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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="package_gsl_1_16" version="1.16">
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4 <repository changeset_revision="48e3daecb97f" name="package_gsl_1_16" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="art" version="2014_11_03">
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_by_url">http://www.niehs.nih.gov/research/resources/assets/docs/artsrcvanillaicecream031114linuxtgz.tgz</action>
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10 <action type="set_environment_for_install">
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11 <repository changeset_revision="48e3daecb97f" name="package_gsl_1_16" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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12 <package name="gsl" version="1.16" />
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13 </repository>
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14 </action>
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15 <action type="autoconf" />
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16 <action type="set_environment">
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17 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
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18 </action>
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19 </actions>
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20 </install>
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21 <readme>ART is a set of simulation tools to generate synthetic next-generation
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22 sequencing reads. ART simulates sequencing reads by mimicking real
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23 sequencing process with empirical error models or quality profiles summarized
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24 from large recalibrated sequencing data. ART can also simulate reads using user
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25 own read error model or quality profiles. ART supports simulation of
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26 single-end, paired-end/mate-pair reads of three major commercial
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27 next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and
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28 Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety
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29 of method or tools for next-generation sequencing data analysis, including
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30 read alignment, de novo assembly, SNP and structure variation discovery.
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31 ART was used as a primary tool for the simulation study of the 1000 Genomes
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32 Project . ART is implemented in C++ with optimized algorithms and is highly
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33 efficient in read simulation. ART outputs reads in the FASTQ format, and
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34 alignments in the ALN format. ART can also generate alignments in the SAM
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35 alignment or UCSC BED file format.
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36 </readme>
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37 </package>
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38 </tool_dependency>
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