On Wed, Jun 26, 2013 at 10:01 PM, Dave Bouvier wrote:
> Peter,
>
> The empty failed tests folder issue has been resolved in 10171:eaa5112fefcd,
> and the test tool shed has been updated to that revision.
>
>--Dave B.
Great - currently all the missing test failures have been resolved :)
The ba
Hi Brad,
In your Galaxy installation directory, try copying
shed_tool_data_table_conf.xml.sample to shed_tool_data_table_conf.xml.
Hopefully that will resolve the problem.
Greg Von Kuster
On Jun 26, 2013, at 6:22 PM, Brad Zeitner wrote:
> I've started up an instance using cloudman, and it s
I've started up an instance using cloudman, and it seemed to be running fine.
When I tried to install a tool from the toolshed I got an error, and in trying
to resolve the error I used the admin console to update galaxy.
Now when Galaxy tries to start I get the following error:
galaxy.datatype
I've started up an instance using cloudman, and it seemed to be running fine.
When I tried to install a tool from the toolshed I got an error, and in trying
to resolve the error I used the admin console to update galaxy.
Now when Galaxy tries to start I get the following error:
galaxy.datatype
>
> To have Trackster visualization working properly in Galaxy, one needs
> bedtools.
> Yet in our instance (running under Ubuntu OS), installing bedtools in the
> galaxy home directory and setting the environmental variable PATH in the
> .profile file so that it includes the path to ~/bin/bedt
Bart,
I believe drmaa://-q somehost@queue-name
will work. However I could be very wrong. It has been a while since I
messed with the actual drmaa runners.
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Peter,
The empty failed tests folder issue has been resolved in
10171:eaa5112fefcd, and the test tool shed has been updated to that
revision.
--Dave B.
On 6/26/13 11:34:38.000, Dave Bouvier wrote:
Peter,
It looks like the failed tests container is being populated, but there
is some odd
Is it possible to specify the torque host as part of a DRMAA runner URL? I
haven't been able to find a *native_options *parameter to allow for this.
I'm using the old style cluster configuration.
*drmaa://[native_options]/*
*
*
Also, I haven't been able to find a list of native_options anywhere.
Is it possible to specify the torque host as part of a DRMAA runner URL? I
haven't been able to find a *native_options *parameter to allow for this.
I'm using the old style cluster configuration.
*drmaa://[native_options]/*
*
*
Also, I haven't been able to find a list of native_options anywhere.
Graham, this is not supported. The goal with the tool config is not to
specify any particular user interface format so that we are not locked
into a particular UI technology in the future. It is an abstract
description from which we can generate HTML, but also potentially
other interfaces.
--
Jame
Peter,
It looks like the failed tests container is being populated, but there
is some odd behavior with displaying it. As soon as we've tracked down
the issue, I'll update you.
--Dave B.
On 6/26/13 02:00:30.000, Peter Cock wrote:
On Tue, Jun 25, 2013 at 9:43 PM, Dave Bouvier wrote:
Pet
Hello,
Regards your comment about keeping history but deleting data, I suggest
you convert your history into a Workflow.
You could then delete the history and therefore all files attached to it
but keep a copy of the protocol for future use.
Hope it helps
Best
Jean-François
Also is there
Dear Developers,
I am using GATK for first time. I am doing Targeted reseq Analysis. while i
am running Unified Genotyper in Galaxy interface. it gives error message as
mentioned below..
"ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-WBrGTf) does
not exist."
But i places the Fasta f
I've tried updating a couple of times to the latest stable release and each
time I find that I can no longer see my saved histories. Roll back my machine
to an earlier snapshot and it is fine. The thing that may be different about
our system is that we're using Apache authentication rather tha
Hi everybody,
This is not a big issue but I am curious to know about it:
To have Trackster visualization working properly in Galaxy, one needs
bedtools.
Yet in our instance (running under Ubuntu OS), installing bedtools in the
galaxy home directory and setting the environmental variable PATH in t
> I was looking at galaxy/dist/tools/sr_mapping/bowtie2_wrapper.* and it
> does not seem to challenging to add another field where a user could
> specify some integer value that we simply pass to the the
> tag in the xml file.
>
> Would this be the correct way to go about this?
Yes, this is corr
Dear all,
We are running a local Galaxy instance up-to-date against galaxy/galaxy-dist.
When we edit attributes of a dataset in current history and request a datatype
change (Datatype tab), the selected dataset appears as a running job (yellow
box with spinning icon) for ever. The type has been
Hi guys,
we are currently establishing our own local Galaxy instance. However, after we
tried to install the "mothur toolsuite" we could not enter the admin pages
anymore. Every time we try we we obtain the following error:
"Internal Server Error
Galaxy was unable to successfully complete your
Hi Bjorn ,
thanks for reply ...my problem has solved ...it's working now ..
regards
shashi
From: Björn Grüning
To: shashi shekhar
Cc: Peter Cock ; Galaxy Dev
Sent: Tuesday, 25 June 2013 9:44 PM
Subject: Re: [galaxy-dev] How to enable auto option for newly
On Tue, Jun 25, 2013 at 9:43 PM, Dave Bouvier wrote:
> Peter,
>
> It turns out that the automated functional testing framework was not
> actually running. I suggest having a look in the morning, and if there are
> still any missing test results, I'll get them resolved then.
>
>--Dave B.
Thank
Hello,
I found two mistakes in the code of the bwa wrapper .
The first one comes from the following error message:
---
File "/galaxy-dist/tools/bwa_wrappers/bwa_wrapper.py", line 79
parser.add_option( '-y', '--ion', dest='ion', action="store_true,
help='Ion Torrent data mode usin
Hello,
When I install from binary files the boost problem doesn't go away and I
get one extra error message in the beginning.
Error running cuffdiff. cuffdiff: /usr/lib64/libz.so.1: no version
information available (required by cuffdiff)
[14:51:54] Loading reference annotation.
Warning: No condit
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