Mercurial > repos > stheil > taxonomy_sqlite
diff tool_dependencies.xml @ 0:4ecb2ce50254 draft default tip
Uploaded
| author | stheil |
|---|---|
| date | Mon, 26 Oct 2015 10:59:07 -0400 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Oct 26 10:59:07 2015 -0400 @@ -0,0 +1,49 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="perl" version="5.18.1"> + <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"/> + </package> + <package name="loadTaxonomy" version="1.0"> + <install version="1.0"> + <actions> + <action type="set_environment_for_install"> + <repository changeset_revision="114b6af405fa" 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="setup_perl_environment"> + <package>Data::Dumper</package> + <package>File::Basename</package> + <package>Getopt::Long</package> + <package>DBI</package> + <package>SQL::SplitStatement</package> + <package>$INSTALL_DIR/perl/lib</package> + </action> + <action type="download_by_url"> + ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz + </action> + <action type="shell_command"> + gunzip gi_taxid_nucl.dmp.gz + </action> + <action type="download_by_url"> + ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_prot.dmp.gz + </action> + <action type="shell_command"> + gunzip gi_taxid_prot.dmp.gz + </action> + <action type="download_by_url"> + ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip + </action> + <action type="shell_command"> + gunzip taxdmp.zip + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/perl/scripts</environment_variable> + </action> + <action type="shell_command"> + loadTaxonomy.pl + </action> + </actions> + </install> + </package> +</tool_dependency>