For the job related stuff, I’m doing this in my tools that provide statistics for the Galaxy ChIP-exo instance I’m setting up for a lab here at Penn State. You can see variations of tool examples here:
https://github.com/gregvonkuster/cegr-galaxy/tree/master/tools/cegr_statistics.
These tools are all included in workflows where the tool is generating metadata about the tool that executed immediatly prior to one of these metadata-generating tools. I use the while loop in the command to keep the this tool from executing in the workflow
before its immediate predecessor is completed. I assume you are doing something similar, where your tool will generate metadata for some different tool that has already been executed.
Here is an example of a basic command line in one of these tool configs that will provide the job stuff to the underlying script.
<command>
<![CDATA[
#set non_ready_states = ['new', 'queued', 'running', 'setting_metadata', 'upload']
#while $input.dataset.state in $non_ready_states:
time.sleep(60)
#end while
#set history_id = $__app__.security.encode_id($input.history.id)
#set history_name = $input.history.name
#set job = $input.creating_job
#set tool_id = $job.tool_id
#set tool_parameters = ""
#for p in $job.parameters:
#set tool_parameters = $tool_parameters + "__SeP__" + $p.name
#set tool_parameters = $tool_parameters + "__SeP__" + $p.value
#end for
python $__tool_directory__/bam_to_scidx_output_stats.py
--config_file $__tool_directory__/stats_config.ini
--input "$input"
--input_id "$__app__.security.encode_id($input.id)"
--input_datatype "$input.ext"
--dbkey "$input.metadata.dbkey"
--chrom_len_file ${chromInfo}
--history_id "$history_id"
--history_name "$history_name"
--tool_id "$tool_id"
--tool_parameters "$tool_parameters"
--output "$output"
]]>
</command>
Cheers!
Greg Von Kuster
Hi everyone,
I am working on a tool which attempts to create a file which stores all the metadata associated with a job execution. The things I know how to access right now are the file extension, name history id, dataset id. I'd like to know how to access other things
like the job id, uuid, file size, job command-line, job end time, job start time, core allocated, job runtime and any other important information associated with tool execution. I would prefer to get this information from the tool config file or my tool script
and not have the user create an api key which they have to submit as a parameter to my tool. Let me know if you guys have any ideas!
Katherine
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/