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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="dfaacc4bf896" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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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="f6efd799dc70" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://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="https://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="bzlib" version="1.0.6">
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13 <repository changeset_revision="087298adb1fa" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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14 </package>
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15 <package name="libpng" version="1.2.5">
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16 <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="https://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 <action type="setup_perl_environment">
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22 <repository changeset_revision="f6efd799dc70" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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23 <package name="perl" version="5.18.1" />
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24 </repository>
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25 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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26 <package name="expat" version="2.1.0" />
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27 </repository>
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28 <!-- allow downloading and installing an Perl package from cpan.org-->
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29 <package>http://cpan.metacpan.org/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package>
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30 <!-- Also possible but not reproducible, due to the fact that always the latest version is installed.
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31 <package>XML::Parser</package>
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32 -->
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33 <package>http://cpan.metacpan.org/authors/id/L/LD/LDS/CGI.pm-3.49.tar.gz</package>
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34 </action>
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35 <action type="change_directory">..</action>
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36 <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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37 <!-- populate the environment variables from the dependend repos -->
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38 <action type="set_environment_for_install">
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39 <repository changeset_revision="dfaacc4bf896" name="package_libgd_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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40 <package name="libgd" version="2.1.0" />
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41 </repository>
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42 <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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43 <package name="libpng" version="1.2.5" />
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44 </repository>
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45 <repository changeset_revision="087298adb1fa" name="package_bzlib_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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46 <package name="bzlib" version="1.0.6" />
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47 </repository>
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48 <repository changeset_revision="f6efd799dc70" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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49 <package name="perl" version="5.18.1" />
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50 </repository>
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51 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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52 <package name="expat" version="2.1.0" />
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53 </repository>
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54 </action>
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55 <action type="shell_command">tar xfz TPP-4.6.3.tgz</action>
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56 <!-- doanload patched version of htmldoc to prevent a TPP crashed during compilation -->
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57 <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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58 <action type="shell_command">rm ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action>
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59 <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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60 <!--
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61 <action type="move_file" rename_to="htmldoc.tgz">
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62 <source>htmldoc-1.8.27-8.debian.patched.tar.gz</source>
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63 <destination>./TPP-4.6.3/trans_proteomic_pipeline/extern/</destination>
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64 </action>
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65 -->
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66 <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action>
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67 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' > Makefile.config.incl</action>
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68 <action type="shell_command">echo 'TPP_WEB=/tpp/' >> Makefile.config.incl</action>
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69 <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' >> Makefile.config.incl</action>
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70
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71 <!--
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72 TPP is fails with a error due to an deprecated use of qw()
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73 See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html
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74 -->
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75 <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../perl/tpp_models.pl</action>
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76 <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../CGI/show_nspbin.pl</action>
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77 <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../perl/exporTPP.pl</action>
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78 <!--action type="shell_command">echo '' > ../perl/tpp_models.pl</action-->
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79
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80 <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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81 <action type="shell_command">make install</action>
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82 <action type="set_environment">
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83 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tpp/bin</environment_variable>
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84 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
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85 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
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86 </action>
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87 </actions>
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88 </install>
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89 <readme>
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90 Installs and complils the trans proteomic pipeline in version 4.6.3.
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91 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
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92
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93 http://tools.proteomecenter.org/
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94
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95 Dependencies: e2fslibs-dev (e2fsprogs-devel)
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96
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97 PATH will be set.
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98 TPP_ROOT_PATH will point to the root path of the installation.
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99 </readme>
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100 </package>
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101 </tool_dependency>
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