Mercurial > repos > iuc > package_trinity_2_0_6

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
author iuc
date Fri, 20 Nov 2015 06:49:06 -0500
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e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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1 <?xml version="1.0"?>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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2 <tool_dependency>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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3 <package name="ncurses" version="5.9">
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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4 <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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5 </package>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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6 <package name="zlib" version="1.2.8">
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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7 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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8 </package>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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9 <package name="trinity" version="2.0.6">
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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10 <install version="1.0">
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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11 <actions>
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12 <action sha256sum="e0c3ec885fdcfe3422ea492372518ddf5d1aed3daa187c69c4254516b0845de1" type="download_by_url">https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.6.tar.gz</action>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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13 <action type="set_environment_for_install">
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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14 <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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15 <package name="ncurses" version="5.9" />
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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16 </repository>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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17 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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18 <package name="zlib" version="1.2.8" />
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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19 </repository>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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20 </action>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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21 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/' trinity-plugins/Makefile</action>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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22 <action type="shell_command">sed -i.bak -e 's/-ltinfo//' trinity-plugins/Makefile</action> <!-- tinfo is included in ncurses lib-->
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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23 <action type="shell_command">sed -i.bak -e '/tar -zxvf ${RSEM_CODE}.tar.gz/a \\tsed -i.bak -e "s|-lz|-lz -L${ZLIB_ROOT_PATH}/lib|" ${RSEM_CODE}/Makefile ${RSEM_CODE}/sam/Makefile' trinity-plugins/Makefile</action> <!-- In case you have an obsolete zlib in /usr/lib -->
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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24 <action type="shell_command">make</action>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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25 <action type="shell_command">make plugins</action>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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26
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27 <action type="move_file">
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28 <source>Trinity</source>
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29 <destination>$INSTALL_DIR</destination>
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30 </action>
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31 <action type="move_directory_files">
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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32 <source_directory>Analysis</source_directory>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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33 <destination_directory>$INSTALL_DIR/Analysis</destination_directory>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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34 </action>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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35 <action type="move_directory_files">
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36 <source_directory>Butterfly</source_directory>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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37 <destination_directory>$INSTALL_DIR/Butterfly</destination_directory>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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38 </action>
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39 <action type="move_directory_files">
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40 <source_directory>Chrysalis</source_directory>
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41 <destination_directory>$INSTALL_DIR/Chrysalis</destination_directory>
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42 </action>
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43 <action type="move_directory_files">
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44 <source_directory>Inchworm</source_directory>
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45 <destination_directory>$INSTALL_DIR/Inchworm</destination_directory>
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46 </action>
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47 <action type="move_directory_files">
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48 <source_directory>PerlLib</source_directory>
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49 <destination_directory>$INSTALL_DIR/PerlLib</destination_directory>
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50 </action>
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51 <action type="move_directory_files">
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52 <source_directory>trinity-plugins</source_directory>
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53 <destination_directory>$INSTALL_DIR/trinity-plugins</destination_directory>
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54 </action>
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55 <action type="move_directory_files">
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56 <source_directory>util</source_directory>
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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57 <destination_directory>$INSTALL_DIR/util</destination_directory>
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58 </action>
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59
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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60 <action type="shell_command">rm $INSTALL_DIR/trinity-plugins/*tar.gz</action>
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61
e65cf857feb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
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62 <action type="set_environment">
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63 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/</environment_variable>
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64 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/util</environment_variable>
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65 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/collectl/bin</environment_variable>
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66 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/fastool</environment_variable>
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67 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/jellyfish/bin</environment_variable>
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68 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/parafly/bin</environment_variable>
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69 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/transdecoder</environment_variable>
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70 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/Trimmomatic</environment_variable>
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71 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/slclust/bin</environment_variable>
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72 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/GAL_0.2.1</environment_variable>
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73 </action>
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74 </actions>
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75 </install>
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76 </package>
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77 </tool_dependency>