Hi,
Thanks for the input.
I've attached code (tool xml and perl script tool) and a test file for a
simple example that creates variable amounts of files after tool
execution. The test file is a simple 4 line text file for which new file
is created for each line in it and then that line is written
Thanks Jeremy, that changeset fixed the issue :)
Cheers,
Liisa
From:
Jeremy Goecks jeremy.goe...@emory.edu
To:
Liisa Koski liisa.ko...@dnalandmarks.ca
Cc:
galaxy-dev@lists.bx.psu.edu
Date:
2011-11-30 18:07
Subject:
Re: [galaxy-dev] Can't view data files from published histories, only
David,
There are many steps in Tophat, only some of which can be parallelized. Hence,
utilization appears low in many instances when Tophat is doing a step that
cannot be parallelized.
I'm not aware of anything that can be done to optimize Tophat further, but you
could contact the Tophat
On Dec 6, 2011, at 7:31 AM, Leon Mei wrote:
Hi Nate,
Here's the schema dump from our current Galaxy. Maybe this can help you to
identify something fishy.
Is it safe to do a manual DB upgrade based on the scripts in
./lib/galaxy/model/migrate/versions/?
Anything is safe as long as you
Hello,
Since our local Galaxy is a little sluggish, we were wondering if it
could be related to broken or missing database indexes (we're using
PostgreSQL), so we would like to know how they are managed in Galaxy,
and if there is a way to restore them automatically.
Thanks,
L-A
I don't know anything about the tool or parameters in question , but it looks
like the expected output filename is well formatted enough that you can derive
it from the input filename and parameters.
You could write a small python wrapper to grant you full control over
manipulating output
On Nov 30, 2011, at 2:24 PM, Mary Anne Alliegro wrote:
Hi Galaxy Users,
I have permanently deleted numerous files.
My usage % has decreased, but this is NOT reflected in my Gb report (upper
right)- it remains the same.
Am I missing some phantom trash bin?
If not, will Galaxy recalculate my
On Dec 1, 2011, at 8:37 AM, Glen Beane wrote:
You aren't the only one having problem in the disk-usage reported in the
upper right. I've also had problems with this total disk usage in our local
instance of Galaxy
I've deleted all but a handful of files, and we have a cron job that
Hi Nate,
That's awesome; thanks a million!
I just took a look at the auto generated emails on galaxy-commits; nicely done.
Even if it wasn't much work, I think the general benefit to the quality of
Galaxy as a platform and to the developer community is palpable.
And definitely thanks for
On Dec 6, 2011, at 10:16 AM, Louise-Amélie Schmitt wrote:
Hello,
Since our local Galaxy is a little sluggish, we were wondering if it could be
related to broken or missing database indexes (we're using PostgreSQL), so we
would like to know how they are managed in Galaxy, and if there is a
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