Mercurial > repos > iuc > package_tpp_4_6_3
changeset 3:679b2c6a6e19 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tpp_4_6_3 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty
| author | iuc |
|---|---|
| date | Fri, 17 Jul 2015 14:17:32 -0400 |
| parents | aa519f1dda68 |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 61 insertions(+), 36 deletions(-) [+] |
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--- a/tool_dependencies.xml Thu Oct 09 06:55:57 2014 -0500 +++ b/tool_dependencies.xml Fri Jul 17 14:17:32 2015 -0400 @@ -1,74 +1,99 @@ <?xml version="1.0"?> <tool_dependency> <package name="libgd" version="2.1.0"> - <repository changeset_revision="99a41bc40067" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="9ff7903354f2" name="package_libgd_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="perl" version="5.18.1"> + <repository changeset_revision="fd34b72b501b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="expat" version="2.1.0"> + <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bzlib" version="1.0.6"> + <repository changeset_revision="c494aad769a8" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="libpng" version="1.2.5"> <repository changeset_revision="e0719be25969" name="package_libpng_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="bzlib" version="1.0.6"> - <repository changeset_revision="a8d7180642fa" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="perl" version="5.18.1"> - <repository changeset_revision="34b039b3943b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="expat" version="2.1.0"> - <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> <package name="trans_proteomic_pipeline" version="4.6.3"> <install version="1.0"> <actions> - <!-- populate the environment variables from the dependent repos --> + <action type="setup_perl_environment"> + <repository changeset_revision="fd34b72b501b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="perl" version="5.18.1" /> + </repository> + <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="expat" version="2.1.0" /> + </repository> + <!-- allow downloading and installing an Perl package from cpan.org--> + <package>http://cpan.metacpan.org/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://cpan.metacpan.org/authors/id/L/LD/LDS/CGI.pm-3.49.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"> - <repository changeset_revision="99a41bc40067" name="package_libgd_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <repository changeset_revision="9ff7903354f2" name="package_libgd_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="libgd" version="2.1.0" /> </repository> <repository changeset_revision="e0719be25969" name="package_libpng_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="libpng" version="1.2.5" /> </repository> - <repository changeset_revision="a8d7180642fa" name="package_bzlib_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <repository changeset_revision="c494aad769a8" name="package_bzlib_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="bzlib" version="1.0.6" /> </repository> + <repository changeset_revision="fd34b72b501b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="perl" version="5.18.1" /> + </repository> <repository changeset_revision="0b8d0fa6cea6" name="package_expat_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="expat" version="2.1.0" /> </repository> - <repository changeset_revision="34b039b3943b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.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-4.6.3.tgz</action> - <action type="shell_command">tar -zxf TPP-4.6.3.tgz</action> - - <!-- Change deprecated CGI endform to end_form --> - <action type="shell_command">sed -i.orig 's/endform/end_form/' TPP-4.6.3/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl</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_1.8.27-8ubuntu1.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=$INSTALL_DIR/" > Makefile.config.incl</action> - <action type="shell_command">echo "TPP_WEB=/tpp/" >> Makefile.config.incl</action> - <action type="shell_command">echo "XSLT_PROC=/usr/bin/xsltproc" >> Makefile.config.incl</action> - <action type="shell_command">echo "CGI_USER_DIR=$INSTALL_DIR/cgi-bin/" >> Makefile.config.incl</action> + <action type="shell_command">echo 'TPP_ROOT=$INSTALL_DIR/tpp/' > Makefile.config.incl</action> + <action type="shell_command">echo 'TPP_WEB=/tpp/' >> Makefile.config.incl</action> + <action type="shell_command">echo 'CGI_USER_DIR=$INSTALL_DIR/cgi-bin/' >> Makefile.config.incl</action> - <action type="shell_command">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">echo '' > ../perl/tpp_models.pl</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.bak -e 's/qw(.*) /(&) /' ../perl/tpp_models.pl</action> + <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&) /' ../CGI/show_nspbin.pl</action> + <action type="shell_command">sed -i.bak -e 's/qw(.*) /(&) /' ../perl/exporTPP.pl</action> + <!--action type="shell_command">echo '' > ../perl/tpp_models.pl</action--> - <action type="shell_command">eval $(perl -I$PERL_LOCALLIB_DIR/lib/perl5 -Mlocal::lib=$PERL_LOCALLIB_DIR); make; make install</action> - + <action type="shell_command">export PERL5LIB=$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> </install> <readme> - Installs and compiles the trans proteomic pipeline in version 4.6.3 + Installs and complils the trans proteomic pipeline in version 4.6.3. 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>