Mercurial > repos > iuc > package_tpp_4_6_3
annotate tool_dependencies.xml @ 8:7fb7c8a17c87 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_6_3 commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
| author | iuc |
|---|---|
| date | Fri, 09 Oct 2015 05:27:03 -0400 |
| parents | 6ad62d7ded0c |
| children | 00f7d0264bcf |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 3 <package name="libgd" version="2.1.0"> | |
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e8d19d226f14
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_6_3 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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7fb7c8a17c87
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_6_3 commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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7 <repository changeset_revision="2590d4683481" 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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7fb7c8a17c87
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_6_3 commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
parents:
7
diff
changeset
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13 <repository changeset_revision="6ebf4fdf5359" 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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7fb7c8a17c87
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_6_3 commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
parents:
7
diff
changeset
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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="trans_proteomic_pipeline" version="4.6.3"> | |
| 19 <install version="1.0"> | |
| 20 <actions> | |
| 21 <action type="setup_perl_environment"> | |
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7fb7c8a17c87
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_6_3 commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
parents:
7
diff
changeset
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22 <repository changeset_revision="2590d4683481" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 0 | 23 <package name="perl" version="5.18.1" /> |
| 24 </repository> | |
| 25 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> | |
| 26 <package name="expat" version="2.1.0" /> | |
| 27 </repository> | |
| 28 <!-- allow downloading and installing an Perl package from cpan.org--> | |
| 29 <package>http://cpan.metacpan.org/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package> | |
| 30 <!-- Also possible but not reproducible, due to the fact that always the latest version is installed. | |
| 31 <package>XML::Parser</package> | |
| 32 --> | |
| 33 <package>http://cpan.metacpan.org/authors/id/L/LD/LDS/CGI.pm-3.49.tar.gz</package> | |
| 34 </action> | |
| 35 <action type="change_directory">..</action> | |
| 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> | |
| 37 <!-- populate the environment variables from the dependend repos --> | |
| 38 <action type="set_environment_for_install"> | |
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e8d19d226f14
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_6_3 commit 37b7d29c0289e00c0b36f3523134880aa45ce26d
iuc
parents:
1
diff
changeset
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39 <repository changeset_revision="88f469bfafbf" name="package_libgd_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 0 | 40 <package name="libgd" version="2.1.0" /> |
| 41 </repository> | |
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7fb7c8a17c87
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_6_3 commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
parents:
7
diff
changeset
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42 <repository changeset_revision="8813649bf702" name="package_libpng_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 0 | 43 <package name="libpng" version="1.2.5" /> |
| 44 </repository> | |
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8
7fb7c8a17c87
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_6_3 commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
parents:
7
diff
changeset
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45 <repository changeset_revision="6ebf4fdf5359" name="package_bzlib_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 0 | 46 <package name="bzlib" version="1.0.6" /> |
| 47 </repository> | |
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8
7fb7c8a17c87
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_6_3 commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
parents:
7
diff
changeset
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48 <repository changeset_revision="2590d4683481" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 0 | 49 <package name="perl" version="5.18.1" /> |
| 50 </repository> | |
| 51 <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> | |
| 52 <package name="expat" version="2.1.0" /> | |
| 53 </repository> | |
| 54 </action> | |
| 55 <action type="shell_command">tar xfz TPP-4.6.3.tgz</action> | |
| 56 <!-- doanload patched version of htmldoc to prevent a TPP crashed during compilation --> | |
| 57 <action type="download_file">https://github.com/bgruening/download_store/raw/master/htmldoc/htmldoc_1.8.27-8ubuntu1.debian.tar.gz</action> | |
| 58 <action type="shell_command">rm ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action> | |
| 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> | |
| 60 <!-- | |
| 61 <action type="move_file" rename_to="htmldoc.tgz"> | |
| 62 <source>htmldoc-1.8.27-8.debian.patched.tar.gz</source> | |
| 63 <destination>./TPP-4.6.3/trans_proteomic_pipeline/extern/</destination> | |
| 64 </action> | |
| 65 --> | |
| 66 <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action> | |
| 67 <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' > Makefile.config.incl</action> | |
| 68 <action type="shell_command">echo 'TPP_WEB=/tpp/' >> Makefile.config.incl</action> | |
| 69 <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' >> Makefile.config.incl</action> | |
| 70 | |
| 71 <!-- | |
| 72 TPP is fails with a error due to an deprecated use of qw() | |
| 73 See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html | |
| 74 --> | |
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6ad62d7ded0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_6_3 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
parents:
6
diff
changeset
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75 <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&) /' ../perl/tpp_models.pl</action> |
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6ad62d7ded0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_6_3 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
parents:
6
diff
changeset
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76 <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&) /' ../CGI/show_nspbin.pl</action> |
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6ad62d7ded0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_6_3 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
parents:
6
diff
changeset
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77 <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&) /' ../perl/exporTPP.pl</action> |
| 0 | 78 <!--action type="shell_command">echo '' > ../perl/tpp_models.pl</action--> |
| 79 | |
| 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> | |
| 81 <action type="shell_command">make install</action> | |
| 82 <action type="set_environment"> | |
| 83 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tpp/bin</environment_variable> | |
| 84 <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable> | |
| 85 <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable> | |
| 86 </action> | |
| 87 </actions> | |
| 88 </install> | |
| 89 <readme> | |
| 90 Installs and complils the trans proteomic pipeline in version 4.6.3. | |
| 91 The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC. | |
| 92 | |
| 93 http://tools.proteomecenter.org/ | |
| 94 | |
| 95 Dependencies: e2fslibs-dev (e2fsprogs-devel) | |
| 96 | |
| 97 PATH will be set. | |
| 98 TPP_ROOT_PATH will point to the root path of the installation. | |
| 99 </readme> | |
| 100 </package> | |
| 101 </tool_dependency> |