Mercurial > repos > nick > dunovo
view tool_dependencies.xml @ 9:fa563fa9b330 draft
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
author | nick |
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date | Fri, 23 Mar 2018 22:26:23 -0400 |
parents | 658eefb99fd7 |
children | 9dc43bf7d1db |
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<?xml version="1.0"?> <tool_dependency> <package name="bowtie" version="1.1.2"> <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="mafft" version="7.221"> <repository changeset_revision="c5908940967d" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="networkx" version="1.10"> <repository changeset_revision="e761775277c1" name="package_networkx_1_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="dunovo" version="2.14"> <install version="1.0"> <actions> <!-- download the main dunovo package files --> <action sha256sum="e517a12794e7cac31b4ebcad99e6a6c0789027ace7d33f89d06ff2bc961515fc" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.14.tar.gz</action> <!-- TODO: Store dunovo version number in variable instead of hardcoding it everywhere. --> <!-- Move precheck.py and its dependencies into the main source directory. --> <action type="move_file"> <source>utils/precheck.py</source> <destination>$TMP_WORK_DIR/dunovo-2.14</destination> </action> <action type="move_file"> <source>utils/getreads.py</source> <destination>$TMP_WORK_DIR/dunovo-2.14</destination> </action> <!-- install submodules --> <action type="shell_command">rmdir kalign utillib ET</action> <!-- download the utillib submodule --> <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action> <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action> <action type="shell_command">rm v0.1.0.tar.gz</action> <action rename_to="utillib" type="move_file"> <source>utillib-0.1.0</source> <destination>$TMP_WORK_DIR/dunovo-2.14</destination> </action> <!-- download the kalign submodule --> <action type="download_file">https://github.com/makrutenko/kalign-dunovo/archive/v0.2.0.tar.gz</action> <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action> <action type="shell_command">rm v0.2.0.tar.gz</action> <action rename_to="kalign" type="move_file"> <source>kalign-dunovo-0.2.0</source> <destination>$TMP_WORK_DIR/dunovo-2.14</destination> </action> <!-- download the ET submodule --> <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action> <action type="shell_command">tar -zxvpf v0.2.2.tar.gz</action> <action type="shell_command">rm v0.2.2.tar.gz</action> <action rename_to="ET" type="move_file"> <source>ET-0.2.2</source> <destination>$TMP_WORK_DIR/dunovo-2.14</destination> </action> <!-- make and install --> <action type="shell_command">make clean</action> <action type="shell_command">make</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> </action> <action type="set_environment"> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> </action> </actions> </install> </package> </tool_dependency>