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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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19
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6 <package name="perl" version="5.18.1">
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7 <repository changeset_revision="978287122b91" 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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17
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12 <package name="trans_proteomic_pipeline" version="4.6.3">
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16
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13 <install version="1.0">
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14 <actions>
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18
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15 <action type="setup_perl_environment">
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19
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16 <repository changeset_revision="978287122b91" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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18
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17 <package name="perl" version="5.18.1" />
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18 </repository>
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19
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19 <!-- allow downloading and installing an Perl package from cpan.org-->
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18
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20
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19
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21 <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package>
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22 <!-- Also possible but not reproducible, due to the fact that always the latest version is installed.
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23 <package>XML::Parser</package>
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24 -->
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18
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25 <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package>
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26
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27
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28 </action>
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19
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29 <action type="change_directory">..</action>
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18
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30 <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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31 <!-- populate the environment variables from the dependend repos -->
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32 <action type="set_environment_for_install">
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17
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33 <repository changeset_revision="dcbab64c0429" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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34 <package name="libgd" version="2.1.0" />
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16
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35 </repository>
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36 </action>
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18
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37 <action type="shell_command">tar xfz TPP-4.6.3.tgz</action>
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38 <!-- doanload patched version of htmldoc to prevent a TPP crashed during compilation -->
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19
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39 <action type="download_file">https://github.com/bgruening/download_store/raw/master/htmldoc/htmldoc_1.8.27-8ubuntu1.debian.tar.gz</action>
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40 <action type="shell_command">rm ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action>
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41 <action type="shell_command">mv htmldoc_1.8.27-8ubuntu1.debian.tar.gz ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action>
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42 <!--
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43 <action type="move_file" rename_to="htmldoc.tgz">
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18
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44 <source>htmldoc-1.8.27-8.debian.patched.tar.gz</source>
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19
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45 <destination>./TPP-4.6.3/trans_proteomic_pipeline/extern/</destination>
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18
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46 </action>
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19
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47 -->
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18
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48 <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action>
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19
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49 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' > Makefile.config.incl</action>
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50 <action type="shell_command">echo 'TPP_WEB=/tpp/' >> Makefile.config.incl</action>
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51 <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' >> Makefile.config.incl</action>
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52
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53 <!--
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54 TPP is fails with a error due to an deprecated use of qw()
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55 See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html
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56 -->
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57 <action type="shell_command">sed -i -e 's/ /(&) /' ../perl/tpp_models.pl</action>
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58 <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../CGI/show_nspbin.pl</action>
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59 <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../perl/exporTPP.pl</action>
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60
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61 <action type="shell_command">export PERL5LIB=$INSTALL_DIR/lib/perl5/:$PERL5LIB && export PATH=$PERL_ROOT_DIR/bin/:$PATH && export PERL5LIB=$PERL_ROOT_DIR/lib/perl5:$PERL5LIB && make</action>
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18
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62 <action type="shell_command">make install</action>
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16
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63 <action type="set_environment">
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19
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64 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tpp/bin</environment_variable>
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65 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
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17
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66 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
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16
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67 </action>
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68 </actions>
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69 </install>
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70 <readme>
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17
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71 Installs and complils the trans proteomic pipeline in version 4.6.3.
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72 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
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73
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74 http://tools.proteomecenter.org/
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75
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19
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76 Dependencies: e2fslibs-dev (e2fsprogs-devel)
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77
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17
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78 PATH will be set.
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79 TPP_ROOT_PATH will point to the root path of the installation.
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80 </readme>
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81 </package>
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16
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82 </tool_dependency>
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