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16
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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17
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3 <package name="libgd" version="2.1.0">
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4 <repository changeset_revision="dcbab64c0429" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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17
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6 <package name="trans_proteomic_pipeline" version="4.6.3">
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16
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_by_url">https://downloads.sourceforge.net/project/sashimi/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v4.6%20%28occupy%29%20rev%203/TPP-4.6.3.tgz</action>
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16
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10 <!-- populate the environment variables from the dependend repos -->
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11 <action type="set_environment_for_install">
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12 <repository changeset_revision="dcbab64c0429" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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13 <package name="libgd" version="2.1.0" />
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16
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14 </repository>
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15 </action>
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17
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16 <action type="change_directory">./trans_proteomic_pipeline/src/</action>
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17 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR' > Makefile.config.incl</action>
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18 <action type="make_install" />
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16
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19 <action type="set_environment">
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20 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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17
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21 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
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16
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22 </action>
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23 </actions>
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24 </install>
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25 <readme>
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17
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26 Installs and complils the trans proteomic pipeline in version 4.6.3.
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27 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
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28
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29 http://tools.proteomecenter.org/
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30
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31 PATH will be set.
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32 TPP_ROOT_PATH will point to the root path of the installation.
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33 </readme>
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34 </package>
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35 <package name="tpp_perllibs" version="4.6.3">
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36 <install version="1.0">
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37 <actions>
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38 <action type="setup_perl_environment">
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39 <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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40 <package name="perl" version="5.18.1" />
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41 </repository>
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42 <!-- allow downloading and installing an Perl package from cpan.org-->
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43
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44 <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package>
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45 <!-- Also possible but not reproducible, due to the fact that always the latest version is installed.
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46 <package>XML::Parser</package>
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47 -->
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48 <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package>
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49
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50
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51 </action>
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52 </actions>
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53 </install>
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54 <readme>
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55 TPP Perl dependencies.
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56 </readme>
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57 </package>
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58 </tool_dependency>
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