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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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16
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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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18
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9 <action type="setup_perl_environment">
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10 <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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11 <package name="perl" version="5.18.1" />
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12 </repository>
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13 <!-- allow downloading and installing an Perl package from cpan.org-->
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14
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15 <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package>
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16 <!-- Also possible but not reproducible, due to the fact that always the latest version is installed.
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17 <package>XML::Parser</package>
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18 -->
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19 <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package>
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20
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21
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22 </action>
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23 <action type="download_file">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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24 <!-- populate the environment variables from the dependend repos -->
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25 <action type="set_environment_for_install">
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17
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26 <repository changeset_revision="dcbab64c0429" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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27 <package name="libgd" version="2.1.0" />
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16
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28 </repository>
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29 </action>
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18
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30 <action type="shell_command">tar xfz TPP-4.6.3.tgz</action>
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31 <!-- doanload patched version of htmldoc to prevent a TPP crashed during compilation -->
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32 <action type="download_file">https://github.com/bgruening/download_store/raw/master/htmldoc/htmldoc-1.8.27-8.debian.patched.tar.gz</action>
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33
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34 <action type="move_file">
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35 <source>htmldoc-1.8.27-8.debian.patched.tar.gz</source>
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36 <destination>./TPP-4.6.3/extern/htmldoc.tgz</destination>
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37 </action>
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38
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39 <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action>
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40 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp' > Makefile.config.incl</action>
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41 <action type="shell_command">ls -l > $INSTALL_DIR/foo.txt</action>
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42 <action type="shell_command">cat Makefile.config.incl > $INSTALL_DIR/foo2.txt</action>
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43 <action type="shell_command">export PERL5LIB=$INSTALL_DIR/lib/perl5/:$PERL5LIB && export PATH=$PERL_ROOT_DIR/bin/:$PATH && make</action>
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44 <action type="shell_command">make install</action>
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16
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45 <action type="set_environment">
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46 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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17
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47 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
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16
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48 </action>
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49 </actions>
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50 </install>
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51 <readme>
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17
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52 Installs and complils the trans proteomic pipeline in version 4.6.3.
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53 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
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54
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55 http://tools.proteomecenter.org/
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56
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57 PATH will be set.
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58 TPP_ROOT_PATH will point to the root path of the installation.
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59 </readme>
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60 </package>
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16
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61 </tool_dependency>
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