2:55 p.m.
Hello all,
Re: BitBucket Issue 538 - Admin action to reload ".loc" files without
restarting Galaxy
https://trello.com/card/538-admin-action-to-reload-loc-files-without-rest...
Currently Galaxy administrators can reload a tool's XML configuration
file, which is very helpful (especially as a developer working on
changes to a single tool). Similarly it would be useful to be able to
reload one (or all) of the *.loc files (e.g. if a new BLAST database
is added), without having to restart Galaxy.
Further to this, it would be useful to trigger this from a script via
the Galaxy API or otherwise. Should this be filed as a new issue, or a
comment on the existing issue?
Another idea for enhancement would be to monitor the loc files for
*automatic* reloading without user or script intervention (but that
might be too much magic), or simply (re)loading loc files on demand
rather than at startup.
Do the Galaxy team have any plans in this area?
Thanks,
Peter
11:55 a.m.
On Fri, Mar 1, 2013 at 2:55 PM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
Hello all,
Re: BitBucket Issue 538 - Admin action to reload ".loc" files without
restarting Galaxy
https://trello.com/card/538-admin-action-to-reload-loc-files-without-rest...
Currently Galaxy administrators can reload a tool's XML configuration
file, which is very helpful (especially as a developer working on
changes to a single tool). Similarly it would be useful to be able to
reload one (or all) of the *.loc files (e.g. if a new BLAST database
is added), without having to restart Galaxy.
Further to this, it would be useful to trigger this from a script via
the Galaxy API or otherwise. Should this be filed as a new issue, or a
comment on the existing issue?
Another idea for enhancement would be to monitor the loc files for
*automatic* reloading without user or script intervention (but that
might be too much magic), or simply (re)loading loc files on demand
rather than at startup.
Do the Galaxy team have any plans in this area?
Thanks,
Peter
One example I had in mind was a tool using a loc file for a list of
databases, with a special entry "latest". If told to use the latest
DB, the tool would check the source website/FTP site. If the
latest file is already downloaded locally, it would just use that.
If not, it would download the latest file and use it. That part is
all quite doable in a tool wrapper script (assuming write
permissions in the desired database folder).
Now for the 'clever' part - the new database could be added to
the loc file for explicit selection by future users. It could be added
at the top to make it the default if desired. Then somehow we'd
need Galaxy to reload the loc file.
Of course, from a reproducibility point of view, the 'latest' version
of a database is not ideal (especially when there are versioned
or dated snapshots), but it is commonly requested all the same.
Peter
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Peter Cock