Mercurial > repos > iracooke > package_tpp_4_6_1
changeset 7:82e26fa61b00
Merge heads at 0:4819d276ffaf and 6:c0e73546cd42 which were created as a result of a recently fixed bug.
| author | devteam <devteam@galaxyproject.org> |
|---|---|
| date | Mon, 13 Jan 2014 12:32:27 -0500 |
| parents | c0e73546cd42 (diff) 4819d276ffaf (current diff) |
| children | c2fd1ff3a7f9 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 66 insertions(+), 17 deletions(-) [+] |
line wrap: on
line diff
--- a/tool_dependencies.xml Thu Oct 24 13:10:37 2013 +1100 +++ b/tool_dependencies.xml Mon Jan 13 12:32:27 2014 -0500 @@ -1,20 +1,69 @@ <?xml version="1.0"?> <tool_dependency> - <package name="trans_proteomic_pipeline" version="4.6.1"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://dl.dropboxusercontent.com/u/226794/galaxy/tpp_4.6.1.tar.gz</action> - <action language="cheetah" type="template_command"> - sh install.sh $env.INSTALL_DIR - </action> - <action type="set_environment"> - <environment_variable action="set_to" name="TPP_PERL_DIR">$INSTALL_DIR/perl5</environment_variable> - <environment_variable action="set_to" name="PROTK_TPP_ROOT">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme> - This part of the installer is extremely minimal. It just downloads and runs a shell script that does the install. - </readme> - </package> + <package name="libgd" version="2.1.0"> + <repository changeset_revision="016ad1de8f18" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="libpng" version="1.2.5"> + <repository changeset_revision="a80a3062f066" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="bzlib" version="1.0.6"> + <repository changeset_revision="04e1967b1722" name="package_bzlib_1_0" 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="trans_proteomic_pipeline" version="4.6.1"> + <install version="1.0"> + <actions> + <!-- populate the environment variables from the dependend repos --> + <action type="set_environment_for_install"> + <repository changeset_revision="016ad1de8f18" 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="a80a3062f066" 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="04e1967b1722" 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="8fc96166cddd" name="package_expat_2_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="expat" version="2.1.0" /> + </repository> + <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> + </action> + <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" XML::Parser</action> + <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); cpanm --local-lib=$PERL_LOCALLIB_DIR --configure-args="EXPATLIBPATH=$EXPAT_ROOT_DIR/lib EXPATINCPATH=$EXPAT_ROOT_DIR/include" CGI --force</action> + <action type="download_file">https://dl.dropbox.com/u/226794/TPP-4.6.1.tgz</action> + <action type="shell_command">tar -zxf TPP-4.6.1.tgz</action> + + <action type="change_directory">./TPP-4.6.1/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 "TPP_ROOT=$INSTALL_DIR/\nTPP_WEB=/tpp/\nXSLT_PROC=/usr/bin/xsltproc\nCGI_USERS_DIR=$INSTALL_DIR/cgi-bin/" > "Makefile.config.incl"</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">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); make; make install</action> + + </actions> + </install> + <readme> + Installs and compiles the trans proteomic pipeline in version 4.6.1 + The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC. + + http://tools.proteomecenter.org/ + + PATH will be set. + TPP_ROOT_PATH will point to the root path of the installation. + </readme> + </package> </tool_dependency>