Mercurial > repos > iuc > package_stringtie_1_1_0

annotate tool_dependencies.xml @ 0:62a98ebf406f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
author iuc
date Wed, 21 Oct 2015 16:06:33 -0400
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children 4e8dc3ecc62f
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62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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1 <?xml version="1.0"?>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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2 <tool_dependency>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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3 <package name="stringtie" version="1.1.0">
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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4 <install version="1.0">
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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5 <actions_group>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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6 <actions architecture="x86_64" os="linux">
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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7 <action type="download_by_url" sha256sum="a457dbfee8f66204b17401ac1c4f3c67896ab77f142bad5ac555bfec0d59f613">
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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8 http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.1.0.Linux_x86_64.tar.gz
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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9 </action>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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10 <action type="move_file">
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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11 <source>stringtie</source>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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12 <destination>$INSTALL_DIR/bin</destination>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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13 </action>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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14 </actions>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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15 <actions architecture="x86_64" os="darwin">
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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16 <action type="download_by_url" sha256sum="2ccd09274e9c5be1121e55950e6510d7c62a0994266ebfce784c1f493a6c5719">
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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17 http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.1.0.OSX_x86_64.tar.gz
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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18 </action>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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19 <action type="move_file">
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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20 <source>stringtie</source>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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21 <destination>$INSTALL_DIR/bin</destination>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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22 </action>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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23 </actions>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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24 <actions>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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25 <action type="download_by_url" sha256sum="75178e57620abec8e3e544f0430a5f1cdd7fc5faa484fadd8318b5dce90b4fb7">
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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26 http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.1.0.tar.gz
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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27 </action>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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28 <action type="shell_command">make release</action>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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29 <action type="move_file">
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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30 <source>stringtie</source>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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31 <destination>$INSTALL_DIR/bin</destination>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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32 </action>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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33 </actions>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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34 <action type="set_environment">
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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35 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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36 <environment_variable action="set_to" name="STRINGTIE_ROOT_PATH">$INSTALL_DIR</environment_variable>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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37 </action>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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38 </actions_group>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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39 </install>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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40 <readme>
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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41 StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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42 It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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43 quantitate full-length transcripts representing multiple splice variants for each gene locus.
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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44 Its input can include not only the alignments of raw reads used by other transcript assemblers,
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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45 but also alignments longer sequences that have been assembled from those reads.
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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46 To identify differentially expressed genes between experiments, StringTie's
62a98ebf406f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_1_0 commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a
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47 output can be processed either by the Cuffdiff or Ballgown programs.
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48 </readme>
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49 </package>
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50 </tool_dependency>