Mercurial > repos > devteam > package_emboss_5_0_0
changeset 0:cf998ddc0542 draft default tip
Uploaded tool dependency definition.
| author | devteam |
|---|---|
| date | Wed, 11 Dec 2013 16:23:37 -0500 |
| parents | |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 94 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Dec 11 16:23:37 2013 -0500 @@ -0,0 +1,94 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="emboss" version="5.0.0"> + <install version="1.0"> + <actions_group> + <actions architecture="i386" os="linux"> + <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/emboss/emboss-5.0.0-Linux-i686.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/emboss/emboss-5.0.0-Linux-x86_64.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions architecture="x86_64" os="darwin"> + <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/emboss/emboss-5.0.0-Darwin-x86_64.tgz</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + </actions> + <actions> + <package name="libx11" version="1.5.0"> + <repository changeset_revision="bfb1f66b1402" name="package_libx11_1_5_0" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="libgd" version="2.1.0"> + <repository changeset_revision="3918b86c4f1f" name="package_libgd_2_1_0" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="libxproto" version="7.0.23"> + <repository changeset_revision="6a512bc84b0d" name="package_libxproto_7_0_23" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="libxcb" version="1.9.1"> + <repository changeset_revision="283d04f807f7" name="package_libxcb_1_9_1" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <action type="download_by_url">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/EMBOSS-5.0.0.tar.gz</action> + <action type="set_environment_for_install"> + <repository changeset_revision="3918b86c4f1f" name="package_libgd_2_1_0" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="libgd" version="2.1.0" /> + </repository> + <repository changeset_revision="bfb1f66b1402" name="package_libx11_1_5_0" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="libx11" version="1.5.0" /> + </repository> + <repository changeset_revision="6a512bc84b0d" name="package_libxproto_7_0_23" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="libxproto" version="7.0.23" /> + </repository> + <repository changeset_revision="283d04f807f7" name="package_libxcb_1_9_1" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu"> + <package name="libxcb" version="1.9.1" /> + </repository> + </action> + <action type="shell_command"> + export LDFLAGS="-L$XCB_LIBS -lm" + export CFLAGS="-I$XPROTO_INCLUDES" && \ + ./configure --prefix=$INSTALL_DIR \ + --x-includes=$X11_INCLUDE_DIR \ + --x-libraries=$X11_LIB_DIR \ + --with-pngdriver=$GD_ROOT + </action> + <action type="shell_command">make && make install</action> + <action extract="true" type="download_file">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/PHYLIP-3.6b.tar.gz</action> + <action type="change_directory">PHYLIP-3.6b</action> + <action type="shell_command"> + export LDFLAGS="-L$XCB_LIBS -lm" + export CFLAGS="-I$XPROTO_INCLUDES" && \ + ./configure --prefix=$INSTALL_DIR \ + --x-includes=$X11_INCLUDE_DIR \ + --x-libraries=$X11_LIB_DIR \ + --with-pngdriver=$GD_ROOT + </action> + <action type="shell_command">make && make install</action> + </actions> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="set_to" name="EMBOSS_ACDROOT">$INSTALL_DIR/share/EMBOSS/acd</environment_variable> + <environment_variable action="set_to" name="EMBOSS_DATA">$INSTALL_DIR/share/EMBOSS/data</environment_variable> + <environment_variable action="set_to" name="PLPLOT_LIB">$INSTALL_DIR/share/EMBOSS</environment_variable> + </action> + </actions_group> + </install> + <readme> +These links provide information for building the Emboss package in most environments. + +System requirements +http://emboss.sourceforge.net/download/#Requirements + +Platform-dependent notes +http://emboss.sourceforge.net/download/#Platforms + </readme> + </package> +</tool_dependency>