Hello all,
For those interested in more flexible tabular output from BLAST+,
please try out the wrappers on the *Test* Tool Shed which I have
also just updated to wrap BLAST+ 2.2.29 as well:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
One open question is should the interface
Hey Greg and Pieter,
Thanks for the report. This would seem to be an important feature if
there are going to be a lot of tools producing rich HTML output -
though I wonder if in some of these cases the visualization plugin
framework might be the superior way to render these results (though
First I am not the best person to respond to this - I hope someone
like Dan or JJ can follow up. In my past tool development I have tried
to limit my use of .loc files because they can be impediments to
reproduciblity (they are getting better though).
I have a pet peeve - it is when I ask a
Hello Rui,
The problems you are describing have to do with the format of the input
wig dataset.
It looks as if you have corrected the chromosome names to be identical
to the reference genome build used (required). There are options to
overcome the other issues:
1. verify that your data
Galaxy can do some these and maybe not others. This is a really big
topic, and I hope you let us all know how progress on this goes - it
is a really interesting use case. I can comment a little on each part
of this, but they are all connected and there are different ways to
approach each of these
Hi Jennifer,
Thanks for the note.
A related question, do we have a 'ucsc_tool'? I sometimes saw the warning
of failed dependency on ucsc_tool, but I'm not sure what it is. I found
that there are many binary/script utilities:
https://github.com/adamlabadorf/ucsc_tools
should I install all these
Hello,
Is it possible to share a history with a user (by user name) or change
ownership through the Galaxy API?
I didn't see any example doing this.
Thanks.
Cheers,
Daniel
--
Daniel Sobral,
Bioinformatics Unit
Instituto Gulbenkian de Ciência
Hi Daniel,
I am sorry but Galaxy API doesn't support sharing of histories yet.
For further notice these two parts of the API documentation are the most
relevant for the histories API:
Thanks Martin,
I saw that you can upload a file directly to a history using the API
through the upload tool, but then it has limitations in terms of file
size, no?
Would it be useable with large files?
Thanks,
Daniel
On 01/15/2014 07:05 PM, Martin Čech wrote:
Hi Daniel,
I am sorry but Galaxy
Hello John,
Thank you very much for your answer!
It's sounds logical and do-able.
However, I've thought of the following and I would like your opinion about it:
(this is to create a workspace for each student which is accessible only by
them and their teacher)
1. create a data library for each
Hi Rui,
This error probably means that the binaries from UCSC are not installed
or the path to the tools is incorrect. ucsc_tools is a package
requirement for the tools that use these binaries in the .xml portion of
the wrapper (for those in the dist/devteam).
If you are running your own
I am a total galaxy newbie who is setting up a galaxy server for a group of
internal researchers in order to do RNASeq analysis.
I can see where I can upload libraries from the galaxy server, but I can’t
figure out how to load the “available” data (fastqs) — to clarify instead of
asking users
On Wed, Jan 15, 2014 at 3:04 PM, Cantarel, Brandi L.
brandi.canta...@baylorhealth.edu wrote:
I can see where I can upload libraries from the galaxy server, but I
can’t figure out how to load the “available” data (fastqs) — to clarify
instead of asking users to upload 5GB fastq files, which
Hey Sheldon,
My first guess is that something's going wrong with your nginx proxy/cookie
configuration. Did you happen to change this when you updated the galaxy
server at all? Have you checked the steps at
https://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy and
verified that
Hi Dannon,
Thanks for the reply. I didn't change anything with my nginx configuration. I
reinstalled only the galaxy side of things thinking that I had somehow messed
up the update. It was working before the update. I also tested to see if I
had the problem by accessing the galaxy process
Hi,
I double checked directly trying the galaxy process. It turns out I never
tried it. I only thought that I had. So it is obviously a config problem or
permissions problem with nginx. Since I hadn't changed the nginx config I find
that strange.
Anyway the problem is between my keyboard
Daniel: You can create a history item through API by importing dataset from
library (that would be this method:
https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#galaxy.webapps.galaxy.api.history_contents.HistoryContentsController.create
).
For uploading bigger
On Wed, Jan 15, 2014 at 12:03 PM, Fernandez Edgar
edgar.fernan...@umontreal.ca wrote:
Hello John,
Thank you very much for your answer!
It's sounds logical and do-able.
However, I've thought of the following and I would like your opinion about it:
(this is to create a workspace for each
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