Thanks! This looks very useful for me. I'm also interested in fleshing out the
wrapper, (implementing all possible options, like bowtie's full parameter
list), but this should fit my purposes for now.
Best regards,
Patrick
Von: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Gesendet: Freitag,
Hi
I hope I have the correct place to ask for assistance.
I've been trying to use a local install of Galaxy. I can upload data and
convert formats (FASTq to FASTA) but can't use fasta manipulation tools like
width formatter or collapse. I am told No such file or directory /bin/sh:
Hi,
I've put together some exempels for activating and using the api. You can find
them here:
http://geertvandeweyer.zymichost.com/index.php?page=readid=29
Best regards,
Geert vandeweyer
Op 16-jan.-2013 om 02:52 heeft neil.burd...@csiro.au het volgende geschreven:
Hi
Sorry if these
Hello,
I've encountered a problem uploading some .xlsx files to Galaxy. None of
the files I've tried uploading today, via html or ftp, have been
successfully uploaded. Instead, the box turns grey and says the Job is
waiting to run. If I try to refresh, I get the error: The 'Upload File'
tool does
Dear Galaxy Team
We recently bagan to use galaxy in our lab. I uploaded the whole SNPs
several times but the number of them showed difference in every time .
Would you please do me a favor and let me know why the number of SNPs
differ in every times and what is the reason of this?
Best regards,
I've searched the list to see if anyone specifically mentions not being able to
use the cloud launchhttps://main.g2.bx.psu.edu/cloudlaunch feature on the
main public instance, but no one seems to address it. I have no trouble
launching Galaxy-cloudman using an AMI and pasting in my own user
Hello,
Is anyone having trouble with the UCSC data browser? I got the following
from one of my users:
Hi guys,
I try to fetch data from UCSC browser. A summary of my query shows that I
am getting what I ask for, but when I Send the data to Galaxy I am
returned to the channing galaxy home page
Cloudlaunch on the main public instance is fully supported and should work fine
-- I use it regularly for launching instances without issue.
There was a brief EC2 API outage yesterday (on the Amazon end) that caused
intermittent errors to all users of the API (including cloudlaunch), but that
Do you know how I can read in gzipped FASTQ files in the STAR wrapper without
writing an external Python script or the like?
Thanks,
Patrick
Von: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Gesendet: Freitag, 18. Januar 2013 04:37
An: Sorn, Patrick
Cc: 'galaxy-dev@lists.bx.psu.edu';
Geert, this is great stuff!
One small correction -- the API is enabled by default as of revision
7022:8376ad08ae41 (April 2012).
-Dannon
On Jan 16, 2013, at 1:17 AM, Geert Vandeweyer geertvandewe...@gmail.com wrote:
Hi,
I've put together some exempels for activating and using the api.
The display icon has been re-enabled in revision 8634:b9d44cf4b68e.
Thanks for the catch/feedback.
On Wed, Jan 9, 2013 at 12:00 PM, Langhorst, Brad langho...@neb.com wrote:
In some cases (e.g. mira) it's nice to be able to follow what's going on
in the log file…
Does anybody else miss
On Wed, Jan 9, 2013 at 5:00 PM, Langhorst, Brad langho...@neb.com wrote:
In some cases (e.g. mira) it's nice to be able to follow what's going on in
the log file…
Does anybody else miss being able to view files as they're running?
brad
I remember specifically testing that I could read
Hi Matthew,
Would you like to try out what we put together for modENCODE DCC?
Please see the README file in the docs folder at
https://github.com/modENCODE-DCC/Galaxy
Thanks,
Q
On Fri, Jan 18, 2013 at 10:17 AM, Dannon Baker dannonba...@me.com wrote:
Cloudlaunch on the main public instance
Does anyone have any experience running Galaxy using Amazon's EC2 spot
pricing? It seems like that could save a lot of money as compared to
on-demand pricing, and it appears that there are ways to mix on-demand and
spot instances within one processing cluster:
While it isn't bulletproof yet (restarting jobs that fail due to spot instance
reclaims, etc), Cloudman (usegalaxy.org/cloud) does currently have support for
running worker nodes as spot instances. When you go to add nodes, just click
Use Spot Instances, and add your spot price.
For obvious
Hi Andrew,
If this was on Main at Penn State, there was a problem with uploads that we
believe has now been resolved.
Dave C
On Wed, Jan 16, 2013 at 5:21 PM, Andrew Gorzalski gorzal...@gmail.comwrote:
Hello,
I've encountered a problem uploading some .xlsx files to Galaxy. None of
the files
Should definitely be stable enough to use in a classroom and that it isn't
working for you is definitely unexpected; it's the only way I've launched
instances for many months now. I'm digging through logs to see if I can find
any indication of why your particular requests are having issues.
Hello,
I am trying to connect to ftp with my username and password that I registered
in galaxy.
I am doing this through Filezilla. I am getting the error could not connect
to server.
Do you know what the problem is, please?
Thank you.
Eleanne
Hi All,
Thanks to this email[1] from Peter Cock I was able to find what was
causing the error I initially described here[2]. I also now have a
theory of why this is happening.
My unconfirmed guess. When a colon is present in the standard output
or standard error file, someone betweent Galaxy,
I hope I have the correct place to ask for assistance.
Yes, this list is a great place to ask questions about local Galaxy instances.
I've been trying to use a local install of Galaxy. I can upload data and
convert formats (FASTq to FASTA) but can't use fasta manipulation tools like
width
The wrapper isn't set up to support gzipped FASTQ because Galaxy unzips
datasets when they are uploaded, so the wrapper won't ever see a gzipped FASTQ
dataset. We plan to dataset gzip support to Galaxy in the future.
J.
On Jan 18, 2013, at 10:21 AM, Sorn, Patrick wrote:
Do you know how I can
Thanks. The requests will be coming from kennedykrieger.org.
On Jan 18, 2013, at 12:36 PM, Dannon Baker dannonba...@me.com
wrote:
Should definitely be stable enough to use in a classroom and that it isn't
working for you is definitely unexpected; it's the only way I've launched
instances
Thanks, Quang. That's not exactly what I'm looking for. My motivation is to
teach an entire class how to start a Galaxy cluster on their own, with minimal
knowledge of AWS or systems administration. The cloudlaunch feature on the
main psx site seems to fit this purpose exactly, but does not
Just an update on this issue. Upon further investigation, it looks like
the dynamic job runner code in commit 6f3b4e8 broke this. I haven't been
able to parse through everything going on yet to propose a fix, but I've
discovered two things:
1) Moving the self.__clear_user_job_count() call
Hi Eleanne,
Take a look at http://wiki.galaxyproject.org/FTPUpload.
FTP also needs to be enabled on the Galaxy server you are using. Which
server are you trying to connect to?
Thanks,
Dave C.
On Fri, Jan 18, 2013 at 10:42 AM, Solorzano, Eleanne
eleanne.solorz...@unh.edu wrote:
Hello,
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