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Uploaded tool dependency definition that downloads and installs EMBOSS 5.0.0 and PHYLIP 3.6b.
author devteam
date Thu, 20 Jun 2013 15:18:09 -0400
parents
children f117a9d9dc9c
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<?xml version="1.0"?>
<tool_dependency>
    <package name="libx11" version="1.5.0">
        <repository changeset_revision="90c1cbb8095a" name="package_x11_client_1_5_proto_7_0" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="emboss" version="5.0.0">
        <install version="1.0">
            <actions>
                <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="90c1cbb8095a" name="package_x11_client_1_5_proto_7_0" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
                        <package name="libx11" version="1.5.0" />
                    </repository>
                </action>
                <action type="shell_command">
                    if [ -z $X11_LIB_DIR ] || [ -z $X11_INCLUDE_DIR ]; then
                        ./configure --prefix=$INSTALL_DIR
                    else
                        ./configure --prefix=$INSTALL_DIR --x-includes=$X11_INCLUDE_DIR --x-libraries=$X11_LIB_DIR
                    fi
                </action>
                <action type="shell_command">make</action>
                <action type="shell_command">make install</action>
            </actions>
            <actions>
                <action type="download_by_url">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/PHYLIP-3.6b.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="90c1cbb8095a" name="package_x11_client_1_5_proto_7_0" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
                        <package name="libx11" version="1.5.0" />
                    </repository>
                </action>
                <action type="shell_command">
                    if [ -z $X11_LIB_DIR ] || [ -z $X11_INCLUDE_DIR ]; then
                        ./configure --prefix=$INSTALL_DIR
                    else
                        ./configure --prefix=$INSTALL_DIR --x-includes=$X11_INCLUDE_DIR --x-libraries=$X11_LIB_DIR CFLAGS='-I$INSTALL_DIR/include'
                    fi
                </action>
                <action type="shell_command">make</action>
                <action type="shell_command">make install</action>
            </actions>
        </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>