annotate tool_dependencies.xml @ 1:6bbb95b43f62 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_1_1 commit a7154599629e0f552495d91166648c3398acc10e

<?xml version="1.0"?>
<tool_dependency>
    <package name="ncurses" version="6.0">
        <repository changeset_revision="0efde9889efd" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="zlib" version="1.2.8">
        <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="lapack" version="3.4.2">
        <repository changeset_revision="5686c79a72d5" name="package_lapack_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="bzlib" version="1.0.6">
        <repository changeset_revision="af4887e1f595" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="trinity" version="2.1.1">
        <install version="1.0">
            <actions>
                <action sha256sum="012ccb42e1eab8a5b14c4e78becf3e7e69964d76c17fcca8110db6ffe63d3e0b" type="download_by_url">
                    https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.1.1.tar.gz
                </action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="0efde9889efd" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="ncurses" version="6.0" />
                    </repository>
                    <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="zlib" version="1.2.8" />
                    </repository>
                    <repository changeset_revision="5686c79a72d5" name="package_lapack_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="lapack" version="3.4.2" />
                    </repository>
                    <repository changeset_revision="af4887e1f595" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="bzlib" version="1.0.6" />
                    </repository>
                </action>

                <action type="setup_r_environment">
                    <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="R" version="3.2.1" />
                    </repository>
                    <repository changeset_revision="5686c79a72d5" name="package_lapack_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="lapack" version="3.4.2" />
                    </repository>
                    <package sha256sum="68782050f5252c4246f1b5b335105eccf4c804d57a0cd41eb63a300f7e0241a0">
                        https://depot.galaxyproject.org/software/Rcpp/Rcpp_0.12.0_src_all.tar.gz
                    </package>
                    <package sha256sum="f30155fdd4745b4c9a548a25a30b6ae5fe3e3f6cf4136ac485a75c90555934a0">
                        https://depot.galaxyproject.org/software/RcppArmadillo/RcppArmadillo_0.5.500.2.0_src_all.tar.gz
                    </package>
                    <package sha256sum="560be08f12ff92bab2aa926dd4dc22f05b6edd9e87afb22e2f52ef7d7d1fd103">
                        https://depot.galaxyproject.org/software/ape/ape_3.0-11_src_all.tar.gz
                    </package>
                    <package sha256sum="f3e9781e84e114b7a88eb099825936cc5ae7276bbba5af94d35adb1b3ea2ccdd">
                        https://depot.galaxyproject.org/software/RColorBrewer/RColorBrewer_1.1-2_src_all.tar.gz
                    </package>
                    <package sha256sum="f31afae9b1998dcf806d9ec82474fac49837082e310a2c6e3ee3cbcb55ff641b">
                        https://depot.galaxyproject.org/software/plyr/plyr_1.8.3_src_all.tar.gz
                    </package>
                    <package sha256sum="3062422c2ca917e52749464d63084a0d3cc061f59083f069280ec26336ce2f55">
                        https://depot.galaxyproject.org/software/digest/digest_0.6.8_src_all.tar.gz
                    </package>
                    <package sha256sum="b08ba8e62e0ce05e7a4c07ba3ffa67719161db62438b04f14343f8928d74304d">
                        https://depot.galaxyproject.org/software/gtable/gtable_0.1.2_src_all.tar.gz
                    </package>
                    <package sha256sum="1cd67b64f287aac9e8fd95dd4a0cab829e0fb7870fd264ede281be0b65ce7ca0">
                        https://depot.galaxyproject.org/software/stringi/stringi_0.5-5_src_all.tar.gz
                    </package>
                    <package sha256sum="05c45943ada9443134caa0ab24db4a962b629f00b755ccf039a2a2a7b2c92ae8">
                        https://depot.galaxyproject.org/software/magrittr/magrittr_1.5_src_all.tar.gz
                    </package>
                    <package sha256sum="f8267db85b83c0fc8904009719c93296934775b0d6890c996ec779ec5336df4a">
                        https://depot.galaxyproject.org/software/stringr/stringr_1.0.0_src_all.tar.gz
                    </package>
                    <package sha256sum="fbd49f75a5b0b7266378515af98db310cf6c772bf6e68bed01f38ee99b408042">
                        https://depot.galaxyproject.org/software/reshape2/reshape2_1.4.1_src_all.tar.gz
                    </package>
                    <package sha256sum="31151eaf36f70bdc1172da5ff5088ee51cc0a3db4ead59c7c38c25316d580dd1">
                        https://depot.galaxyproject.org/software/dichromat/dichromat_2.0-0_src_all.tar.gz
                    </package>
                    <package sha256sum="ba3165c5b906edadcd1c37cad0ef58f780b0af651f3fdeb49fbb2dc825251679">
                        https://depot.galaxyproject.org/software/colorspace/colorspace_1.2-6_src_all.tar.gz
                    </package>
                    <package sha256sum="84e787f58f626c52a1e3fc1201f724835dfa8023358bfed742e7001441f425ae">
                        https://depot.galaxyproject.org/software/munsell/munsell_0.4.2_src_all.tar.gz
                    </package>
                    <package sha256sum="0d8069eb48e91f6f6d6a9148f4e2dc5026cabead15dd15fc343eff9cf33f538f">
                        https://depot.galaxyproject.org/software/labeling/labeling_0.3_src_all.tar.gz
                    </package>
                    <package sha256sum="f4e1b98e3501b3a27b1a86ecc622a4653aff31c9f93248d7b5d428b03ebe6fce">
                        https://depot.galaxyproject.org/software/scales/scales_0.3.0_src_all.tar.gz
                    </package>
                    <package sha256sum="d0d941bfbf247879b3510c8ef3e35853b1fbe83ff3ce952e93d3f8244afcbb0e">
                        https://depot.galaxyproject.org/software/proto/proto_0.3-10_src_all.tar.gz
                    </package>
                    <package sha256sum="835fe22547222742fa84b8bf77774432abe3dff267932b8b8ed06de554f8e79b">
                        https://depot.galaxyproject.org/software/MASS/MASS_7.3-44_src_all.tar.gz
                    </package>
                    <package sha256sum="40248e6b31307787e44e45d806e7a33095844a9bbe864cc7583dd311b19c241d">
                        https://depot.galaxyproject.org/software/ggplot2/ggplot2_1.0.1_src_all.tar.gz
                    </package>
                    <package sha256sum="fbd49f75a5b0b7266378515af98db310cf6c772bf6e68bed01f38ee99b408042">
                        https://depot.galaxyproject.org/software/reshape2/reshape2_1.4.1_src_all.tar.gz
                    </package>
                    <package sha256sum="36f8bec5831ceedde3d3ab21d9db87cf1a32133a04f46e1803c833a510b8d17d">
                        https://depot.galaxyproject.org/software/qvalue/qvalue_2.2.2_src_all.tar.gz
                    </package>
                    <package sha256sum="02fb5178555e0288c4ec8f9b564721e31198dbf647aca0d3957c886f4c3b84a4">
                        https://depot.galaxyproject.org/software/amap/amap_0.8-7_src_all.tar.gz
                    </package>
                    <package sha256sum="0f67391d3fd6bc970293b5eb11dcd14f15686b61bce1c6da03e16dc3a60e93f2">
                        https://depot.galaxyproject.org/software/ctc/ctc_1.44.0_src_all.tar.gz
                    </package>
                    <package sha256sum="f16b6316fdbd7ab0077644d41a3286a688b0b75cc34686383e10f139f0955ae1">
                        https://depot.galaxyproject.org/software/Biobase/Biobase_2.30.0_src_all.tar.gz
                    </package>
                </action>

                <action type="shell_command">sed -i.bak -e 's/-ltinfo//' trinity-plugins/Makefile</action> <!-- tinfo is included in ncurses lib-->
                <action type="shell_command">sed -i.bak -e '/tar xvf samtools-0.1.19.tar.bz2/a \\tsed -i.bak -e "s|-lcurses|-lncurses|" samtools-0.1.19/Makefile samtools-0.1.19/Makefile' trinity-plugins/Makefile</action> <!-- ncurses instead of curses -->

                <action type="shell_command">make</action>
                <action type="shell_command">make plugins</action>

                <action type="move_file">
                    <source>Trinity</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_directory_files">
                    <source_directory>Analysis</source_directory>
                    <destination_directory>$INSTALL_DIR/Analysis</destination_directory>
                </action>
                <action type="move_directory_files">
                    <source_directory>Butterfly</source_directory>
                    <destination_directory>$INSTALL_DIR/Butterfly</destination_directory>
                </action>
                <action type="move_directory_files">
                    <source_directory>Chrysalis</source_directory>
                    <destination_directory>$INSTALL_DIR/Chrysalis</destination_directory>
                </action>
                <action type="move_directory_files">
                    <source_directory>Inchworm</source_directory>
                    <destination_directory>$INSTALL_DIR/Inchworm</destination_directory>
                </action>
                <action type="move_directory_files">
                    <source_directory>PerlLib</source_directory>
                    <destination_directory>$INSTALL_DIR/PerlLib</destination_directory>
                </action>
                <action type="move_directory_files">
                    <source_directory>trinity-plugins</source_directory>
                    <destination_directory>$INSTALL_DIR/trinity-plugins</destination_directory>
                </action>
                <action type="move_directory_files">
                    <source_directory>util</source_directory>
                    <destination_directory>$INSTALL_DIR/util</destination_directory>
                </action>

                <action type="shell_command">rm $INSTALL_DIR/trinity-plugins/*tar.gz</action>

                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/util</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/collectl/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/fastool</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/jellyfish/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/parafly/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/Trimmomatic</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/slclust/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/GAL_0.2.1</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/BIN</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/htslib</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/Analysis/DifferentialExpression</environment_variable>
                </action>
            </actions>
        </install>
    </package>
</tool_dependency>