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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="samtools" version="0.1.18">
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4 <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="numpy" version="1.7.1">
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7 <repository changeset_revision="40db34c904df" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="matplotlib" version="1.2.1">
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10 <repository changeset_revision="dd81b71dff1b" name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="scipy" version="0.12.0">
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13 <repository changeset_revision="cd2e7872a8eb" name="package_scipy_0_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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14 </package>
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15
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16
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17 <package name="ucsc_tools" version="0.1">
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18 <install version="1.0">
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19 <actions>
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20 <action type="download_binary">
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21 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
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22 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
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23 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
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24 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
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25 </action>
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26 <action type="chmod">
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27 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
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28 </action>
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29 <action type="download_binary">
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30 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
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31 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
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32 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
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33 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
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34 </action>
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35 <action type="chmod">
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36 <file mode="755">$INSTALL_DIR/bigWigInfo</file>
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37 </action>
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38 <action type="set_environment">
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39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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40 </action>
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41 </actions>
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42 </install>
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43 <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
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44 </package>
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45
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46
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47 <package name="deepTools" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">
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48 <install version="1.0">
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49 <actions>
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50
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51 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
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52 <action type="shell_command">git reset --hard 98e5d8a61431ea8605c0643d991a1a5d8999b4dc</action>
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53 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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54 <action type="shell_command">
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55 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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56 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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57 </action>
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58
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59 <action type="set_environment">
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60 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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61 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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62 </action>
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63 </actions>
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64 </install>
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65 <readme>Installation of deepTools from Fidel Ramirez.</readme>
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66 </package>
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67 </tool_dependency>
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