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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="boost" version="1.55.0">
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19 <repository changeset_revision="336ab080d1d4" name="package_boost_1_55" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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20 </package>
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21 <package name="e2fsprogs" version="1.42.9">
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22 <repository changeset_revision="13445e8c7fd8" name="package_e2fsprogs_1_42_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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23 </package>
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24 <package name="trans_proteomic_pipeline" version="4.7.0">
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25 <install version="1.0">
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26 <actions>
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27 <action type="setup_perl_environment">
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28 <repository changeset_revision="f6efd799dc70" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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29 <package name="perl" version="5.18.1" />
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30 </repository>
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31 <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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32 <package name="expat" version="2.1.0" />
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33 </repository>
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34 <!-- allow downloading and installing an Perl package from cpan.org-->
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35
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36 <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package>
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37 <!-- Also possible but not reproducible, due to the fact that always the latest version is installed.
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38 <package>XML::Parser</package>
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39 -->
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40 <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package>
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41 <!--<package>http://search.cpan.org/CPAN/authors/id/S/SK/SKIMO/FCGI-0.67.tar.gz</package>-->
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42 </action>
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43 <action type="change_directory">..</action>
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44 <action type="download_file">http://downloads.sourceforge.net/project/sashimi/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v4.7%20%28polar%20vortex%29%20rev%200/TPP_4.7.0-src.tgz</action>
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45 <!-- populate the environment variables from the dependend repos -->
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46 <action type="set_environment_for_install">
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47 <repository changeset_revision="dfaacc4bf896" name="package_libgd_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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48 <package name="libgd" version="2.1.0" />
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49 </repository>
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50 <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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51 <package name="libpng" version="1.2.5" />
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52 </repository>
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53 <repository changeset_revision="087298adb1fa" name="package_bzlib_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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54 <package name="bzlib" version="1.0.6" />
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55 </repository>
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56 <repository changeset_revision="336ab080d1d4" name="package_boost_1_55" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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57 <package name="boost" version="1.55.0" />
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58 </repository>
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59 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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60 <package name="expat" version="2.1.0" />
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61 </repository>
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62 <repository changeset_revision="13445e8c7fd8" name="package_e2fsprogs_1_42_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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63 <package name="e2fsprogs" version="1.42.9" />
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64 </repository>
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65 </action>
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66 <action type="shell_command">tar xfz TPP_4.7.0-src.tgz</action>
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67
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68 <action type="change_directory">./TPP-4.7.0/trans_proteomic_pipeline/src/</action>
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69 <action type="make_directory">../build/</action>
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70 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' > Makefile.config.incl</action>
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71 <action type="shell_command">echo 'TPP_WEB=/tpp/' >> Makefile.config.incl</action>
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72 <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' >> Makefile.config.incl</action>
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73 <action type="shell_command">echo 'OBJ_ARCH=../build' >> Makefile.config.incl</action>
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74
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75 <!-- define some BOOST variables to link against the toolshed boost version -->
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76 <action type="shell_command">echo "BOOST_DIR=$BOOST_ROOT_DIR" >> Makefile.config.incl</action>
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77 <action type="shell_command">echo "BOOST_LIBDIR=$BOOST_ROOT_DIR/lib/" >> Makefile.config.incl</action>
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78 <action type="shell_command">echo 'BOOST_LIB_EXT=so' >> Makefile.config.incl</action>
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79 <action type="shell_command">echo 'BOOST_INCL=-isystem $(BOOST_DIR) -isystem $(BOOST_DIR)/.. -I$(SRC_ROOT).' >> Makefile.config.incl</action>
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80 <action type="shell_command">echo 'BOOST_LIBS=$(BOOST_LIBDIR)*' >> Makefile.config.incl</action>
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81 <action type="shell_command">echo 'HTMLDOC_BIN=' >> Makefile.config.incl</action>
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82
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83 <action type="shell_command">echo 'LINK=shared' >> Makefile.config.incl</action>
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84 <action type="shell_command">echo 'LIBEXT=a' >> Makefile.config.incl</action>
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85 <!--action type="shell_command">echo "BZ2_LIB=$BZLIB_LIB_DIR/libbz2.a" >> Makefile.config.incl</action-->
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86
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87 <action type="shell_command">echo "EXPAT_LIB=$EXPAT_ROOT_DIR/lib/libexpat.a" >> Makefile.config.incl</action>
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88 <action type="shell_command">echo "EXPAT_INCL=$EXPAT_ROOT_DIR/include/" >> Makefile.config.incl</action>
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89
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90 <action type="shell_command">cat Makefile.config.incl > /home/bag/blablabla.txt</action>
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91
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92
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93 <!-- do not use the build-in boost version
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94 Boost version 1.54 is known to have a build bug and can't be used on some systems without a patch.
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95 -->
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96 <action type="shell_command">sed -i -e 's/# www.boost.org/ifeq "$(strip $(BOOST_LIBDIR))" ""/' Makefile.incl</action>
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97 <action type="shell_command">sed -i -e 's/# Proteowizrd/endif/' Makefile.incl</action>
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98 <!-- replace build-in expat library with the more recent toolshed one -->
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99 <action type="shell_command">sed -i -e 's/# Build expat library/ifeq "$(strip $(EXPAT_LIB))" ""/' Makefile.incl</action>
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100 <action type="shell_command">sed -i -e 's/# Build HDF5/endif\n# Build HDF5/' Makefile.incl</action>
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101
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102 <action type="shell_command">sed -i -e 's/# HTMLDOC/ifeq "$(strip $(HTMLDOC_BIN))" "not-needed"/' Makefile.incl</action>
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103 <action type="shell_command">sed -i -e 's/# put common.*/endif/' Makefile.incl</action>
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104
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105 <action type="shell_command">cat Makefile.incl > /home/bag/makefile.incl.txt</action>
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106
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107
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108
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109 <!--
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110 TPP is fails with a error due to an deprecated use of qw()
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111 See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html
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112 -->
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113 <!--<action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../perl/tpp_models.pl</action>-->
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114 <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../CGI/show_nspbin.pl</action>
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115 <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../perl/exporTPP.pl</action>
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116 <action type="shell_command">echo '' > ../perl/tpp_models.pl</action>
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117
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118 <action type="shell_command">make</action>
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119 <action type="shell_command">make install</action>
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120 <action type="set_environment">
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121 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tpp/bin</environment_variable>
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122 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
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123 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable>
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124 </action>
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125 </actions>
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126 </install>
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127 <readme>
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128 Installs and complils the trans proteomic pipeline in version 4.7.0.
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129 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
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130
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131 http://tools.proteomecenter.org/
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132
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133 PATH will be set.
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134 TPP_ROOT_PATH will point to the root path of the installation.
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135 </readme>
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136 </package>
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137 </tool_dependency>
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