Mercurial > repos > jjohnson > defuse
diff tool_dependencies.xml @ 8:06675bd664ee
Update to DeFuse verion 0.6.1 and change tool dependencies for autoinstall
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 05 Jun 2013 15:37:57 -0500 |
| parents | 5545ec69acbd |
| children | d9017e11cde5 |
line wrap: on
line diff
--- a/tool_dependencies.xml Fri Jan 18 14:56:40 2013 -0600 +++ b/tool_dependencies.xml Wed Jun 05 15:37:57 2013 -0500 @@ -1,10 +1,31 @@ <?xml version="1.0"?> <tool_dependency> - <package name="defuse" version="0.6.0"> + <package name="boost" version="1.53.0"> + <repository changeset_revision="f5b13e56a321" name="package_boost_1_53" owner="bgruening" prior_installation_required="True" toolshed="http://localhost:19009" /> + </package> + <package name="samtools" version="0.1.18"> + <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="bowtie" version="1.0.0"> + <repository changeset_revision="e682af6a72cd" name="package_bowtie_1_0_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="gmap" version="2013-05-09"> + <repository changeset_revision="03bb09b717ae" name="package_gmap_2013_05_09" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="kent" version="283"> + <repository changeset_revision="d4c8accb9a57" name="package_kent_283" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="defuse" version="0.6.1"> <install version="1.0"> <actions> - <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.6/defuse-0.6.0.tar.gz</action> - <action type="shell_command">cd tools && make</action> + <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.6/defuse-0.6.1.tar.gz</action> + <!-- populate the environment variables from the dependent repos --> + <action type="set_environment_for_install"> + <repository changeset_revision="f5b13e56a321" name="package_boost_1_53" owner="bgruening" prior_installation_required="True" toolshed="http://localhost:19009" > + <package name="boost" version="1.53.0" /> + </repository> + </action> + <action type="shell_command">export CPLUS_INCLUDE_PATH=$BOOST_ROOT_DIR:$CPLUS_INCLUDE_PATH && cd tools && make</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> @@ -20,161 +41,4 @@ </readme> </package> - <package name="samtools" version="0.1.18"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> - <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>misc/maq2sam-long</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -Compiling SAMtools requires the ncurses and zlib development libraries. - </readme> - </package> - - - <package name="bowtie" version="0.12.7"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>bowtie</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>bowtie-build</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>bowtie-inspect</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - Compiling Bowtie requires libpthread to be present on your system. - </readme> - </package> - - <package name="gmap" version="2012-07-20"> - <install version="1.0"> - <actions> - <action type="download_by_url" target_filename="gmap-2012-07-20.tar.gz">http://research-pub.gene.com/gmap/src/gmap-gsnap-2012-07-20.v2.tar.gz</action> - <action type="shell_command">./configure</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>src/gmap</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>src/gmapindex</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>src/gsnap</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>src/uniqscan</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>src/iit_store</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>src/iit_get</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>src/atoiindex</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>src/snpindex</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>src/cmetindex</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>src/get-genome</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_directory_files"> - <source_directory>util</source_directory> - <destination_directory>$INSTALL_DIR/bin</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - </readme> - </package> - - <package name="blat" version="34x10"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action> - <action type="shell_command">chmod 755 blat</action> - <action type="move_file"> - <source>blat</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -This only handles blat for a non-commercial linux system. - -Please note that the Blat source and executables are freely available for -academic, nonprofit and personal use. Commercial licensing information is -available on the Kent Informatics website (http://www.kentinformatics.com/). - </readme> - </package> - - <package name="fatotwobit" version="34x10"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit</action> - <action type="shell_command">chmod 755 faToTwoBit</action> - <action type="move_file"> - <source>faToTwoBit</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -This only handles faToTwoBit for a non-commercial linux system. - -Please note that the source and executables are freely available for -academic, nonprofit and personal use. Commercial licensing information is -available on the Kent Informatics website (http://www.kentinformatics.com/). - </readme> - </package> - </tool_dependency>