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1st Uploaded |
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tool_dependencies.xml |
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| diff -r 000000000000 -r f3b6009634b1 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Feb 06 13:05:10 2017 -0500 |
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| @@ -0,0 +1,30 @@ +<?xml version="1.0"?> +<tool_dependency version="1.0"> + <package name="repet" version="2.5"> + <install version="1.0"> + <actions> + <action type="set_environment"> + <environment_variable name="REPET_HOST" action="set_to">bdd_server</environment_variable> + <environment_variable name="REPET_USER" action="set_to">orepet_galaxy</environment_variable> + <environment_variable name="REPET_PW" action="set_to">"blabla"</environment_variable> + <environment_variable name="REPET_DB" action="set_to">repet_galaxy</environment_variable> + <environment_variable name="REPET_PORT" action="set_to">3615</environment_variable> + <environment_variable name="REPET_PATH" action="set_to">~/tools/repet_pipe</environment_variable> + <environment_variable name="REPET_JOB_MANAGER" action="set_to">SGE</environment_variable> + <environment_variable name="REPET_QUEUE" action="set_to">SGE</environment_variable> + <environment_variable name="REPET_JOBS" action="set_to">MySQL</environment_variable> + <environment_variable name="REPET_TMP_DIR" action="set_to">/tmp</environment_variable> + <environment_variable name="PYTHONPATH" action="set_to">$REPET_PATH</environment_variable> + <environment_variable name="PATH" action="prepend_to">$REPET_PATH/bin</environment_variable> + <environment_variable name="REPET_NUCL_BANK" action="set_to">/path/to/nucl/bank</environment_variable> + <environment_variable name="REPET_PROT_BANK" action="set_to">/path/to/prot/bank</environment_variable> + <environment_variable name="REPET_HMM_PROFILES" action="set_to">/path/to/hmm_profiles/bank</environment_variable> + <environment_variable name="REPET_RDNA_BANK" action="set_to">/path/to/rdna/bank</environment_variable> + <environment_variable name="LIB_GCC4_8_2" action="set_to"></environment_variable> + <environment_variable name="LD_LIBRARY_PATH" action="set_to"></environment_variable> + </action> + </actions> + </install> + <readme> Please verify if environment variables match to your configuration : galaxy_dist/tool_dependency_dir/repet/2.5/.../env.sh</readme> + </package> +</tool_dependency> |