I tried using IE 11.0.9600.17280 and updated to the latest Galaxy but am still
having the problems listed below. It’s not a big deal for us – we’ve just told
users not to use IE.
Dori
**
Dori Sajdak
Senior Systems Administrator
State University of NY at Buffalo
Hi all,
I am trying to install the Genome Diversity tools from the Miller Lab that are
in the Galaxy toolshed. I've been able to get all dependencies installed
except Quicktree. Whenever I try to install it, I get the error:
Error downloading from URL
ftp://ftp.sanger.ac.uk/pub4/resources/sof
I also was able to download quicktree.tar.gz by clicking on the URL in your
message. However, when I manually ftp into ftp.sanger.ac.uk, there is no
/pub4 directory. I'm a bit confused about how those two statements are both
true, but maybe it will help someone else figure this out. Removing the '4
I've just looked at this as well, it appears that /pub4 is not exposed and
does not allow you to change into it, but it does allow you to fetch if you
request files under it via the full path.
e.g.:
nate@victory% ncftp ftp.sanger.ac.uk
...
Logged in to ftp.sanger.ac.uk.
ncftp / > ls
ls-lR.gz
Hey all,
This fix is in the galaxy-central, but does not exist in galaxy-dist yet.
It will in the next release, and hopefully this is resolved for you at that
point.
-Dannon
On Wed, Sep 24, 2014 at 1:40 PM, Sajdak, Doris wrote:
> I tried using IE 11.0.9600.17280 and updated to the latest Gala
Hi,
I am developing a tool for STAR (https://code.google.com/p/rna-star/), and I
realize I may be reinventing another wheel. Has anyone else created a tool for
STAR? There's nothing else in the toolsheds for it yet.
David
David Hoover, PhD
Helix Systems Staff
SCB/DCSS/CI
Hi David,
yes there is inital code in the https://testtoolshed.g2.bx.psu.edu/. I
think Ross has done some work on it.
The main problem with Star is that is needs special indices (and a lot
of it) and it would be great to offer data managers for it.
Cheers,
Bjoern
Am 24.09.2014 um 22:05 schri
Why didn't I see these before? Hmm, I thought I had searched both toolsheds...
I was kind of hoping someone had tackled this in a different way. It would be
nice if there was a composite datatype for the reference genome. It is
important for users to generate their own personal genome referen
Hi,
Am 24.09.2014 um 22:39 schrieb David Hoover:
Why didn't I see these before? Hmm, I thought I had searched both toolsheds...
I was kind of hoping someone had tackled this in a different way. It would be
nice if there was a composite datatype for the reference genome. It is
important for
Bjorn
We'd be interested in this tool, as well. Any idea how close to functional it
is?
I see it's only on TEST toolshed, and not on production, at this point.
I don't see any related Trello card when searching on "star"
Regards,
Curtis
Galaxy Admin @ University of Alabama at Birmingham
--
Hi all,
I do have a version 0.1 wrapper for STAR under our oqtans package, however
it is not yet in toolshed.
https://github.com/ratschlab/oqtans_tools/tree/master/STAR/2.3/
Feel free to comment,
Vipin | Rätsch Lab
On Wed, Sep 24, 2014 at 4:55 PM, Curtis Hendrickson (Campus) <
curt...@uab.e
On a local instance of Galaxy, I get this error when attempting to
reset my password:
Failed to reset password: (501, '5.1.7 Bad sender address syntax',
'galaxy-no-reply@10.32.16.121')
I am told my mail server requires the from address to either have a
domain name, or the IP address to be in brac
When I run a workflow and multiple steps fail, does Galaxy have the
option to send a digest of all problems, or does each failed step
result in another email? Or maybe only the first failed task results
in an email alert?
I'm trying not to get spammed when a workflow fails.
Cheers,
-Evan Bollig
Hi All,
That (fubar in testtoolshed) star wrapper was derived from one originally
written by Jeremy Goecks. I modified it for multiple inputs and added a few
tweaks and it has been in production use in our group for about 6 months so
I'm pretty sure it works reasonably well in our hands at least.
Hi David,
-1 on the composite datatype for star reference genomes idea
Let's use the existing reference genome and index file infrastructure -
star is not sufficiently different from bwa or bowtie to warrant anything
different IMHO - it works for us but generating the index files manually is
a pai
Hi,
I have configured a new galaxy-project site with SLURM (version 14). I have one
server with a Galaxy-Project instance, one node with SLURM server and two SLURM
worker nodes. I have compile SLURM-DRMAA from source codes. When I run
“drmaa-run /bin/hostname” it’s work. But, when I try to run
16 matches
Mail list logo
