Hi all, I can't use the public interface in an effective way: items in history
(i.e. the green boxes) cannot be expanded. More important, names of the items
remind me something that has to deal with the tool/library path (e.g.
2010_03/pilot2/README_pilot2_snps).
This happens on OS X and MS Wind
Hello Galaxy Team,
I am writing to request that the genome of *Sinorhizobium meliloti *1021 be
added to the "Map with Bowtie for Illumina" tool. I am using the main
server http://main.g2.bx.psu.edu/ and my user name is mbiggs.
Please let me know if this email is received.
Thanks,
Matt Biggs
I am a non-programmer working on Prochlorococcus (a marine
bacteria) for which UCSC and Ensembl do not yet have
genome/transcriptome available or uploaded. However, the genome
and transcriptome of this organism have been solved and annotated
and are available on
Likewise. I can get to my "Saved Histories", but when i click on one, very few
items (if any) show up in the rightside panel. ive also tried multiple
browsers, etc.
rich
From: Cittaro Davide
To: "galaxy-u...@bx.psu.edu"
Sent: Monday, December 5, 2011 7:39 A
closing on galaxy-user list (posted to dev, too)
On 12/2/11 12:19 PM, Toqa Manasrah wrote:
Hi everybody,
I am integrating a new tool which depends on several other libraries
(part of the tool). when galaxy run my tool, it can find main command
but not the deepest. where should I define the path
Hi Matt,
The quickest way to use new genomes with most tools, including Bowtie,
is to use them as a custom reference genome. To do this, load the genome
in fasta format into your history.
Then, on the tool form (for Bowtie, will vary slightly between tools), set:
Will you select a re
Dear Galaxy experts,
I have a question regarding uploading my illumina data (over 3G) using
FTP. It was not uploaded completely and stopped. I tried a couple of
times..still not working. Can anyone tell me what can cause the problems?
Many thanks,
Bao
Same here; I can't initiate "Generate Pileup" from Sam tools. When I select
"Execute" the brower just stalls and does not add to my workflow. Also, I can't
download bam or bai files when use right-click "save targe as." I have tried
Internet Explorer and Firefox.
--- On Mon, 12/5/11, Richard
Hi,
Sorry to add to the list of problems but I can't see "my history" at all, I can
only see the main pane and the list of tools.
Best Wishes,
David.
__
Dr David A. Matthews
Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
Sch
Dear Gretel,
I am copying this question to the Galaxy-User mailing list, which is the
best place to discuss it. Also, see
http://galaxyproject.org/wiki/Supportfor other ways to get
information.
Can you post some additional information to this thread? In particular:
* What steps are missing from
Hi Gretel,
I just read the rest of my inbox. It appears that you are not the only
person experiencing problems with the history panel today.
Someone from Galaxy will get back to you once we have this figured out.
Thanks,
Dave C.
On Mon, Dec 5, 2011 at 8:44 AM, Dave Clements wrote:
> Dear Gr
Hello Gretel,
There was a temporary problem that has now been resolved. The History
panel should now load as expected. Jobs will also be started, however
the time to start and will likely be longer than usual due to many users
starting their jobs at the same time.
Very sorry for any inconven
Hello,
There was a temporary problem that has now been resolved. The History
panel should now load as expected. Jobs will also be started, however
the time to start and complete will likely be longer than usual due to
many users initiating jobs at the same time.
Very sorry for any inconvenie
Hello,
There was a temporary problem that has now been resolved. The History
panel should now load as expected. Jobs will also be started, including
Upload jobs, however the time to start and complete will likely be
longer than usual due to many users initiating jobs at the same time.
Very s
Hello,
There was a temporary problem that has now been resolved. The History
panel should now load as expected and jobs will start. However, the time
for a job to initiate, run, and complete will likely be longer than
usual due to many users initiating jobs at the same time.
Very sorry for t
Hi Everybody,
I am running a tool which is not defining the output file name as parameter.
the tool is running and I can see the output file in the history directory but
not in the history frame.
how could I solve the problem? I should see and download the output file from
the history but I see
Toqa,
Just to make sure I've understood your question: the problem is that a tool
that you're trying to wrap doesn't provide a way to specify a particular output
filename? Take a look at the from_work_dir attribute of a element.
Or are you asking how to define outputs in general? For that, s
On Nov 30, 2011, at 12:49 PM, Richard Mark White wrote:
> Hi,
> I was nearing my disk quota (at 97%), so I deleted a large number of
> datasets using "delete permanently". But my usage did not go down at all.
> Is there a delay in this happening, or is there some way to purge the files?
Hi
Thank you so much Dannon.
I appreciate your help but I need some more clarification.
in the tool I am integrating (which is java classes) if the input parameters are
./main.bash eps0.3_40reads.fa population10_ref.fa 15 6 120
Then teh output is in eps0.3_40reads_I_6_15_CNTGS_DIST0_EM20.txt
As
I posted this question previously- IS there any work flow for analysis of
microRNA/ small RNA in galaxy, please. I have run microRNA sequencing for
control and treated cells.
Thanks
___
The Galaxy User list should be used for the discussion o
Hi,
I have been using Galaxy for manipulation of data sets and you can
run analysis on DSAP http://dsap.cgu.edu.tw/index.htm or use miRNAkey http://ibis.tau.ac.il/miRNAkey/
. Well there are other options as well, but these are pretty easy to
use.
Luciano
On Dec 5, 2011, at 3:10 PM, sha
Hi all,
I have a a bed file that I would like sort for chromosome 1 ONLY? Would
you tell me the syntax to "select" lines that are chromosome 1 only
instead of 1 or 10,11-19?
Thank you very much,
Di Nguyen
U of Washington
___
The Galaxy
Hi,
I open my galaxy and found the history was empty, I could not found my previous
history, so how can I find it? Thanks a lot!
Reards
weimin zhao___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other fea
Hi,
I opened my galaxy and found the history was empty, I could not found my
previous history, so how could I find it? Thanks a lot!
Reards
weimin zhao___
The Galaxy User list should be used for the discussion of
Galaxy analysis and othe
Hi, Weimin,
What do you see when you select Options | Saved Histories (top right of the
history panel)?
If that doesn't show your old histories to re-open, please let us know
exactly which galaxy URL you were using and what login name you used so we
can take a look.
Note that you need to be logg
yup...took a while, but eventually resolved. thanks.
rich
From: Nate Coraor
To: Richard Mark White
Cc: Jennifer Jackson ; "galaxy-u...@bx.psu.edu"
Sent: Monday, December 5, 2011 3:39 PM
Subject: Re: [galaxy-user] disk quota not updating
On Nov 30, 2011,
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