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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_transtermhp_2_09 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty |
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tool_dependencies.xml |
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| diff -r 000000000000 -r 0a21f73e2f15 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jul 17 14:33:36 2015 -0400 |
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| @@ -0,0 +1,59 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="transtermhp" version="2.09"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://transterm.cbcb.umd.edu/transterm_hp_v2.09.zip</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>transterm</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>2ndscore</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>calibrate.sh</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>make_expterm.py</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>mfold_rna.sh</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>expterm.dat</source> + <destination>$INSTALL_DIR/data</destination> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable> + <environment_variable action="set_to" name="TRANSTERM_EXPTERM_DAT">$INSTALL_DIR/data/expterm.dat</environment_variable> + <environment_variable action="set_to" name="TRANSTERMHP_ROOT_PATH">$INSTALL_DIR/</environment_variable> + </action> + </actions> + </install> + <readme> +TransTermHP v. 2.0 is a complete rewrite by Carl Kingsford of TransTerm v. 1.0, +originally written by Maria D. Ermolaeva. The first TransTermHP was described in +the paper: + + [1] Maria D. Ermolaeva, Hanif G. Khalak, Owen White, Hamilton O. Smith and + Steven L. Salzberg. Prediction of Transcription Terminators in Bacterial + Genomes. J Mol Biol 301, (1), 27-33 (2000) + +TransTermHP v 2.0 is free software and is distributed under the GNU Public +License. See the file LICENSE.txt included with TransTermHP for complete +details. + +This package ships with the built-in experm.dat file which ships with +transterm. In tools, this may be used as:: + + transterm -p \$TRANSTERM_EXPTERM_DAT + + </readme> + </package> +</tool_dependency> |