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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_6_2 commit d04a4c3b62d9a9decc3e27e6bee7a007f47b3d73
author iuc
date Tue, 17 May 2016 06:57:10 -0400
parents 4503178d0713
children
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<?xml version="1.0"?>
<tool_dependency>
    <package name="perl" version="5.18.1">
        <repository changeset_revision="95dad0955d7e" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="libmagic" version="5.25">
        <repository changeset_revision="c7b9857a1522" name="package_libmagic_5_25" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="ncbi_vdb" version="2.6.2">
        <repository changeset_revision="1b2990f1663b" name="package_ncbi_vdb_2_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="ngs_sdk" version="1.2.3">
        <repository changeset_revision="03bfda5a7f9f" name="package_ngs_sdk_1_2_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="sra_toolkit" version="2.6.2">
        <install version="1.0">
            <actions>
                <action sha256sum="7aa1ec118486cd877bf2976818a3f319674584f3d04931a6ce2a92f6a9defbc1" type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.6.2.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="95dad0955d7e" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="perl" version="5.18.1" />
                    </repository>
                    <repository changeset_revision="c7b9857a1522" name="package_libmagic_5_25" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="libmagic" version="5.25" />
                    </repository>
                    <repository changeset_revision="1b2990f1663b" name="package_ncbi_vdb_2_6_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="ncbi_vdb" version="2.6.2" />
                    </repository>
                    <repository changeset_revision="03bfda5a7f9f" name="package_ngs_sdk_1_2_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="ngs_sdk" version="1.2.3" />
                    </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>
            </actions>
        </install>
        <readme>
            Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
            This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
            When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a
            download of a large SRA data set.

            Build Requirements:
            - make
            - git
            - gcc
            - g++
            - libxml2
            - libcurl4
            - zlib

            On a debian based Linux OS use:

            apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev

        </readme>
    </package>
</tool_dependency>