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annotate tool_dependencies.xml @ 1:f77ce4f92b46 draft

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Use $GALAXY_SLOTS instead of $EDGE_PRO_SITE_OPTIONS. Add dependency on bowtie2. Add readme.rst .
author crs4
date Fri, 31 Jan 2014 05:44:03 -0500
parents 7af33315bc5e
children ddcbf8732706
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="bowtie2" version="2.1.0">
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4 <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="edge-pro" version="1.3.1">
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_by_url">http://ccb.jhu.edu/software/EDGE-pro/EDGE_pro_v1.3.1.tar.gz</action>
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10 <action type="shell_command">make</action>
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11 <action type="move_file">
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12 <source>count</source>
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13 <destination>$INSTALL_DIR/bin</destination>
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14 </action>
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15 <action type="move_file">
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16 <source>edge.pl</source>
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17 <destination>$INSTALL_DIR/bin</destination>
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18 </action>
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19 <action type="set_environment">
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20 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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21 </action>
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22 </actions>
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23 </install>
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24 <readme>
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25 Dependencies of EDGE-pro which needs to be installed separately:
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26 - Switch Perl module ( http://search.cpan.org/~rgarcia/Switch/Switch.pm ).
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28 Configuration: Previously (until Release 0), the EDGE_PRO_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of threads to use (--num-threads). This is not used anymore and may be removed.
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29 </readme>
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30 </package>
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31 </tool_dependency>