Mercurial > repos > iuc > package_tpp_4_7_0
annotate tool_dependencies.xml @ 11:9f606e975d00 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit bd736b6361ba659a1251dd1a1a05f7e3b633bdf5
| author | iuc |
|---|---|
| date | Tue, 22 Dec 2015 19:42:53 -0500 |
| parents | a5d93ac27cfe |
| children |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 3 <package name="libgd" version="2.1.0"> | |
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a374b047268a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit 37b7d29c0289e00c0b36f3523134880aa45ce26d
iuc
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4 <repository changeset_revision="88f469bfafbf" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 0 | 5 </package> |
| 6 <package name="perl" version="5.18.1"> | |
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9f606e975d00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit bd736b6361ba659a1251dd1a1a05f7e3b633bdf5
iuc
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7 <repository changeset_revision="d5193a5f6203" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 0 | 8 </package> |
| 9 <package name="expat" version="2.1.0"> | |
| 10 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | |
| 11 </package> | |
| 12 <package name="bzlib" version="1.0.6"> | |
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a5d93ac27cfe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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13 <repository changeset_revision="29f79feefc77" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 0 | 14 </package> |
| 15 <package name="libpng" version="1.2.5"> | |
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5d695df7cfa1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit c5b99dd9482d52035bbfec5ac717f60ef968e989-dirty
iuc
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16 <repository changeset_revision="8813649bf702" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 0 | 17 </package> |
| 18 <package name="boost" version="1.55.0"> | |
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9f606e975d00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit bd736b6361ba659a1251dd1a1a05f7e3b633bdf5
iuc
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19 <repository changeset_revision="18bf2e8cf06e" name="package_boost_1_55" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 0 | 20 </package> |
| 21 <package name="e2fsprogs" version="1.42.9"> | |
| 22 <repository changeset_revision="13445e8c7fd8" name="package_e2fsprogs_1_42_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | |
| 23 </package> | |
| 24 <package name="trans_proteomic_pipeline" version="4.7.0"> | |
| 25 <install version="1.0"> | |
| 26 <actions> | |
| 27 <action type="setup_perl_environment"> | |
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9f606e975d00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit bd736b6361ba659a1251dd1a1a05f7e3b633bdf5
iuc
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diff
changeset
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28 <repository changeset_revision="d5193a5f6203" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 0 | 29 <package name="perl" version="5.18.1" /> |
| 30 </repository> | |
| 31 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> | |
| 32 <package name="expat" version="2.1.0" /> | |
| 33 </repository> | |
| 34 <!-- allow downloading and installing an Perl package from cpan.org--> | |
| 35 | |
| 36 <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package> | |
| 37 <!-- Also possible but not reproducible, due to the fact that always the latest version is installed. | |
| 38 <package>XML::Parser</package> | |
| 39 --> | |
| 40 <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package> | |
| 41 <!--<package>http://search.cpan.org/CPAN/authors/id/S/SK/SKIMO/FCGI-0.67.tar.gz</package>--> | |
| 42 </action> | |
| 43 <action type="change_directory">..</action> | |
| 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> | |
| 45 <!-- populate the environment variables from the dependend repos --> | |
| 46 <action type="set_environment_for_install"> | |
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a374b047268a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit 37b7d29c0289e00c0b36f3523134880aa45ce26d
iuc
parents:
1
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changeset
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47 <repository changeset_revision="88f469bfafbf" name="package_libgd_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 0 | 48 <package name="libgd" version="2.1.0" /> |
| 49 </repository> | |
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5d695df7cfa1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit c5b99dd9482d52035bbfec5ac717f60ef968e989-dirty
iuc
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50 <repository changeset_revision="8813649bf702" name="package_libpng_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 0 | 51 <package name="libpng" version="1.2.5" /> |
| 52 </repository> | |
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a5d93ac27cfe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
parents:
9
diff
changeset
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53 <repository changeset_revision="29f79feefc77" name="package_bzlib_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 0 | 54 <package name="bzlib" version="1.0.6" /> |
| 55 </repository> | |
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9f606e975d00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit bd736b6361ba659a1251dd1a1a05f7e3b633bdf5
iuc
parents:
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diff
changeset
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56 <repository changeset_revision="18bf2e8cf06e" name="package_boost_1_55" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 0 | 57 <package name="boost" version="1.55.0" /> |
| 58 </repository> | |
| 59 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> | |
| 60 <package name="expat" version="2.1.0" /> | |
| 61 </repository> | |
| 62 <repository changeset_revision="13445e8c7fd8" name="package_e2fsprogs_1_42_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> | |
| 63 <package name="e2fsprogs" version="1.42.9" /> | |
| 64 </repository> | |
| 65 </action> | |
| 66 <action type="shell_command">tar xfz TPP_4.7.0-src.tgz</action> | |
| 67 | |
| 68 <action type="change_directory">./TPP-4.7.0/trans_proteomic_pipeline/src/</action> | |
| 69 <action type="make_directory">../build/</action> | |
| 70 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' > Makefile.config.incl</action> | |
| 71 <action type="shell_command">echo 'TPP_WEB=/tpp/' >> Makefile.config.incl</action> | |
| 72 <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' >> Makefile.config.incl</action> | |
| 73 <action type="shell_command">echo 'OBJ_ARCH=../build' >> Makefile.config.incl</action> | |
| 74 | |
| 75 <!-- define some BOOST variables to link against the toolshed boost version --> | |
| 76 <action type="shell_command">echo "BOOST_DIR=$BOOST_ROOT_DIR" >> Makefile.config.incl</action> | |
| 77 <action type="shell_command">echo "BOOST_LIBDIR=$BOOST_ROOT_DIR/lib/" >> Makefile.config.incl</action> | |
| 78 <action type="shell_command">echo 'BOOST_LIB_EXT=so' >> Makefile.config.incl</action> | |
| 79 <action type="shell_command">echo 'BOOST_INCL=-isystem $(BOOST_DIR) -isystem $(BOOST_DIR)/.. -I$(SRC_ROOT).' >> Makefile.config.incl</action> | |
| 80 <action type="shell_command">echo 'BOOST_LIBS=$(BOOST_LIBDIR)*' >> Makefile.config.incl</action> | |
| 81 <action type="shell_command">echo 'HTMLDOC_BIN=' >> Makefile.config.incl</action> | |
| 82 | |
| 83 <action type="shell_command">echo 'LINK=shared' >> Makefile.config.incl</action> | |
| 84 <action type="shell_command">echo 'LIBEXT=a' >> Makefile.config.incl</action> | |
| 85 <!--action type="shell_command">echo "BZ2_LIB=$BZLIB_LIB_DIR/libbz2.a" >> Makefile.config.incl</action--> | |
| 86 | |
| 87 <action type="shell_command">echo "EXPAT_LIB=$EXPAT_ROOT_DIR/lib/libexpat.a" >> Makefile.config.incl</action> | |
| 88 <action type="shell_command">echo "EXPAT_INCL=$EXPAT_ROOT_DIR/include/" >> Makefile.config.incl</action> | |
| 89 | |
| 90 <!-- do not use the build-in boost version | |
| 91 Boost version 1.54 is known to have a build bug and can't be used on some systems without a patch. | |
| 92 --> | |
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f732cb0203cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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93 <action type="shell_command">sed -i.bak -e 's/# www.boost.org/ifeq "$(strip $(BOOST_LIBDIR))" ""/' Makefile.incl</action> |
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f732cb0203cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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94 <action type="shell_command">sed -i.bak -e 's/# Proteowizrd/endif/' Makefile.incl</action> |
| 0 | 95 <!-- replace build-in expat library with the more recent toolshed one --> |
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7
f732cb0203cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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changeset
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96 <action type="shell_command">sed -i.bak -e 's/# Build expat library/ifeq "$(strip $(EXPAT_LIB))" ""/' Makefile.incl</action> |
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f732cb0203cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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97 <action type="shell_command">sed -i.bak -e 's/# Build HDF5/endif\n# Build HDF5/' Makefile.incl</action> |
| 0 | 98 |
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f732cb0203cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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changeset
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99 <action type="shell_command">sed -i.bak -e 's/# HTMLDOC/ifeq "$(strip $(HTMLDOC_BIN))" "not-needed"/' Makefile.incl</action> |
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f732cb0203cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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100 <action type="shell_command">sed -i.bak -e 's/# put common.*/endif/' Makefile.incl</action> |
| 0 | 101 |
| 102 <action type="shell_command">cat Makefile.incl > /home/bag/makefile.incl.txt</action> | |
| 103 | |
| 104 | |
| 105 | |
| 106 <!-- | |
| 107 TPP is fails with a error due to an deprecated use of qw() | |
| 108 See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html | |
| 109 --> | |
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f732cb0203cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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110 <!--<action type="shell_command">sed -i.bak -e 's/qw(.*) /(&) /' ../perl/tpp_models.pl</action>--> |
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f732cb0203cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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111 <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&) /' ../CGI/show_nspbin.pl</action> |
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f732cb0203cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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112 <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&) /' ../perl/exporTPP.pl</action> |
| 0 | 113 <action type="shell_command">echo '' > ../perl/tpp_models.pl</action> |
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a5d93ac27cfe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_7_0 commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
parents:
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changeset
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114 <action type="make_install" /> |
| 0 | 115 <action type="set_environment"> |
| 116 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tpp/bin</environment_variable> | |
| 117 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable> | |
| 118 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable> | |
| 119 </action> | |
| 120 </actions> | |
| 121 </install> | |
| 122 <readme> | |
| 123 Installs and complils the trans proteomic pipeline in version 4.7.0. | |
| 124 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC. | |
| 125 | |
| 126 http://tools.proteomecenter.org/ | |
| 127 | |
| 128 PATH will be set. | |
| 129 TPP_ROOT_PATH will point to the root path of the installation. | |
| 130 </readme> | |
| 131 </package> | |
| 132 </tool_dependency> |