Mercurial > repos > vmarcon > package_repet_2_5

changeset 0:f3b6009634b1 draft default tip

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1st Uploaded
author vmarcon
date Mon, 06 Feb 2017 13:05:10 -0500
parents
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files tool_dependencies.xml
diffstat 1 files changed, 30 insertions(+), 0 deletions(-) [+]
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--- /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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+<?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>