Hi "ngsf...@hygenomics.com"
You ask four different questions. I strongly recommend you ask them in
four different mails each with an appropriate subject line, next time.
This will make it much easier for the community to help you.
Also, copy paste the logs and don't use screenshots, as they wil
Dear all,
this problem has been mentioned before by mcdow...@vims.ed, but there was no
solution so far posted.
I'm using the current cloudman on Amazon AWS. When I download a fastq.gz file
via an EBI-SRA ftp link using the "Upload File" function, although the file
itself is loading to the /mnt
Hi all,
Running galaxy-central default branch, I've seen a couple of cases where
what otherwise appears to be a successful job has failed with:
Traceback (most recent call last):
File "./scripts/set_metadata.py", line 122, in
__main__()
File "./scripts/set_metadata.py", line 72, in __mai
On Mon, Oct 14, 2013 at 9:20 PM, UMD Bioinformatics
wrote:
> On Oct 14, 2013, at 9:16 PM, Brad Chapman wrote:
>
>>
>> Ian;
>>
>>> I have my PATH set as well as the env.sh and my ./bash_profile. Again
>>> this all works fine from the command line. I don't know where else
>>> Galaxy is trying to fi
Dear all,
this problem has been mentioned before by mcdow...@vims.ed, but there was no
solution so far posted.
I'm using the current cloudman on Amazon AWS. When I download a fastq.gz file
via an EBI-SRA ftp link using the "Upload File" function, although the file
itself is loading to the /mnt
Hi Vipin,
It seems there are too many volumes (or too much volume storage) in your
AWS account and AWS is preventing any more from being created. You can
either delete some volumes if you don't need them or send a request to AWS
to increase your volume limit:
https://aws.amazon.com/contact-us/ebs_v
On Tue, Oct 15, 2013 at 10:13 AM, Stanislas Werfel
wrote:
>
> I'm also having another issue: when I delete files in the history in galaxy,
> they don't acually get deleted in the files/000/ folder. And galaxy is still
> showing them under "Using ..." in the total space used. So if I download
> a 3
Björn, Peter,
In the course of my investigation, I've discovered a possible
improvement to the lapack build recipe. If you change the cmake command
from:
cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/lapack
to:
cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/lapack
-DCMAKE_Fortran_FLAGS='-O2 -
And I can answer the first part; this is a known issue we're trying to
nail down and get a fix out for this week, along with a base volume update
to address other issues. Trello card: https://trello.com/c/8XSIeoG0
On Tue, Oct 15, 2013 at 10:23 AM, Peter Cock wrote:
> On Tue, Oct 15, 2013 at 10
Carlos,
Thank you very much. What I ended up doing to fix this issue was to uninstall
fastx_toolkit from the tool shed then I created a .bashrc file for galaxy. I
added this to the environmental_setup_file path and restarted galaxy. This was
the fix I needed. Things seem to be working now. Here
Hi Dave,
thanks for the pointer.
I updated the testtoolshed package. For me installing fine. I will wait
one more day and have a look at Peter's Testcases. I will than migrate
it to the main toolshed. Changes are now also in github.
Thanks,
Björn
> Björn, Peter,
>
> In the course of my investi
Hi Rhea,
Are you using the new server address? This is noted on the upload form:
"usegalaxy.org"
We will be updating the screencasts and such soon, there are other small
changes that will go along with this one and we want to capture it all
in one place. Meanwhile, I'll try to make this more
Hi all,
I think what we have are two similar, but somewhat separate problems:
1.) We need a way via the UI for an admin to be able to add additional
configuration entries to data tables / .loc files.
2.) We need a way to bootstrap/initialize a Galaxy installation with data
table/ .loc file entri
Hi Enis,
Thank you for the information! I saw many GalaxyIndicesFS are accumulated
on my account and cleaned up.
Later I tried to launch cloudman ami, a different message I saw in
paster.log:
18:35:32 - Master starting
18:35:33 - Successfully retrieved root user's public key from file.
Hi List,
I've sprouted some grays in the last week after my Galaxy instances all
simultaneously ceased to submit jobs to our main cluster.
Some Galaxy instances are running the PBS job runner, and others use DRMAA. For
the DRMAA runner I was getting:
galaxy.jobs.runners ERROR 2013-10-15 08:40:1
Hi Jennifer,
Thank you for your response.
The server address I have been using is main.g2.bx.psu.edu. I don't see the
new address on the website. Can you let me know what it is?
Thanks again
Rhea
On Tue, Oct 15, 2013 at 2:20 PM, Jennifer Jackson wrote:
> Hi Rhea,
>
> Are you using the new se
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Hello all,
I've been digging through the available galaxy tool config files and
have been unable to find a solution, so I bring my problem to you.
I have the following (pretty generic) repeat section in a tool config
I'm working on
Hi,
Is there any way to make collaboration on pages possible. I would like user
to be able to modify an existing and publicly shared page when the creator
of the page wants to offer this opportunity. It might be a bit complicated
and out of the scope of Galaxy right now but I wanted to hear what y
Hi Eric,
> Hello all,
>
> I've been digging through the available galaxy tool config files and
> have been unable to find a solution, so I bring my problem to you.
>
> I have the following (pretty generic) repeat section in a tool config
> I'm working on
>
>
> label="String of letters
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Hi Bjoern,
On 10/16/2013 01:26 AM, Bjoern Gruening wrote:
> Hi Eric,
>
>> Hello all,
>>
>> I've been digging through the available galaxy tool config files and
>> have been unable to find a solution, so I bring my problem to you.
>>
>> I have the fol
Am Mittwoch, den 16.10.2013, 01:41 -0500 schrieb Eric Rasche:
> Hi Bjoern,
>
> On 10/16/2013 01:26 AM, Bjoern Gruening wrote:
> > Hi Eric,
> >
> >> Hello all,
> >>
> >> I've been digging through the available galaxy tool config files and
> >> have been unable to find a solution, so I bring my pro
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