comparison tool_dependencies.xml @ 39:c6f1a059bc7d

Uploaded

38:1a78aa9ea234

<?xml version="1.0"?>
<tool_dependency>
    <package name="R_3_0_1" version="3.0.1">
        <repository changeset_revision="564b46e4fda7" name="precommit_test" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>


    <package name="deseq2" version="1.0.17">
        <install version="1.0">
            <actions>
                <action type="download_file">http://bioconductor.org/packages/release/bioc/src/contrib/DESeq2_1.0.17.tar.gz</action>

                <action type="set_environment_for_install">
                    <repository changeset_revision="564b46e4fda7" name="precommit_test" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu">
                        <package name="R_3_0_1" version="3.0.1" />
                    </repository>
                </action>

                <action type="make_directory">$INSTALL_DIR/deseq2/</action>
                <action type="shell_command">
                    Rscript -e "source('http://bioconductor.org/biocLite.R'); install.packages('DESeq2', lib='$INSTALL_DIR/deseq2/', repos='http://cran.us.r-project.org')"
                </action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="R_LIBS">$INSTALL_DIR/deseq2/</environment_variable>
                </action>
            </actions>
        </install>
        <readme>DESeq2</readme>
    </package>
</tool_dependency>

39:c6f1a059bc7d

<?xml version="1.0"?>
<tool_dependency>
    <package name="samtools" version="0.1.18">
        <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="numpy" version="1.7.1">
        <repository changeset_revision="40db34c904df" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="matplotlib" version="1.2.1">
        <repository changeset_revision="dd81b71dff1b" name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="scipy" version="0.12.0">
        <repository changeset_revision="cd2e7872a8eb" name="package_scipy_0_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>


    <package name="ucsc_tools" version="0.1">
        <install version="1.0">
            <actions>
                <action type="download_binary">
                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
                </action>
                <action type="chmod">
                    <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
                </action>
                <action type="download_binary">
                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
                </action>
                <action type="chmod">
                    <file mode="755">$INSTALL_DIR/bigWigInfo</file>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
                </action>
             </actions>
         </install>
         <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
     </package>


    <package name="deepTools" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">
        <install version="1.0">
            <actions>

                <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
                <action type="shell_command">git reset --hard 98e5d8a61431ea8605c0643d991a1a5d8999b4dc</action>
                <action type="shell_command">
                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
                    python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
                </action>

                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                </action>
             </actions>
         </install>
         <readme>Installation of deepTools from Fidel Ramirez.</readme>
     </package>
</tool_dependency>