Mercurial > repos > pjbriggs > macs21

annotate tool_dependencies.xml @ 2:15889783e759 draft

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Fix bugs in tool operation and update dependencies.
author pjbriggs
date Thu, 12 Feb 2015 08:29:07 -0500
parents d0986d2be693
children 881a48588832
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <!-- Dependencies from local toolshed
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4 <package name="numpy" version="1.9">
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5 <repository name="package_numpy_1_9" prior_installation_required="True" owner="pjbriggs" />
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6 </package>
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7 -->
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8 <!-- Dependencies from main/test toolsheds -->
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9 <package name="numpy" version="1.9">
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10 <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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11 </package>
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12 <!-- Subset of UCSC tools -->
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13 <package name="ucsc_tools" version="1.0">
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14 <install version="1.0">
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15 <actions>
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16 <!-- fetchChromSizes -->
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17 <action type="download_binary">
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18 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template>
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19 </action>
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20 <action type="chmod">
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21 <file mode="755">$INSTALL_DIR/fetchChromSizes</file>
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22 </action>
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23 <!-- bedClip -->
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24 <action type="download_binary">
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25 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip</url_template>
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26 </action>
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27 <action type="chmod">
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28 <file mode="755">$INSTALL_DIR/bedClip</file>
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29 </action>
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30 <!-- bedGraphToBigWig -->
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31 <action type="download_binary">
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32 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
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33 </action>
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34 <action type="chmod">
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35 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
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36 </action>
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37 </actions>
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38 </install>
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39 </package>
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40 <!-- MACS 2.1.0 -->
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41 <package name="macs2" version="2.1.0.20140616">
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42 <install version="1.0">
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43 <actions>
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44 <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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45 <!-- Install environment for local toolshed
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46 <repository name="package_numpy_1_9" owner="pjbriggs">
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47 <package name="python_numpy" version="1.9" />
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48 </repository>
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49 </action>
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50 -->
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51 <!-- Install environment for main & test toolsheds -->
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52 <action type="set_environment_for_install">
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53 <repository changeset_revision="266529386609" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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54 <package name="numpy" version="1.9" />
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55 </repository>
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56 </action>
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57 --&gt;
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58 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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59 <action type="shell_command">
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60 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
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61 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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62 </action>
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63 <action type="set_environment">
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64 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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65 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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66 </action>
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67 </actions>
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68 </install>
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69 <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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70 </package>
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71 </tool_dependency>