Mercurial > repos > iuc > package_stringtie_1_2_3

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
author iuc
date Wed, 13 Jul 2016 14:47:52 -0400
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ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
iuc
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1 <?xml version="1.0"?>
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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2 <tool_dependency>
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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3 <package name="stringtie" version="1.2.3">
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
iuc
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4 <install version="1.0">
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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5 <actions>
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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6 <action type="download_by_url" sha256sum="1a323fd17c24889748c645b3dfe5a06305236d9899e87a27939a68404d2d9d09">https://ccb.jhu.edu/software/stringtie/dl/stringtie-1.2.3.tar.gz</action>
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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7 <action type="shell_command">make release</action>
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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8 <action type="move_file">
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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9 <source>stringtie</source>
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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10 <destination>$INSTALL_DIR/bin</destination>
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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11 </action>
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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12 <action type="set_environment">
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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13 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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14 <environment_variable action="set_to" name="STRINGTIE_ROOT_PATH">$INSTALL_DIR</environment_variable>
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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15 </action>
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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16 </actions>
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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17 </install>
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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18 <readme>
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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19 StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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20 It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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21 quantitate full-length transcripts representing multiple splice variants for each gene locus.
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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22 Its input can include not only the alignments of raw reads used by other transcript assemblers,
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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23 but also alignments longer sequences that have been assembled from those reads.
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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24 To identify differentially expressed genes between experiments, StringTie's
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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25 output can be processed either by the Cuffdiff or Ballgown programs.
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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26 </readme>
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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27 </package>
ee804c6f3b97 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
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28 </tool_dependency>