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1 <?xml version="1.0"?>
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2 <tool_dependency>
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2
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3 <package name="libgd" version="2.1.0">
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4 <repository changeset_revision="b17bbb1a41da" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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2
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5 </package>
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6 <package name="perl" version="5.18.1">
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7 <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="expat" version="2.1.0">
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10 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="trans_proteomic_pipeline" version="4.6.1">
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13 <install version="1.0">
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14 <actions>
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15 <!-- populate the environment variables from the dependend repos -->
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16 <action type="set_environment_for_install">
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17 <repository changeset_revision="b17bbb1a41da" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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2
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18 <package name="libgd" version="2.1.0" />
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19 </repository>
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20 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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21 <package name="expat" version="2.1.0" />
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22 </repository>
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23 <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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24 <package name="perl" version="5.18.1" />
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25 </repository>
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26 </action>
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27 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" XML::Parser</action>
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28 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" CGI --force</action>
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29 <action type="download-file">https://dl.dropbox.com/u/226794/TPP-4.6.1.tgz</action>
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30 <action type="shell_command">tar -zxf TPP-4.6.1.tgz</action>
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31
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32 <action type="change_directory">./TPP-4.6.1/trans_proteomic_pipeline/src/</action>
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33 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' > Makefile.config.incl</action>
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34 <action type="shell_command">echo 'TPP_WEB=/tpp/' >> Makefile.config.incl</action>
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35 <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' >> Makefile.config.incl</action>
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36
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37 <action type="shell_command">echo "TPP_ROOT=$INSTALL_DIR/\nTPP_WEB=/tpp/\nXSLT_PROC=/usr/bin/xsltproc\nCGI_USERS_DIR=$INSTALL_DIR/cgi-bin/" > "TPP-$tpp_version/trans_proteomic_pipeline/src/Makefile.config.incl"</action>
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38
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39 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); make; make install</action>
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40
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2
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41 </actions>
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42 </install>
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43 <readme>
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44 Installs and complils the trans proteomic pipeline in version 4.6.3.
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45 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
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46
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47 http://tools.proteomecenter.org/
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48
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49 Dependencies: e2fslibs-dev (e2fsprogs-devel)
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50
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51 PATH will be set.
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52 TPP_ROOT_PATH will point to the root path of the installation.
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53 </readme>
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54 </package>
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55 </tool_dependency>
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