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annotate tool_dependencies.xml @ 32:580ee0c4bc4e

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Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
author lparsons
date Mon, 07 Oct 2013 15:01:13 -0400
parents cc5eaa9376d8
children 073c77ce5e94
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="R" version="3.0.1">
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4 <repository changeset_revision="7473992d1f38" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
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5 </package>
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lparsons
parents: 31
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6 <package name="numpy" version="1.7.1">
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7 <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
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lparsons
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8 </package>
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parents: 31
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9 <package name="rseqc" version="2.3.7">
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10 <install version="1.0">
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11 <actions>
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12 <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action>
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13 <action type="shell_command">python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
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14 <action type="set_environment">
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15 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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16 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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17 </action>
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18 </actions>
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19 </install>
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20 <readme>
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21 RSeQC version 2.3.7, documentation available at http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html.
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22 Requires gcc and python.
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23 </readme>
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24 </package>
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26 </tool_dependency>