Hello John,
Thank you for your answer.
We shall thus wait.
Julie
2014-07-29 22:43 GMT+02:00 David Kelly davidke...@uchicago.edu:
Hi John,
Is there any documentation that explains how dataset collections work? I'd
like to learn more about it.
Thanks,
David
On Tue, Jul 29, 2014 at 3:20
Hello,
In our old version of Galaxy (July,2012), we have this file
GalaxyDIR/templates/webapps/galaxy/base_panels.mako that has changed a
lot of to actual version (latest_2014.06.02).
Do you have some documentation about this? Because when we used an
iframe, all upper menu disappear,
Any
Hi all,
I'm not sure when this started (having hardly looked at my Tool Shed
test results since GCC2014), but I think this is a fairly recent problem
with my BLAST RBH tests failing (which has held me back from posting
this to the main Tool Shed).
This could be some silly mistake in my tar-ball,
Hi John,
Following the work at the BOSC 2014 CodeFest to support
embedded citations within Galaxy Tool XML files [1], and your
work adding this to the BLAST tools as an example [2], I tried
uploading a minor tool using this to the Tool Shed.
The upload seems to have worked, but there was a scary
Hi everyone,
Is there any standard or commonly used way to package tools that have
language specific dependencies.
I know that with Python libraries one can use setup_virtualenv and with
Java jars the JAVA_JAR_LIB strategy is used.
Is there anything equivalent for R, Perl and Ruby libraries?
Dear Nate, dear Peter
Again, sorry for the delay in replying.
Yes I can. It looks like this
[galaxy@srv ~]$ cat /galaxy/database/files/081/dataset_81002.dat
[galaxy@srv ~]$ ls /galaxy/database/files/081/dataset_81002_files/
blastdb.nhd blastdb.nhi blastdb.nhr blastdb.nin blastdb.nog
Hi,
is there any current functionality or plans to enforce secure
passwords when registering a new account? By secure I mean tests on
length, use of capitals and alphanumeric characters etc.
Thanks
Shaun Webb
--
The University of Edinburgh is a charitable body, registered in
Scotland,
Hi Renato,
Am 30.07.2014 um 12:21 schrieb Renato Alves:
Hi everyone,
Is there any standard or commonly used way to package tools that have
language specific dependencies.
I know that with Python libraries one can use setup_virtualenv and with
Java jars the JAVA_JAR_LIB strategy is used.
Is
On Wed, Jul 30, 2014 at 11:52 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear Nate, dear Peter
Again, sorry for the delay in replying.
Yes I can. It looks like this
[galaxy@srv ~]$ cat /galaxy/database/files/081/dataset_81002.dat
[galaxy@srv ~]$ ls
Hey Peter,
Opps sorry about that and thanks for the bug report. The tool shed
code should be fixed with
https://bitbucket.org/galaxy/galaxy-central/commits/38ba45d6ba5be65b3b743fc08739e16cd6e0ac8f
- it is in next-stable so I think the tool shed should pick up that
fix at next tool shed update.
Thanks John - is there any point/benefit to re-uploading
my tool once the fix is live on the Tool Shed?
i.e. Was it a harmless warning?
Peter
On Wed, Jul 30, 2014 at 12:12 PM, John Chilton jmchil...@gmail.com wrote:
Hey Peter,
Opps sorry about that and thanks for the bug report. The tool
... that might be a Greg question. The tool shed isn't going to use
the citation information in anyway at this time
(https://trello.com/c/R8vKH4PQ) - so you won't gain anything from a
citation-y perspective by re-uploading. That bug might have interfered
with the tool shed metadata generation
Both Galaxy Tool Sheds have been updated with this fix.
Greg
On Jul 30, 2014, at 7:14 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Thanks John - is there any point/benefit to re-uploading
my tool once the fix is live on the Tool Shed?
i.e. Was it a harmless warning?
Peter
On
Yes, it looks like metadata just needs to be regenerated on the affected
repositories. Let me know if doing so uncovers something else.
Greg
On Jul 30, 2014, at 7:20 AM, John Chilton jmchil...@gmail.com wrote:
... that might be a Greg question. The tool shed isn't going to use
the citation
Hi Björn,
Thanks, this is exactly what I was looking for.
Cheers,
Renato
Quoting Björn Grüning on 30-07-2014 12:04:
Hi Renato,
Am 30.07.2014 um 12:21 schrieb Renato Alves:
Hi everyone,
Is there any standard or commonly used way to package tools that have
language specific dependencies.
Hey David,
Nothing on the wiki yet - the documentation I have been pointing
people at is my GCC 2014 presentation on this work
http://bit.ly/gcc2014workflows. It has details on tool developer side
of this as well as some end-user screenshots. There was some initial
support for dataset
I don't believe this is possible and I am aware of not active plans to
work on this. But if you are willing to hack on Galaxy I think you
could enforce arbitrary constraints pretty easily (if you know Python)
by modifying the validate_password function in
Thanks for tracking down the problem - it sounds like it is a Galaxy
bug then so I have created a Trello card
(https://trello.com/c/bNEKfOWR).
-John
On Wed, Jul 30, 2014 at 7:06 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Wed, Jul 30, 2014 at 11:52 AM, Ulf Schaefer
Peter,
I believe part of the problem is that the install and test framework is unable
to resolve the dependency on blast+ 2.2.29 because it is defined as a
repository dependency, not a tool dependency. I would recommend replacing the
repository dependency in the blast_rbh repository with a
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