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annotate tool_dependencies.xml @ 2:00d73c812399 draft

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Version 2.1.0-6: add sorting step in bigWig generation, and explicitly terminate tool on error from MACS2.
author pjbriggs
date Wed, 22 Mar 2017 11:36:07 -0400
parents 02a01ea54722
children
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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="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.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="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.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="2.0">
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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 <!-- bedSort -->
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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/bedSort</url_template>
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31 </action>
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32 <action type="chmod">
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33 <file mode="755">$INSTALL_DIR/bedSort</file>
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34 </action>
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35 <!-- bedGraphToBigWig -->
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36 <action type="download_binary">
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37 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
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38 </action>
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39 <action type="chmod">
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40 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
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41 </action>
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42 <action type="set_environment">
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43 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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44 </action>
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45 </actions>
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46 </install>
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47 </package>
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48 <!-- MACS 2.1.0 -->
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49 <package name="macs2" version="2.1.0.20140616">
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50 <install version="1.0">
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51 <actions>
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52 <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20140616.tar.gz</action>
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53 <!-- Install environment for main & test toolsheds -->
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54 <action type="set_environment_for_install">
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55 <repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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56 <package name="numpy" version="1.9" />
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57 </repository>
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58 </action>
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59 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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60 <action type="shell_command">
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61 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
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62 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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63 </action>
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64 <action type="set_environment">
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65 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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66 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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67 </action>
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68 </actions>
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69 </install>
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70 <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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71 </package>
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72 </tool_dependency>