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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="libgd" version="2.1.0">
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4 <repository changeset_revision="2a074c7b442e" 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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4
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6 <package name="libpng" version="1.2.5">
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7 <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" 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="bzlib" version="1.0.6">
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10 <repository changeset_revision="d5188682d08e" name="package_bzlib_1_0" 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="perl" version="5.18.1">
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13 <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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14 </package>
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15 <package name="expat" version="2.1.0">
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16 <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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17 </package>
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18 <package name="trans_proteomic_pipeline" version="4.6.3">
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19 <install version="1.0">
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20 <actions>
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21 <!-- populate the environment variables from the dependent repos -->
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22 <action type="set_environment_for_install">
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23 <repository changeset_revision="2a074c7b442e" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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24 <package name="libgd" version="2.1.0" />
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25 </repository>
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26 <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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27 <package name="libpng" version="1.2.5" />
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28 </repository>
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29 <repository changeset_revision="d5188682d08e" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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30 <package name="bzlib" version="1.0.6" />
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31 </repository>
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3
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32 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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33 <package name="expat" version="2.1.0" />
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34 </repository>
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35 <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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36 <package name="perl" version="5.18.1" />
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37 </repository>
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38 </action>
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4
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39 <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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40 <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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41 <action type="download_file">https://dl.dropbox.com/u/226794/TPP-4.6.3.tgz</action>
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42 <action type="shell_command">tar -zxf TPP-4.6.3.tgz</action>
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43
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44 <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action>
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45 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' > Makefile.config.incl</action>
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46 <action type="shell_command">echo 'TPP_WEB=/tpp/' >> Makefile.config.incl</action>
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47 <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' >> Makefile.config.incl</action>
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48
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4
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49 <action type="shell_command">echo "TPP_ROOT=$INSTALL_DIR/\nTPP_WEB=/tpp/\nXSLT_PROC=/usr/bin/xsltproc\nCGI_USERS_DIR=$INSTALL_DIR/cgi-bin/" > "Makefile.config.incl"</action>
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50
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51
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52 <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../CGI/show_nspbin.pl</action>
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4
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53 <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../perl/exporTPP.pl</action>
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54 <action type="shell_command">echo '' > ../perl/tpp_models.pl</action>
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55
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4
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56 <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); make; make install</action>
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57
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58 <action type="set_environment">
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4
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59 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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60 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
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61 </action>
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4
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62
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63 </actions>
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64 </install>
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65 <readme>
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4
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66 Installs and compiles the trans proteomic pipeline in version 4.6.3
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67 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
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68
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69 http://tools.proteomecenter.org/
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70
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71 PATH will be set.
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72 TPP_ROOT_PATH will point to the root path of the installation.
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73 </readme>
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74 </package>
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75 </tool_dependency>
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