Hi all
I am in the process of updating our galaxy servers (from
release_2014.04.14 to latest_2014.08.11).
when I execute
~/lib/galaxy/model/migrate/versions/0120_dataset_collections.py
as part of the 'manage_db.sh upgrade' I run into a bizarre error:
First, it produces 10 Mysql 1050 Error
Damion,
Thanks a lot - consequently treating the toppic of 'reproducable
science' is a competition, but absolutely required. Björn really touched
my mind when he gave the linked talk in Chicago (GCC 2012). Although for
a longer time things got stuck, I think that Galaxy is still a (the?)
key
Sorry Don, I forgot the https in the proxy line:
RewriteRule ^(.*) https://144.174.51.187:8080$1 [P]
That should do it :)
Iyad Kandalaft
-Original Message-
From: Shrum, Donald C [mailto:dcsh...@admin.fsu.edu]
Sent: Monday, August 25, 2014 9:27 PM
To: Kandalaft, Iyad; Eric Rasche
Cc:
Well it looks like the migration file has these columns listed in a
different order than the mapping Galaxy uses - and the order yours
appeared in were the ones from Galaxy's mapping file. So somehow
Galaxy is automatically creating those tables prior to running the
migration based on the code in
I think I'd also need to change the proxy config to include the https
Proxy *
AddDefaultCharset off
Order Deny,Allow
Allow from all
/Proxy
Proxy https://144.174.51.187:8080
Order deny,allow
Allow from all
/Proxy
Even with that and
What issues are you still seeing? How is it non-functional?
On 08/26/2014 08:32 AM, Shrum, Donald C wrote:
I think I'd also need to change the proxy config to include the https
Proxy *
AddDefaultCharset off
Order Deny,Allow
Allow from all
/Proxy
Proxy
is just an apache page
Is it an error page/the default index.html/other?
Next: Are you doing the proxying with mod_proxy or with mod_rewrite?
mod_rewrite looks like
RewriteRule ^(.*) https://144.174.51.187:8080$1 [P]
while mod_proxy looks like
ProxyPass / http://localhost:8080/
Hi Inge,
There is an implementation for using the AWS S3 object store as the data
store for a given Galaxy instance. The implementation is located here
https://bitbucket.org/galaxy/galaxy-central/src/3a51eaf209f2502bf32dbb421ecabb7fe46243ea/lib/galaxy/objectstore/s3.py?at=default
and it offers
Thanks Enis, just to elaborate on Pulsar - I suspect it would work
with something like configuring Galaxy with S3 object store right now
- but it would do so by having Galaxy cache the data locally and then
Pulsar would negotiate the transfer with Galaxy (many different ways
this could occur
Hi John
Thanks for the insights
Hi Iyad
Yes, the user account has the ability to drop and alter tables.
Hans-Rudolf
On 08/26/2014 03:08 PM, John Chilton wrote:
Well it looks like the migration file has these columns listed in a
different order than the mapping Galaxy uses - and the order
Hello All,
I am running a Galaxy instance on Linux and have installed tools from the
Galaxy Main Tool Shed. However, whenever I run TopHat2, the program is unable
to complete the job before I get the following error message:
Traceback (most recent call last):
File
Hi Hans,
I'll add to John's statement about the ordering - a different ordering than the
model is entirely possible because alters to add columns always add them at the
end. The tables for Galaxy Main are so old that they are in a very different
order than most newer installations. As John
Hey Kevin,
You need to install samtools and bowtie(2) into your system. I assume, the
package you installed to galaxy is just a wrapper to call samtools. It doesn’t
come with samtools binary.
Best,
Alper Kucukural, PhD
Bioinformatics Core,
University of Massachusetts Medical School
368
Hello all,
The *2014 Swiss-German Galaxy Tour
https://wiki.galaxyproject.org/Events/SG2014* is happening from 30
September through 2 October. The tour features 3 events and they will all
be great ways to meet fellow developers, and learn more about defining
tools and deploying and administering
Thanks for the help today Eric...
I'm not sure if this is worth adding to the docs but I thought I'd post it in
case someone would like to.
I have an apache proxy setup for galaxy with ldap authentication. I wanted the
user sign on to be over https as users are using their HPC accounts to
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