Hey Eric,
It looks like you have connection info for both tcp/ip connections and unix
sockets in the connection strings. If you're logging in using psql -h
wigserv5.cshl.edu snip, then you only want the tcp/ip connection info.
Drop the ?host=tmp off the third option you listed and I think
Hi,
I manage a galaxy instance on a local server and I want that users use
only the filesystem paths to create a link to their data by the Admin
Menu. Where can I find the source file to modify the web page in order
to appear directly this option in first in the drop-down menu ?
It will
Cross-post from biostar, answered there:
https://biostar.usegalaxy.org/p/7747/#7760
On Mon, May 26, 2014 at 6:47 AM, Julien Daligault
daliga...@ijm.univ-paris-diderot.fr wrote:
Hi,
I manage a galaxy instance on a local server and I want that users use
only the filesystem paths to create a
Thanks - I'll leave this until next week then.
Peter
On Tue, May 27, 2014 at 3:05 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello peter,
I've looked inot this and discovered what I suspect is a problem with
the buildbot configuration for the Tool Shed's install and test framework.
The
Hi Peter,
I've looked into this as well and again believe it is caused by a problem in
the buildbot configuration for the main Tool Shed's Install and Test framework.
I've created the following Trello card for this, and we'll get it resolved
when Dave B returns next week.
Hi peter,
It seems that we have stopped redirecting the old Tool Shed URL
http://community.g2.bx.psu.edu/ to the new Tool Shed URL
http://toolshed.g2.bx.psu.edu/ . I'm not sure when this happened.
Sorry for the inconvenience.
Greg Von Kuster
On May 21, 2014, at 9:37 AM, Peter Cock
On Tue, May 27, 2014 at 3:39 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi peter,
It seems that we have stopped redirecting the old Tool Shed URL
http://community.g2.bx.psu.edu/ to the new Tool Shed URL
http://toolshed.g2.bx.psu.edu/ . I'm not sure when this happened.
Sorry for the
Peter, sorry, this one is out of my hands. I'm hoping Nate can answer this
when he gets a chance.
Greg Von Kuster
On May 27, 2014, at 11:16 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, May 27, 2014 at 3:39 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi peter,
It seems that we
Hey Dannon,
Thanks for pointing that out! I missed it. I am now connecting to the remote
database. I ran sh manage_db.sh upgrade and it upgraded from schema 114 to
118 without error messages. I then ran sh
./scripts/migrate_tools/0010_tools.sh install_dependencies and received the
Hi Everyone
I'm throwing this out there for some feedback and recommendations.
Objective: Facilitate transferring large files ( 2GB) from an HPC cluster (and
its associated fast tier storage) to galaxy for my clients. I enabled the FTP
upload option in galaxy but it involves users learning
Hi all,
In the conditional param, when sub-element allows you to write specific
parameters for a particular value selected. I am wondering how to write the
help context according to the value selection. For example, if there is a
conditional param called blast_type, when blastn is
On Tue, May 27, 2014 at 4:32 PM, Jun Fan j@qmul.ac.uk wrote:
Hi all,
In the conditional param, when sub-element allows you to write
specific parameters for a particular value selected. I am wondering how to
write the help context according to the value selection. For example, if
On Tue, May 27, 2014 at 11:26 AM, Paniagua, Eric epani...@cshl.edu wrote:
Thanks for pointing that out! I missed it. I am now connecting to the
remote database. I ran sh manage_db.sh upgrade and it upgraded from
schema 114 to 118 without error messages. I then ran sh
On Tue, May 27, 2014 at 4:15 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Peter,
This issue should be resolved in 13630:33b1ff4b9985, which is now running on
the test Tool Shed. Thanks for reporting this!
Greg Von Kuster
Thanks - clearer error messages are a good thing :)
Peter
The dataset table is populated. I looked at the SQL dump file I used to copy
the database, and it has create table and copy into statements for
history_dataset_association, but it looks like there may have been an error
while executing them. Trying to figure out how to get my data in...
Since the database has lost consistency, I'd really try a fresh pg_dump /
import if that's possible. If there's an error this time around, note it
and send it on over and we can figure out where to go from there.
On Tue, May 27, 2014 at 11:48 AM, Paniagua, Eric epani...@cshl.edu wrote:
The
I have created a fresh dump with
$ pg_dump -U galaxyprod galaxyprod
This time the import proceeded cleanly.
Further, using PostgreSQL 9.1, I no longer get the error regarding a read only
database cursor and getting the next history item number. I am currently
running a test job to confirm
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I'd want to open up discussion on a feature I'd like to see. I'll try
and implement it if I can find time this summer. I didn't see a trello
card for anything like this yet, but please feel free to direct me there
if I missed it.
I'd like to see
Restarting the Galaxy server in multiple process mode appears to have helped.
The test job is now running.
From: Paniagua, Eric
Sent: Tuesday, May 27, 2014 12:43 PM
To: Dannon Baker
Cc: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Problem using Galaxy
Peter, this may be the Trello card you were thinking of.
https://trello.com/c/kY7RCnd0/95-tool-shed-citation-for-tools-dois
Greg Von Kuster
On May 27, 2014, at 1:09 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Eric,
I was sure there was a Trello card for this, but I can't find it
As hinted at in the Trello card Greg posted, it could be much simpler if
the citation tag just took a DOI. It appears that the DOI to bibtex
conversion can be done by Crossref:
http://tex.stackexchange.com/questions/6848/automatically-dereference-doi-to-bib
-Will
On Tue, May 27, 2014 at 10:16
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Hi Peter,
What do you know, it has! I should've searched for those emails first.
Nevertheless, I'd like to see this implemented, and may take it on since
there's obviously a need for it.
You raise a good point, I am not familiar with semantic
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Will,
Nice! I follow the tex.SE and missed that one. That's incredibly useful.
I believe the final implementation will include both options (doi/citation)
Jim,
Great, agreed. I want to represent non-published/non-DOI materials, so
this is better
On Tue, May 27, 2014 at 6:21 PM, Jim McCusker
jmccus...@5amsolutions.com wrote:
I would suggest using as much as possible from PROV, especially since other
workflow engines (Taverna and Pegasus come to mind) already support it.
Rather than looking for bibtex mappings in XML, we should be
I'm a semantic web folk (I'm on the PROV Data Model), and I'm willing to
advise as needed. PROV is very generalized, but workflow provenance was one
of the primary use cases for its design (it descends from OPM, which was
almost entirely workflow provenance-oriented).
Workflow tools probably
Hi Peter,
I am afraid that the link you gave me could not solve the problem. The
question I asked is about the help element, not the label attribute for data
element.
To clarify my question, here is the code which does not work, but shows
what I intend to do:
conditional name=blast
Hi all,
Is there any way to unsubscribes from mail lists?
Cheers,
Shari
On Wednesday, 28 May 2014 2:52 AM, Jim McCusker jmccus...@5amsolutions.com
wrote:
I would suggest using as much as possible from PROV, especially since other
workflow engines (Taverna and Pegasus come to mind)
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