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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="samtools" version="0.1.19">
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4 <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="stringtie" version="0.97">
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7 <install version="1.0">
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8 <actions_group>
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9 <actions architecture="x86_64" os="linux">
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10 <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.Linux_x86_64.tar.gz</action>
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11 <action type="move_file">
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12 <source>stringtie</source>
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13 <destination>$INSTALL_DIR/bin</destination>
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14 </action>
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15 </actions>
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16 <actions architecture="x86_64" os="darwin">
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17 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/stringtie/stringtie-0.97-Darwin-x86_64.tgz</action>
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18 <action type="move_file">
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19 <source>stringtie</source>
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20 <destination>$INSTALL_DIR/bin</destination>
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21 </action>
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22 </actions>
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23 <actions>
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24 <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.tar.gz</action>
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25 <action type="set_environment_for_install">
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26 <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
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27 <package name="samtools" version="0.1.19" />
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28 </repository>
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29 </action>
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30 <action type="shell_command">ln -s $SAMTOOLS_ROOT_DIR/src samtools</action>
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31 <action type="shell_command">cp $SAMTOOLS_ROOT_DIR/lib/libbam.* samtools/</action>
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32 <action type="shell_command">make</action>
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33 <action type="move_file">
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34 <source>stringtie</source>
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35 <destination>$INSTALL_DIR/bin</destination>
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36 </action>
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37 </actions>
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38 <action type="set_environment">
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39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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40 </action>
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41 </actions_group>
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42 </install>
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43 <readme>StringTie is a fast and highly efficient assembler of RNA-Seq
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44 alignments into potential transcripts. It is primarily a genome-guided
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45 transcriptome assembler, although it can borrow algorithmic techniques
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46 from de novo genome assembly to help with transcript assembly. Its input
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47 can include not only the spliced read alignments used by reference-based
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48 assemblers, but also longer contigs that were assembled de novo from
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49 unambiguous, non-branching parts of a transcript.</readme>
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50 </package>
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51 </tool_dependency>
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