Dear all,
We are currently using the stable build of Galaxy and we are encountering the
following problem:
When we try to impersonate an user, the user drop down menu hangs in looking up
the user.
In consequence, we can not impersonate the user.
This behaviour started when we upgraded to the F
ry 24, 2014 5:21:56 PM
Subject: Re: [galaxy-dev] Error when searching for tools in local instance.
Hey Ricardo,
Did that fix your issue? Does the problem occur in one of the branches? If yes,
please let me know which one.
Thanks,
Sam
On Wed, Jan 22, 2014 at 10:51 AM, Perez, Ricardo <
t: Re: [galaxy-dev] Error when searching for tools in local instance.
Hi Ricardo,
Are you using the newest version from the stable branch or from default?
Thanks,
Sam
On Tue, Jan 21, 2014 at 3:53 PM, Perez, Ricardo < ricky_...@neo.tamu.edu >
wrote:
Dear All,
When I
Dear All,
When I go to my Galaxy Distibution I go the following place:
Admin -> Manage installed tool shed repositories
When I search for a tool in here with the provided search bar, I get the
following (I believe this is a bug):
URL:
https://galaxy.tamu.edu/admin_toolshed/browse_repositories?
Dear all,
Today when running velvet oprimizer vlsci, we encountered that if you use two
long files as input then the output is a file that its description is "no
peek". However when I run the files seperately the velvet optimizer seems to
work fine. I am not sure if this is a bug or not.
Tha
Dear all,
When trying to run velvet optimizer in galaxy, all the files we get return the
following:
"No peek"
When looking at the output of galaxy, we get the following:
galaxy.jobs.runners.local DEBUG 2013-07-31 09:31:46,829 execution finished:
perl
/usr/local/galaxy/bioinfosoft/shed_tools/
Dear all,
Today we ran some problems when running bowtie2. When we run bowtie2, the run
manages to complete. However, bowtie2 creates a 62kb file.
The error log that we get is the following:
galaxy.jobs DEBUG 2013-07-23 17:09:42,378 (1483) Persisting job destination
(destination id: local:///
Thank you for your quick response. However, I have checked and bedtools are
indeed in the galaxy path. When reviewind the log, I get the following:
galaxy.jobs.runners.local DEBUG 2013-07-09 16:59:15,937 execution
finished: grep -v '^#'
/usr/local/galaxy/galaxy-dist/database/files/000/dataset_5
Dear all,
As I was trying to do visualize my data set in trackster, I get the following
error:
/bin/sh: 1: bedtools: not found
sort: fflush failed: standard output: Broken pipe
sort: write error
needLargeMem: trying to allocate 0 bytes (limit: 1000)
When doing a sudo find / -name "bedto
Dear all,
When I rsync files from let say the following command:
rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/dm3 .
The system will sync files that are related to genome aligments, liftover, and
nibs.
How did the Galaxy team generated this files?
The reason I ask is because I would lather
Dear all,
When adding a genome I understand that the format are added in the following
way:
My question is, what is the difference between the unique_build_id and the
dbkey?
Thank you for your time,
--Ricardo Perez
___
Please keep all
Dear all,
I am currently trying to find a way to decrease the time the users need to wait
to permanently delete their data sets. In galaxy I read the following
"Histories that have been deleted for more than a time period specified by the
Galaxy administrator(s) may be permanently deleted."; I
Dear all,
I am trying to set up trackster for my local instance in galaxy. I did the
following:
Uncommented from the universe_wsgi.ini;
len_file_path = path/to/file/galaxy-dist/tool-data/shared/ucsc/chrom
Also I ran the following commands:
mkdir ./tool-data/shared/ucsc/chrom/
python ./cron/bu
Dear all,
When running Simulate (version 1.0.0)I am missing a graph in the initial
display. Is this a bug or is it my instance problem. On a side note, when
running Simulate I found out that if you don't place parameters in
"Frequency/ies for minor allele:" and "Detection thresholds:" the job
I am sorry, i posted the wrong configuration file above. I am posting now the
updated proftpd.conf , the differences is that some things are commented out
and others are not.
# This is a basic ProFTPD configuration file (rename it to
# 'proftpd.conf' for actual use. It establishes a single se
Hi Mr. Tobias,
We are having a similar problem. It seems that when the galaxy code was
updates, new created/updated passwords are using a different encryption mode.
This new mode, PBKDF2 SHA256 is NOT supported by proftpd 1.3.4d that you see to
be using. We had to compile proftpd from source
Dear all,
I have encountered a problem where my browser does not show the history sidebar
in galaxy. In my configuration I had the following line in universe_wsgi.ini
uncommented, which seem to be the source of the problem.
#filter-with = gzip
Commenting that line will fix my browser and see
Dear all,
I get the following errors when starting galaxy, is there any way to fix this.
Error loading display application (./display_applications/genetrack.xml):
[Errno 2] No such file or directory: './display_applications/genetrack.xml'
Traceback (most recent call last):
File "/usr/local/gal
Hello,
We want to able to distribute Galaxy configured with the UCSC browser,
specially for people who are not too UNIX savvy. We had a question on how to
do this, since we are planning to do it via git. How can we set up the git
server, in such a way that it doesn't compromise important file
Hello,
We are running a local instance of galaxy and we get the following error when
trying to display genes from our history in the ucsc browser. I got the error
as I was following the galaxy 101 video in the galaxy website (last step).
Thanks,
--Ricardo Perez
URL:
http://galaxy.tamu.edu/da
Hello,
I am getting this error when using Extract Genomic DNA (version 2.2.2)
empty
format: fasta, database: hg19
924 warnings, 1st is: Chromosome by name 'chr22' was not found for build
'hg19'. Skipped 924 invalid lines, 1st is #1, "chr22 1625633116287937
NM_001136213 0 -
Hello Galaxy,
We are implementing a fresh instance of Galaxy in the school server for
teaching purposes. So obtaining genomic data from the UCSC servers can present
a problem by overloading the connection. To make things faster, we want to
obtain the data for the genomic data and have it in o
Hi,
We are having problems fetching sequences from our mysql database to galaxy.
Does anyone know how to do so?
Thank you for your help.
--Ricardo Perez.
___
Please keep all replies on the list by using "reply all"
in your mail client.
Hi,
We are implementing a local instance of Galaxy and I had a quick question, is
it wrong to give Galaxy access to the UCSC databases?
Thank you for your time and patience,
--Ricardo Perez
___
Please keep all replies on the list by using "
Hi,
I am sorry for the trivial question. Does anyone know how I can make a local
instance of Galaxy use our local database files? We have downloaded the
database from USCS and would like to use the downloaded files instead of
retrieving it from the UCSC Table Browser when processing data.
Dear all,
I am currently working on downloading the genome data from the UCSC database.
I have figured out how to obtain the genome of one species at a time, however
this would take a bit of time if I have to type every command by hand.
Is there any command that would download the all the data fr
26 matches
Mail list logo
