Mercurial > repos > iuc > package_sailfish_0_7_3

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
author iuc
date Sat, 05 Sep 2015 14:39:39 -0400
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962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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1 <?xml version="1.0"?>
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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2 <tool_dependency>
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3 <package name="boost" version="1.57">
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4 <repository changeset_revision="e3977e321db5" name="package_boost_1_57" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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5 </package>
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6
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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7 <package name="sailfish" version="0.7.3">
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8 <install version="1.0">
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9 <actions_group>
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10 <actions architecture="x86_64" os="linux">
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11 <action type="download_by_url">https://github.com/kingsfordgroup/sailfish/releases/download/v0.7.3/SailfishBeta-0.7.3_Linux-x86-64.tar.gz</action>
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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12 <action type="move_directory_files">
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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13 <source_directory>.</source_directory>
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14 <destination_directory>$INSTALL_DIR</destination_directory>
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15 </action>
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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16 <action type="set_environment">
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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17 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/</environment_variable>
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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18 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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19 </action>
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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20 </actions>
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21 <actions architecture="x86_64" os="darwin">
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22 <action type="download_by_url">https://github.com/kingsfordgroup/sailfish/releases/download/v0.7.3/SailfishBeta-0.7.3_OSX_10.10.tar.gz</action>
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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23 <action type="move_directory_files">
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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24 <source_directory>.</source_directory>
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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25 <destination_directory>$INSTALL_DIR</destination_directory>
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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26 </action>
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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27 <action type="set_environment">
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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28 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/</environment_variable>
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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29 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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30 </action>
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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31 </actions>
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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32 <actions>
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33 <!-- first action is always downloading -->
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34 <action type="download_by_url">https://github.com/kingsfordgroup/sailfish/archive/v0.7.3.tar.gz</action>
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35
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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36 <!-- populate the environment variables from the dependend repos -->
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37 <action type="set_environment_for_install">
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38 <repository changeset_revision="e3977e321db5" name="package_boost_1_57" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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39 <package name="boost" version="1.57" />
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40 </repository>
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41 </action>
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42
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43 <!-- PYTHONPATH_NUMPY is set in the numpy package -->
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44 <action type="shell_command">
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45 mkdir build &amp;&amp;
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46 cd build &amp;&amp;
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47 cmake .. -DBOOST_ROOT=$BOOST_ROOT_DIR -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR</action>
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48 <action type="shell_command">cd ./build &amp;&amp; make </action>
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49 <action type="shell_command">cd ./build &amp;&amp; make install</action>
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50 <action type="set_environment">
962c2b938c58 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_3 commit 963ecc9871de72c9ee5c88de996ce94ee3abc206
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51 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/</environment_variable>
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52 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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53 <environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[BOOST_ROOT_DIR]/lib/</environment_variable>
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54 </action>
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55 </actions>
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56 </actions_group>
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57 </install>
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58 <readme>Compiling sailfish requires cmake and C++11 compiler (usually gcc).</readme>
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59 </package>
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60 </tool_dependency>