update config

Author: qianyuanzhu

template/galaxy.yml

@@ -171,6 +171,7 @@ galaxy:
   # Temporary files are stored in this directory.
   new_file_path: 
 
+  object_store_cache_path:
   # Tool config files, defines what tools are available in Galaxy. Tools
   # can be locally developed or installed from Galaxy tool sheds.
   # (config/tool_conf.xml.sample will be used if left unset and
@@ -197,7 +198,7 @@ galaxy:
   # panel layout.  This file can be changed by the Galaxy administrator
   # to alter the layout of the tool panel.  If not present, Galaxy will
   # create it.
-  #integrated_tool_panel_config: integrated_tool_panel.xml
+  integrated_tool_panel_config: integrated_tool_panel.xml
 
   # Default path to the directory containing the tools defined in
   # tool_conf.xml. Other tool config files must include the tool_path as
@@ -439,15 +440,15 @@ galaxy:
   # Each job is given a unique empty directory as its current working
   # directory. This option defines in what parent directory those
   # directories will be created.
-  #job_working_directory: database/jobs_directory
+  job_working_directory: database/jobs_directory
 
   # If using a cluster, Galaxy will write job scripts and stdout/stderr
   # to this directory.
   cluster_files_directory: 
 
   # Mako templates are compiled as needed and cached for reuse, this
   # directory is used for the cache
-  #template_cache_path: database/compiled_templates
+  template_cache_path: database/compiled_templates
 
   # Set to false to disable various checks Galaxy will do to ensure it
   # can run job scripts before attempting to execute or submit them.
@@ -480,13 +481,13 @@ galaxy:
   # from external sources such as http://dx.doi.org/ by Galaxy - the
   # following parameters can be used to control the caching used to
   # store this information.
-  #citation_cache_data_dir: database/citations/data
+  citation_cache_data_dir: database/citations/data
 
   # Citation related caching.  Tool citations information maybe fetched
   # from external sources such as http://dx.doi.org/ by Galaxy - the
   # following parameters can be used to control the caching used to
   # store this information.
-  #citation_cache_lock_dir: database/citations/lock
+  citation_cache_lock_dir: database/citations/lock
 
   # Tools with a number of outputs not known until runtime can write
   # these outputs to a directory for collection by Galaxy when the job

template/script.sh.erb

@@ -46,15 +46,21 @@ setup_env () {
   EMAIL="${USER}@osc.edu"
   JOB_CONFIG_FILE_PATH="${TEMPLATE_PATH}/job_conf.xml"
   OUTPUT_PATH="<param id='Output_Path'>${TEMPLATE_PATH}/output</param>"
-  
+  INTEGRATED_TOOL_PANEL_CONFIG="${TEMPLATE_PATH}/integrated_tool_panel.xml"
   sed -i -e"s/^\s*mount:.*/  mount: $(echo $MOUNT | sed -e 's/[\/&]/\\&/g')/"  "${TEMPLATE_PATH}/galaxy.yml"
   sed -i -e"s/^\s*cookie_path:.*/  cookie_path: $(echo $COOKIE_PATH | sed -e 's/[\/&]/\\&/g')/"  "${TEMPLATE_PATH}/galaxy.yml"
   sed -i -e"s/^\s*database_connection:.*/  database_connection: $(echo $DATABASE | sed -e 's/[\/&]/\\&/g')/"  "${TEMPLATE_PATH}/galaxy.yml"
   sed -i -e"s/^\s*file_path:.*/  file_path: $(echo ${LOCAL_GALAXY_DIRECTORY}/database/files | sed -e 's/[\/&]/\\&/g')/"  "${TEMPLATE_PATH}/galaxy.yml"
   sed -i -e"s/^\s*new_file_path:.*/  new_file_path: $(echo ${LOCAL_GALAXY_DIRECTORY}/database/tmp | sed -e 's/[\/&]/\\&/g')/"  "${TEMPLATE_PATH}/galaxy.yml"
+  sed -i -e"s/^\s*object_store_cache_path:.*/  object_store_cache_path: $(echo ${LOCAL_GALAXY_DIRECTORY}/database/object_store_cache | sed -e 's/[\/&]/\\&/g')/"  "${TEMPLATE_PATH}/galaxy.yml"
   sed -i -e"s/^\s*single_user:.*/  single_user: $(echo $EMAIL | sed -e 's/[\/&]/\\&/g')/"  "${TEMPLATE_PATH}/galaxy.yml"
   sed -i -e"s/^\s*job_config_file:.*/  job_config_file: $(echo $JOB_CONFIG_FILE_PATH | sed -e 's/[\/&]/\\&/g')/"  "${TEMPLATE_PATH}/galaxy.yml"
+  sed -i -e"s/^\s*integrated_tool_panel_config:.*/  integrated_tool_panel_config: $(echo $INTEGRATED_TOOL_PANEL_CONFIG | sed -e 's/[\/&]/\\&/g')/"  "${TEMPLATE_PATH}/galaxy.yml"
   sed -i -e"s/^\s*cluster_files_directory:.*/  cluster_files_directory: $(echo ${LOCAL_GALAXY_DIRECTORY}/database/pbs | sed -e 's/[\/&]/\\&/g')/"  "${TEMPLATE_PATH}/galaxy.yml"
+  sed -i -e"s/^\s*template_cache_path:.*/  template_cache_path: $(echo ${LOCAL_GALAXY_DIRECTORY}/database/compiled_templates | sed -e 's/[\/&]/\\&/g')/"  "${TEMPLATE_PATH}/galaxy.yml"
+  sed -i -e"s/^\s*citation_cache_data_dir:.*/  citation_cache_data_dir: $(echo ${LOCAL_GALAXY_DIRECTORY}/database/citations/data | sed -e 's/[\/&]/\\&/g')/"  "${TEMPLATE_PATH}/galaxy.yml"
+  sed -i -e"s/^\s*citation_cache_lock_dir:.*/  citation_cache_lock_dir: $(echo ${LOCAL_GALAXY_DIRECTORY}/database/citations/lock | sed -e 's/[\/&]/\\&/g')/"  "${TEMPLATE_PATH}/galaxy.yml"
+  sed -i -e"s/^\s*job_working_directory:.*/  job_working_directory: $(echo ${LOCAL_GALAXY_DIRECTORY}/database/jobs_directory | sed -e 's/[\/&]/\\&/g')/"  "${TEMPLATE_PATH}/galaxy.yml"
   sed -i.bak 's/\(ppn=\).*/\11<\/param>/' "${JOB_CONFIG_FILE_PATH}"
   sed -i -e"s/outputpath/$(echo $OUTPUT_PATH | sed -e 's/[\/&]/\\&/g')/"  "${JOB_CONFIG_FILE_PATH}" 
   sed -i -e"s/^.*Output_Path.*/            $(echo $OUTPUT_PATH | sed -e 's/[\/&]/\\&/g')/"  "${JOB_CONFIG_FILE_PATH}"