One of my colleagues is having trouble developing a peculiar tool: it
has no inputs. This makes sense in our local
context - it fetches some constantly updating remote data for the
current user - but implementing it has escaped our
skill. Galaxy complains about a tool with no params (i.e. an
Thank you so much!!!
It works really fine! I suspected something akin to that but I couldn't
find the right attributes.
But I still have a question: It comprises the datasets stored in
libraries right? Is there a way to ignore them?
Thanks again,
L-A
Greg Von Kuster wrote:
Hello Louise,
Louise,
The original code would not eliminate a dataset file that was pointed to by a
LibraryDatasetDatasetAssociation, and then imported from the data library into
the user's history, creating a HistoryDatasetAssociation that points to the
same file. I've added a bit of code below that
Possibly, but it would require an enable flag in the config since instances
with hundreds of users could pose problems with rendering delays. If someone
will proved the precise specs for what yo9u want, I'll add it to my list, but
it will be awhile before I get to ti. For example, should
Peter Cock wrote:
That sounds really useful - it is something that you plan on adding
to Galaxy officially?
Yes, I'm working on adding a lot of user- and admin- side access to
various numbers about disk usage (used by histories, used by deleted
data, etc. and disk quotas. I hope to have this
Looks like it's working, a couple of values were reduced :)
Thank you so much!!!
L-A
Greg Von Kuster wrote:
Louise,
The original code would not eliminate a dataset file that was pointed to by a
LibraryDatasetDatasetAssociation, and then imported from the data library into
the user's
I'd like to get a better understanding of the point of the database/build
attribute, and pose the question of when is the appropriate time to have it
set?
In our case at the Jackson Laboratory, the most common build is NCBI37/MM9.
However, the feeling of many folks here, is that this should not
I am trying to configure galaxy with sge/drmaa scheduler. The galaxy process is
starting up fine without any drmaa configuration. However the galaxy daemon
doesn't start properly when I add drmaa configuration lines as shown below. I
have set SGE_ROOT and DRMAA_LIBRARY_PATH variables
I'll just chime in quickly with an agreement that FASTQ files should not have
dbkeys set. They don't yet belong to a build/reference genome version. Some
tools/workflows may currently require a FASTQ file to have the dbkey set, but
this should be considered a work-around for a defect in a tool
Dave,
The fact that the Tophat wrapper was not setting the genome based on
the alignment genome was actually a bug, but I just fixed it in
changeset 5570:0c1251f25c6b.
Let us know if you have further questions.
Regards,
Kelly
On May 17, 2011, at 10:57 AM, Dave Walton wrote:
I'd like to
Hi all,
I'm wondering if the following task can be done in Galaxy with the
standard tools. The specific example is selecting the top (e.g. 3)
match sequences for each blast query, but I see this problem as much
more general than a Select top BLAST hits tool.
I want to select the first few (e.g.
Hi,
I'm a Galaxy and Python newbie and I'm working on project that desires
to upload files from a directory to the Galaxy server. We'd like to
physically copy the files rather than maintain references to them.
I'm starting by following the examples in scripts/api/README. All the
display
Hi Peter,
I think the tool shed would be appropriate for this...
-K
On Tue, May 17, 2011 at 6:23 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Wed, May 4, 2011 at 9:59 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hi all,
I mentioned just over a month ago that I had written a
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