comparison tool_dependencies.xml @ 1:bb51af9130ea draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit 09fa2b6129e5d156e22b07287b0c3bb61ac41328

0:ab06c0240705

<?xml version="1.0"?>
<tool_dependency>
    <package name="perl" version="5.18.1">
        <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="ncbi_vdb" version="2.5.2">
        <repository changeset_revision="b980182ad267" name="package_ncbi_vdb_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="ngs_sdk" version="1.1.3">
        <repository changeset_revision="1197d3c98375" name="package_ngs_sdk_1_1_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="sra_toolkit" version="2.5.2">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="perl" version="5.18.1" />
                    </repository>
                    <repository changeset_revision="b980182ad267" name="package_ncbi_vdb_2_5_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="ncbi_vdb" version="2.5.2" />
                    </repository>
                    <repository changeset_revision="1197d3c98375" name="package_ngs_sdk_1_1_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="ngs_sdk" version="1.1.3" />
                    </repository>
                </action>
                <action type="shell_command">
                    ./configure --prefix=$INSTALL_DIR -with-ngs-sdk-prefix=$NGS_SDK_DIR --with-ncbi-vdb-sources=$NCBI_VDB_DIR --with-ncbi-vdb-build=$NCBI_VDB_DIR --build=$INSTALL_DIR/build
                </action>
                <action type="shell_command">
                    sed -i -e "109s/-static//" tools/copycat/Makefile
                </action>
                <action type="make_install" />
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>

1:bb51af9130ea

<?xml version="1.0"?>
<tool_dependency>
    <package name="perl" version="5.18.1">
        <repository changeset_revision="03f5951a9855" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="libmagic" version="5.25">
        <repository changeset_revision="21b08f55a6ac" name="package_libmagic_5_25" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="ncbi_vdb" version="2.5.2">
        <repository changeset_revision="17ae6c0040ea" name="package_ncbi_vdb_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="ngs_sdk" version="1.1.3">
        <repository changeset_revision="1197d3c98375" name="package_ngs_sdk_1_1_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="sra_toolkit" version="2.5.2">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="03f5951a9855" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="perl" version="5.18.1" />
                    </repository>
                    <repository changeset_revision="21b08f55a6ac" name="package_libmagic_5_25" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="libmagic" version="5.25" />
                    </repository>
                    <repository changeset_revision="17ae6c0040ea" name="package_ncbi_vdb_2_5_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="ncbi_vdb" version="2.5.2" />
                    </repository>
                    <repository changeset_revision="1197d3c98375" name="package_ngs_sdk_1_1_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="ngs_sdk" version="1.1.3" />
                    </repository>
                </action>
                <action type="shell_command">
                    ./configure --prefix=$INSTALL_DIR -with-ngs-sdk-prefix=$NGS_SDK_DIR --with-ncbi-vdb-sources=$NCBI_VDB_DIR --with-ncbi-vdb-build=$NCBI_VDB_DIR --build=$INSTALL_DIR
                </action>
                <action type="make_install" />
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>