Hi Katherine,
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
On Jul 7, 2016, at 11:40 AM, Katherine Beaulieu
<katherine.beaulieu...@gmail.com<mailto:katherine.beaulieu...@gmail.com>> wrote:
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
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