Mercurial > repos > hammock > hammock
view tool_dependencies.xml @ 6:2277dd59b9f9 draft
Uploaded
author | hammock |
---|---|
date | Wed, 01 Nov 2017 05:54:28 -0400 |
parents | b7652b7c97bd |
children | 466c62f481d3 |
line wrap: on
line source
<?xml version="1.0"?> <tool_dependency> <package name="clustalomega" version="1.2.0"> <install version="1.0"> <actions_group> <actions architecture="x86_64" os="linux"> <action type="move_file"> <source>$REPOSITORY_INSTALL_DIR/external_tools/linux/clustalo-1.2.0-Ubuntu-x86_64</source> <destination>$INSTALL_DIR</destination> </action> <action type="shell_command">sed -i "s%clustalOmegaCommand=clustalo%clustalOmegaCommand=$INSTALL_DIR/clustalo-1.2.0-Ubuntu-x86_64%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> </actions> <actions architecture="x86_64" os="darwin"> <action type="move_file"> <source>$REPOSITORY_INSTALL_DIR/external_tools/darwin/clustal-omega-1.2.0-macosx</source> <destination>$INSTALL_DIR</destination> </action> <action type="shell_command">sed -i "s%clustalOmegaCommand=clustalo%clustalOmegaCommand=$INSTALL_DIR/clustal-omega-1.2.0-macosx%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> </actions> </actions_group> </install> </package> <package name="hmmer" version="3.1b2"> <install version="1.0"> <actions_group> <actions architecture="x86_64" os="linux"> <action type="move_file"> <source>$REPOSITORY_INSTALL_DIR/external_tools/linux/hmmbuild</source> <destination>$INSTALL_DIR</destination> </action> <action type="move_file"> <source>$REPOSITORY_INSTALL_DIR/external_tools/linux/hmmsearch</source> <destination>$INSTALL_DIR</destination> </action> <action type="shell_command">sed -i "s%hmmbuildCommand=hmmbuild%hmmbuildCommand=$INSTALL_DIR/hmmbuild%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> <action type="shell_command">sed -i "s%hmmsearchCommand=hmmsearch%hmmsearchCommand=$INSTALL_DIR/hmmsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> </actions> <actions architecture="x86_64" os="darwin"> <action type="move_file"> <source>$REPOSITORY_INSTALL_DIR/external_tools/darwin/hmmbuild</source> <destination>$INSTALL_DIR</destination> </action> <action type="move_file"> <source>$REPOSITORY_INSTALL_DIR/external_tools/darwin/hmmsearch</source> <destination>$INSTALL_DIR</destination> </action> <action type="shell_command">sed -i "s%hmmbuildCommand=hmmbuild%hmmbuildCommand=$INSTALL_DIR/hmmbuild%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> <action type="shell_command">sed -i "s%hmmsearchCommand=hmmsearch%hmmsearchCommand=$INSTALL_DIR/hmmsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> </actions> </actions_group> </install> </package> <package name="hhsuite" version="2.0.16"> <install version="1.0"> <actions_group> <actions architecture="x86_64" os="linux"> <action type="move_file"> <source>$REPOSITORY_INSTALL_DIR/external_tools/linux/hhmake</source> <destination>$INSTALL_DIR</destination> </action> <action type="move_file"> <source>$REPOSITORY_INSTALL_DIR/external_tools/linux/hhsearch</source> <destination>$INSTALL_DIR</destination> </action> <action type="move_file"> <source>$REPOSITORY_INSTALL_DIR/external_tools/linux/lib</source> <destination>$INSTALL_DIR</destination> </action> <action type="shell_command">sed -i "s%hhmakeCommand=hhmake%hhmakeCommand=$INSTALL_DIR/hhmake%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> <action type="shell_command">sed -i "s%hhsearchCommand=hhsearch%hhsearchCommand=$INSTALL_DIR/hhsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> <action type="shell_command">sed -i "s%reformatCommand=reformat.pl%reformatCommand=$INSTALL_DIR/lib/hh/scripts/reformat.pl%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> <action type="set_environment"> <environment_variable name="HHLIB" action="set_to">$INSTALL_DIR/lib/hh</environment_variable> </action> </actions> <actions architecture="x86_64" os="darwin"> <action type="move_file"> <source>$REPOSITORY_INSTALL_DIR/external_tools/darwin/hhmake</source> <destination>$INSTALL_DIR</destination> </action> <action type="move_file"> <source>$REPOSITORY_INSTALL_DIR/external_tools/darwin/hhsearch</source> <destination>$INSTALL_DIR</destination> </action> <action type="move_file"> <source>$REPOSITORY_INSTALL_DIR/external_tools/darwin/lib</source> <destination>$INSTALL_DIR</destination> </action> <action type="shell_command">sed -i "s%hhmakeCommand=hhmake%hhmakeCommand=$INSTALL_DIR/hhmake%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> <action type="shell_command">sed -i "s%hhsearchCommand=hhsearch%hhsearchCommand=$INSTALL_DIR/hhsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> <action type="shell_command">sed -i "s%reformatCommand=reformat.pl%reformatCommand=$INSTALL_DIR/lib/hh/scripts/reformat.pl%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> <action type="set_environment"> <environment_variable name="HHLIB" action="set_to">$INSTALL_DIR/lib/hh</environment_variable> </action> </actions> </actions_group> </install> </package> <set_environment version="1.0"> <environment_variable name="HAMMOCK_JAR" action="set_to">$REPOSITORY_INSTALL_DIR/Hammock/dist/Hammock.jar</environment_variable> <environment_variable name="MATRIX_PATH" action="set_to">$REPOSITORY_INSTALL_DIR/Hammock/matrices/</environment_variable> </set_environment> </tool_dependency>