Jun 2015 13:50:21 -0400
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eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
iuc
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1 <?xml version="1.0"?>
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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2 <tool_dependency>
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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3 <package name="package_gsl_1_16" version="1.16">
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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4 <repository changeset_revision="4391a79f86fa" name="package_gsl_1_16" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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5 </package>
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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6 <package name="art" version="2014_11_03">
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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7 <install version="1.0">
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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8 <actions>
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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9 <action type="download_by_url">http://www.niehs.nih.gov/research/resources/assets/docs/artsrcvanillaicecream031114linuxtgz.tgz</action>
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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10 <action type="set_environment_for_install">
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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11 <repository changeset_revision="4391a79f86fa" name="package_gsl_1_16" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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12 <package name="gsl" version="1.16" />
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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13 </repository>
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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14 </action>
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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15 <action type="autoconf" />
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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16 <action type="set_environment">
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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17 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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18 <environment_variable action="set_to" name="ART_ROOT_PATH">$INSTALL_DIR/</environment_variable>
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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19 </action>
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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20 </actions>
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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21 </install>
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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22 <readme>ART is a set of simulation tools to generate synthetic next-generation
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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23 sequencing reads. ART simulates sequencing reads by mimicking real
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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24 sequencing process with empirical error models or quality profiles summarized
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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25 from large recalibrated sequencing data. ART can also simulate reads using user
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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26 own read error model or quality profiles. ART supports simulation of
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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27 single-end, paired-end/mate-pair reads of three major commercial
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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28 next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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29 Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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30 of method or tools for next-generation sequencing data analysis, including
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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31 read alignment, de novo assembly, SNP and structure variation discovery.
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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32 ART was used as a primary tool for the simulation study of the 1000 Genomes
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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33 Project . ART is implemented in C++ with optimized algorithms and is highly
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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34 efficient in read simulation. ART outputs reads in the FASTQ format, and
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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35 alignments in the ALN format. ART can also generate alignments in the SAM
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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36 alignment or UCSC BED file format.
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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37 </readme>
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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38 </package>
eaadf9edc5c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7
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39 </tool_dependency>