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annotate tool_dependencies.xml @ 3:43724ea1c85f

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Add cd-hit for protein fastas
author Jim Johnson <jj@umn.edu>
date Thu, 27 Jun 2013 21:37:08 -0500
parents cca0838c1597
children 88f9e90d9d78
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="cd-hit" version="4.6.1">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">https://cdhit.googlecode.com/files/cd-hit-v4.6.1-2012-08-27.tgz</action>
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7 <action type="shell_command">make openmp=yes</action>
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8 <action type="set_environment">
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9 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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10 <environment_variable name="CDHIT_SITE_OPTIONS" action="set_to">"-M 4000 -T 0"</environment_variable>
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11 </action>
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12 </actions>
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13 </install>
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14 <readme>
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15 These links provide information for building the cdhit package:
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17 http://weizhong-lab.ucsd.edu/cd-hit/
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19 https://code.google.com/p/cdhit/
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21 https://code.google.com/p/cdhit/source/browse/README
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23 Change the CDHIT_SITE_OPTIONS variable in the installed env.sh file to adjust
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24 the maximum memory Mb (-M) or to limit the number of threads (-T)
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25 to match your site
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26 </readme>
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27 </package>
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28 </tool_dependency>
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