On Thu, May 2, 2013 at 7:16 AM, Ira Cooke iraco...@gmail.com wrote:
Hi all,
I've written a script to help deal with the problem of maintaining toolshed
tools
across multiple toolsheds (eg test and release)
The problem I encountered was that switching between test and production
versions
hi,
I'm getting the following error when trying to reach the main/test
toolsheds. Are they down?
This webpage is not available
Chromium's connection attempt to toolshed.g2.bx.psu.edu was rejected.
The website may be down, or your network may not be properly configured.
also from
Hello Geert,
Thanks for reporting this - it looks like our server or network is down. We'll
get this resolved as soon as possible and let you know when it is available.
Greg Von Kuster
On May 2, 2013, at 6:16 AM, Geert Vandeweyer wrote:
hi,
I'm getting the following error when trying to
On Thu, May 2, 2013 at 1:35 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
Standardized Repository Actions menu in the tool shed is available in
changeset revision 9555:fadc4b334f3e which is currently running on
the test tool shed.
Thanks for your request!
Greg Von Kuster
Great -
Hi all,
I've written a script to help deal with the problem of maintaining toolshed
tools across multiple toolsheds (eg test and release)
The problem I encountered was that switching between test and production
versions of a suite of tools can be quite painful because every repository
Hello dev-team,
I would like to add the different type of password encryption to the users
in my galaxy instance. I started working with the current password encoding
script:
/home/apps/galaxy-dist/lib/galaxy/util/hash_util.py
I will keep the current sha1 and add another layer of encryption to
That should be the only place, it is called from the some methods of
the User model object. So you could modify it to always hash new
passwords in a different way, but check old passwords with sha1 first,
then something else.
Although it might be nice to move the functionality into
Both tool shed's should now be accessible. Sorry for the downtime.
On May 2, 2013, at 6:26 AM, Greg Von Kuster wrote:
Hello Geert,
Thanks for reporting this - it looks like our server or network is down.
We'll get this resolved as soon as possible and let you know when it is
Hi all,
For what is I think the second time (fortunately this was only on the
Test Tool Shed), I have managed to upload a tar-ball to the wrong
repository:
2:fae4084a0bc0
http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired
It could have been a glitch, but more likely is was
Hello all,
I'm looking at how best to incorporate Galaxy workflows into a
publication - a standalone *.ga file in supplementary materials
would probably work but is static and I fear likely to bit rot.
I think posting each workflow (or set of workflows) as a
repository on the main Galaxy Tool
Dear galaxy-dev-list,
I am trying to use new-style job configuration whith a load-balancing on 2
web servers and 2 job hanlders.
I have configured load balancing as follows (universe_wsgi.ini):
# Configuration of the internal HTTP server.
[server:web0]
use = egg:Paste#http
port = 8083
host =
On Thu, May 2, 2013 at 4:29 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
For what is I think the second time (fortunately this was only on the
Test Tool Shed), I have managed to upload a tar-ball to the wrong
repository:
2:fae4084a0bc0
Oliver,
The new job running file is also providing me a lot of headaches. The
documentation on site is correct, but some of the items are not yet
implemented, for example, DRMAA external scripts still need to be in
the universe_wsgi.ini, yet the site say to put them in job_conf.xml
file! Lot of
Hi All,
I have noticed that there is no Mpileup available in either of the tool sheds.
Is there a simple way to install it in my instance?
Thanks,
Iry
The information in this email, including attachments, may be confidential and
is intended solely for the addressee(s). If you believe you
Thanks James, I have updated the password of one user in galaxy_user table
with the new algorithm,
I also adjusted the function new_secure_hash
in /lib/galaxy/util/hash_util.py in such a way that it returns
the new hash instead of sha1. Now I tried to login, it fails to get the
account, I think
Hi dev-team,
We have placed our galaxy instance ssl and I need to make sure that the
secure flag is set
on the cookie (commonly represented by the word “secure” under the Security
column) but
I am not able to do the same. something like below:
[image: Inline image 2]
when I checked on my
Hi Peter,
This fix is now running on the test tool shed. Thanks for pointing out this
flaw!
Greg Von Kuster
On May 2, 2013, at 12:54 PM, Peter Cock wrote:
On Thu, May 2, 2013 at 4:29 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Another even simpler change (which would also make a big
Ilya,
Thank you for reporting this issue, a fix has been committed in
9627:8d8368ab03ff, and the test tool shed has been updated.
--Dave B.
On 5/2/13 13:01:54.000, Sytchev, Ilya wrote:
Hi,
I can't install any tools from the test tool shed into the local Galaxy
instances. I can see the
I have started testing with creating a new user and the password hash
created using new algorithm,
galaxy=# select username,email,password from galaxy_user where email = '
fml...@gmail.com';
username | email | password
I am getting similar errors as Brian reported back in March. (Note, we
appear to have the same last name, but no relation)
An error occurred with this dataset: *Job output not returned from cluster*
*
*
- Running on Cloudman with 5-6 nodes. (xlarge)
- The error seems to occur consistently when I
Thanks for getting this fixed so quickly!
Ilya
On 5/2/13 4:32 PM, Dave Bouvier d...@bx.psu.edu wrote:
Ilya,
Thank you for reporting this issue, a fix has been committed in
9627:8d8368ab03ff, and the test tool shed has been updated.
--Dave B.
On 5/2/13 13:01:54.000, Sytchev, Ilya wrote:
I have updated the table schema from the script to adjust the column length
from the following script:
lib/galaxy/model/mapping.py
Now my new registration passwords are encrypted with second layer of
authentication using PBKDF2
new entry from the database table:
galaxy=# select
Thank you.
On Wed, May 1, 2013 at 8:04 PM, Brad Chapman chapm...@50mail.com wrote:
Mic;
(moving to galaxy-dev list so folks there can follow, but future
questions are more appropriate for the Biopython list only since
this isn't a Galaxy question)
I have the following GFF file from a
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