Hello Jan, Thanks for the clarification. Not quite what I was expecting so I am glad I asked - I don't have great answers for either case so hopefully other people will have some ideas. For the first use case - I would just specify some default input to supply to the input wrapper - lets call this N - add a parameter to the tool wrapper "--limit-size=N" - test that and then allow it to be overridden via an environment variable - so in your command block use "--limit-size=\${BLAST_QUERY_LIMIT:N}". This will use N is not limit is set, but deployers can set limits. There are a number of ways to set such variables - DRM specific environment files, login rc files, etc.... Just this last release I added the ability to define environment variables right in job_conf.xml (https://bitbucket.org/galaxy/galaxy-central/pull-request/378/allow-specifica...). I thought the tool shed might have a way to collect such definitions as well and insert them into package files - but Google failed to find this for me. Not sure about how to proceed with the second use case - extending the .loc file should work locally - I am not sure it is feasible within the context of the existing tool shed tools, data manager, etc.... You could certainly duplicate this stuff with your modifications - this how down sides in terms of interoperability though. Sorry I don't have great answers for either question, -John On Sat, Jun 14, 2014 at 5:12 AM, Jan Kanis <jan.code@jankanis.nl> wrote:
I have two use cases: the first is for a modification of the ncbi blast wrapper to limit the query input size (for a publically accessible galaxy instance), so this needs a configuration option for the query size limit. I was thinking about a separate config file in tool-data for this.
The second is is for a tool I have written to convert a blast xml output into a html report. The report contains links for each match to a gene bank (e.g. the ncbi database). These links should be configurable per database that was searched, and preferrably have an option of linking to the location of the match within the gene if the gene bank supports such links. One option is to add an extra column to the blast .loc files (if that doesn't break blast), where the databases are already configured.
Jan
Op 13 jun. 2014 18:02 schreef "John Chilton" <jmchilton@gmail.com> het volgende:
I would have different answers for your depending on what options are available to the server admin. What exactly about the tool is configurable - can you be more specific?
-John
On Fri, Jun 13, 2014 at 10:59 AM, Jan Kanis <jan.code@jankanis.nl> wrote:
I am writing a tool that should be configurable by the server admin. I am considering adding a configuration file, but where should such a file be placed? Is the tool-data directory the right place? Is there another standard way for per-tool configuration?
Jan
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/