Mercurial > repos > iuc > package_trinity_2_0_6
changeset 0:e65cf857feb6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
| author | iuc |
|---|---|
| date | Fri, 20 Nov 2015 06:49:06 -0500 |
| parents | |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 77 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Nov 20 06:49:06 2015 -0500 @@ -0,0 +1,77 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ncurses" version="5.9"> + <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" 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="trinity" version="2.0.6"> + <install version="1.0"> + <actions> + <action sha256sum="e0c3ec885fdcfe3422ea492372518ddf5d1aed3daa187c69c4254516b0845de1" type="download_by_url">https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.6.tar.gz</action> + <action type="set_environment_for_install"> + <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="ncurses" version="5.9" /> + </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> + </action> + <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/' trinity-plugins/Makefile</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 -zxvf ${RSEM_CODE}.tar.gz/a \\tsed -i.bak -e "s|-lz|-lz -L${ZLIB_ROOT_PATH}/lib|" ${RSEM_CODE}/Makefile ${RSEM_CODE}/sam/Makefile' trinity-plugins/Makefile</action> <!-- In case you have an obsolete zlib in /usr/lib --> + <action type="shell_command">make</action> + <action type="shell_command">make plugins</action> + + <action type="move_file"> + <source>Trinity</source> + <destination>$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/transdecoder</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> + </action> + </actions> + </install> + </package> +</tool_dependency>