Mercurial > repos > bgruening > package_tpp_4_7_0
changeset 0:b568a3db8e2c draft
Uploaded
| author | bgruening |
|---|---|
| date | Sat, 15 Mar 2014 06:25:04 -0400 |
| parents | |
| children | 8fb6f74d7db6 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 109 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Mar 15 06:25:04 2014 -0400 @@ -0,0 +1,109 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="libgd" version="2.1.0"> + <repository changeset_revision="2a074c7b442e" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="perl" version="5.18.1"> + <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="expat" version="2.1.0"> + <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="bzlib" version="1.0.6"> + <repository changeset_revision="d5188682d08e" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="libpng" version="1.2.5"> + <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="boost" version="1.53.0"> + <repository changeset_revision="1d696f0a53b9" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="trans_proteomic_pipeline" version="4.7.0"> + <install version="1.0"> + <actions> + <action type="setup_perl_environment"> + <repository changeset_revision="ab58b9f990c5" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="perl" version="5.18.1" /> + </repository> + <repository changeset_revision="8fc96166cddd" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="expat" version="2.1.0" /> + </repository> + <!-- allow downloading and installing an Perl package from cpan.org--> + + <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/XML-Parser-2.41.tar.gz</package> + <!-- Also possible but not reproducible, due to the fact that always the latest version is installed. + <package>XML::Parser</package> + --> + <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/CGI.pm-3.43.tar.gz</package> + </action> + <action type="change_directory">..</action> + <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> + <!-- populate the environment variables from the dependend repos --> + <action type="set_environment_for_install"> + <repository changeset_revision="2a074c7b442e" name="package_libgd_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="libgd" version="2.1.0" /> + </repository> + <repository changeset_revision="821c27341c0e" name="package_libpng_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="libpng" version="1.2.5" /> + </repository> + <repository changeset_revision="d5188682d08e" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="bzlib" version="1.0.6" /> + </repository> + <repository changeset_revision="1d696f0a53b9" name="package_boost_1_53" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="boost" version="1.53.0" /> + </repository> + </action> + <action type="shell_command">tar xfz TPP-4.7.0.tgz</action> + <!-- doanload patched version of htmldoc to prevent a TPP crashed during compilation --> + <!--<action type="download_file">https://github.com/bgruening/download_store/raw/master/htmldoc/htmldoc_1.8.27-8ubuntu1.debian.tar.gz</action> + <action type="shell_command">rm ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action> + <action type="shell_command">mv htmldoc_1.8.27-8ubuntu1.debian.tar.gz ./TPP-4.6.3/trans_proteomic_pipeline/extern/htmldoc.tgz</action> + --> + <!-- + <action type="move_file" rename_to="htmldoc.tgz"> + <source>htmldoc-1.8.27-8.debian.patched.tar.gz</source> + <destination>./TPP-4.6.3/trans_proteomic_pipeline/extern/</destination> + </action> + --> + <action type="change_directory">./TPP-4.6.3/trans_proteomic_pipeline/src/</action> + <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' > Makefile.config.incl</action> + <action type="shell_command">echo 'TPP_WEB=/tpp/' >> Makefile.config.incl</action> + <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' >> Makefile.config.incl</action> + + <action type="shell_command">echo 'BOOST_INCL=-I$BOOST_ROOT_DIR' >> Makefile.config.incl</action> + <action type="shell_command">echo 'BOOST_LIBDIR=$BOOST_ROOT_DIR/lib/' >> Makefile.config.incl</action> + <action type="shell_command">echo 'BOOST_LIBSPEC=-gcc43-mt' >> Makefile.config.incl</action> + <action type="shell_command">echo 'LINK=shared' >> Makefile.config.incl</action> + <action type="shell_command">echo 'LIBEXT=so' >> Makefile.config.incl</action> + + <!-- + TPP is fails with a error due to an deprecated use of qw() + See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html + + <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../perl/tpp_models.pl</action> + <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../CGI/show_nspbin.pl</action> + <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../perl/exporTPP.pl</action> + --> + + <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> + <action type="shell_command">make install</action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tpp/bin</environment_variable> + <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable> + <environment_variable action="set_to" name="TPP_ROOT_PATH">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + Installs and complils the trans proteomic pipeline in version 4.7.0. + The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC. + + http://tools.proteomecenter.org/ + + Dependencies: e2fslibs-dev (e2fsprogs-devel) + + PATH will be set. + TPP_ROOT_PATH will point to the root path of the installation. + </readme> + </package> +</tool_dependency>