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annotate tool_dependencies.xml @ 7:0c6b14f3fefc draft

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Attempt to fix installation of tool dependencies for UCSC/bigwig generation, and trap for undefined genome build.
author pjbriggs
date Tue, 21 Apr 2015 08:29:16 -0400
parents 344dd37d1704
children 7aecd0908b3c
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <!-- Dependencies from main/test toolsheds -->
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4 <package name="numpy" version="1.9">
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5 <repository changeset_revision="266529386609" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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6 </package>
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7 <package name="R" version="3.1.2">
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8 <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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9 </package>
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10 <!-- Subset of UCSC tools -->
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11 <package name="ucsc_tools_for_macs21" version="1.0">
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12 <install version="1.0">
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13 <actions>
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14 <!-- fetchChromSizes -->
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15 <action type="download_binary">
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16 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template>
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17 </action>
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18 <action type="chmod">
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19 <file mode="755">$INSTALL_DIR/fetchChromSizes</file>
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20 </action>
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21 <!-- bedClip -->
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22 <action type="download_binary">
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23 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip</url_template>
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24 </action>
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25 <action type="chmod">
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26 <file mode="755">$INSTALL_DIR/bedClip</file>
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27 </action>
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28 <!-- bedGraphToBigWig -->
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29 <action type="download_binary">
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30 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
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31 </action>
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32 <action type="chmod">
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33 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
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34 </action>
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35 <action type="set_environment">
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36 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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37 </action>
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38 </actions>
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39 </install>
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40 </package>
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41 <!-- MACS 2.1.0 -->
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42 <package name="macs2" version="2.1.0.20140616">
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43 <install version="1.0">
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44 <actions>
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45 <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20140616.tar.gz</action>
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46 <!-- Install environment for main & test toolsheds -->
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47 <action type="set_environment_for_install">
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48 <repository changeset_revision="266529386609" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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49 <package name="numpy" version="1.9" />
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50 </repository>
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51 </action>
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52 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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53 <action type="shell_command">
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54 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
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55 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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56 </action>
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57 <action type="set_environment">
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58 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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59 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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60 </action>
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61 </actions>
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62 </install>
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63 <readme>Macs2.1 depends on having python2.7 and numpy 1.8 installed on all nodes of the work cluster</readme>
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64 </package>
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65 </tool_dependency>