Mercurial > repos > bgruening > precommit_test
changeset 19:4b482f6136c2 draft
Uploaded
| author | bgruening |
|---|---|
| date | Tue, 05 Nov 2013 12:32:08 -0500 |
| parents | 77d6b8ccc046 |
| children | 2ecce0ee7183 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 37 insertions(+), 16 deletions(-) [+] |
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--- a/tool_dependencies.xml Mon Nov 04 04:04:03 2013 -0500 +++ b/tool_dependencies.xml Tue Nov 05 12:32:08 2013 -0500 @@ -3,23 +3,30 @@ <package name="libgd" version="2.1.0"> <repository changeset_revision="dcbab64c0429" 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="978287122b91" 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="4.6.3"> <install version="1.0"> <actions> <action type="setup_perl_environment"> - <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <repository changeset_revision="978287122b91" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> <package name="perl" version="5.18.1" /> </repository> - <!-- allow downloading and installing an Perl package from cpan.org--> + <!-- 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/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">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> <!-- populate the environment variables from the dependend repos --> <action type="set_environment_for_install"> @@ -29,21 +36,33 @@ </action> <action type="shell_command">tar xfz TPP-4.6.3.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-1.8.27-8.debian.patched.tar.gz</action> - - <action type="move_file"> + <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/extern/htmldoc.tgz</destination> + <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">ls -l > $INSTALL_DIR/foo.txt</action> - <action type="shell_command">cat Makefile.config.incl > $INSTALL_DIR/foo2.txt</action> - <action type="shell_command">export PERL5LIB=$INSTALL_DIR/lib/perl5/:$PERL5LIB && export PATH=$PERL_ROOT_DIR/bin/:$PATH && make</action> + <action type="shell_command">echo 'TPP_ROOT=$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=$INSTALL_DIR/cgi-bin/' >> Makefile.config.incl</action> + + <!-- + TPP is fails with a error due to an deprecated use of qw() + See the rant @ http://blogs.perl.org/users/rurban/2010/09/qw-in-list-context-deprecated.html + --> + <action type="shell_command">sed -i -e 's/ /(&) /' ../perl/tpp_models.pl</action> + <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../CGI/show_nspbin.pl</action> + <action type="shell_command">sed -i -e 's/qw(.*) /(&) /' ../perl/exporTPP.pl</action> + + <action type="shell_command">export PERL5LIB=$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/bin</environment_variable> + <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> @@ -54,6 +73,8 @@ 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>