that I am directing the output to a file only to try to find out why
it's not working.
Is this a problem with environment?
Any suggestions what to try would be much appreciated.
Regards
James
J P Mullan
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Hello,
I downloaded Galaxy a few months ago but I just noticed that
the citations tag doesn't work on my download.
The info on the hg pull I have is:
hg tip
changeset: 13771:7a4d321c0e38
branch: stable
tag: tip
user:Nate Coraor n...@bx.psu.edu
date:Wed
Philipp,
Pages are seriously deprecated -- do not use them. Many things will
not work, they are not supported in workflows, the API, et cetera.
They only still exist for backward compatibility with ANCIENT tools.
Thanks,
James
-- jt
On Tue, Aug 12, 2014 at 4:59 AM, Hans-Philipp Brachvogel
Hey Assaf,
For Cite1 (Galaxy): doi:10.1186/gb-2010-11-8-r86
For Cite2 (ToolShed): doi:10.1186/gb4161
Thanks for asking!
-- jt
On Tue, Mar 25, 2014 at 1:15 PM, Assaf Gordon agor...@wi.mit.edu wrote:
Hello Galaxy People!
(it's been a while since I've last been here... a pleasure to be
'PBKDF2$sha256$1$1xx',got Œyy¹
I am not using either PBKDF2 or sha256 see below why are these prefixes
appended? Xxx and are NOT the same alphanumeric strings
Are you sure? Unless you speficically disable it Galaxy now uses
PBKDF2 + SHA256 by default.
I'm not sure if
Would something as simple as showing the input parameter name in a tooltip
inside the workflow editor accomplish what you need?
--
James Taylor
On Fri, Dec 27, 2013 at 4:24 PM, Thon deBoer tdeb...@enzymatics.com wrote:
Hi,
In order to make Galaxy workflows even more useful, it is going
VisiGene only sends gif and jpeg over the wire.
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James Taylor, Associate Professor, Biology/CS, Emory University
On Tue, Dec 3, 2013 at 12:59 PM, Robert Baertsch baert...@soe.ucsc.edu wrote:
I was planning to use server code to tile the large images and then use one
of a number
I have not tested the patch, just read it, but won't this result in
dataset names like:
Some operation on data 27 (Some operation on data 26 (Some other
operation on data 25 (...(...(...
(avoiding this is why we came up with HIDs in the first place).
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? Is there realistically a system that Galaxy
should support that will not have /bin/bash available?
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So far $GALAXY_SLOTS seems to be working nicely for me.
However, I am wondering if it would be possible to use it inside
the configfile section? Is that run at the time of job creation
on the Galaxy server (where determining the number of threads
may be hard) or as part of job execution
has more
than say 50 steps, and switch to just checking on hover.
(but that's just a guess)
The workflow editor doesn't use any library beyond jquery, all the
relevant code to this problem should be in:
static/scripts/galaxy.workflow_editor.canvas.js
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James Taylor, Associate Professor, Biology/CS
As part of this card:
https://trello.com/c/TnSlPz1j/282-55-improvements-to-file-upload
Sam has been completely redoing the UI for upload. Particularly with
the focus on multiple file upload and progress displays. However, it
will be a dedicated UI for upload not using standard tool forms, so I
The paster script distributed with Galaxy is a stripped down Galaxy
specific version. It only supports the command serve and the arguments
--daemon or --reload.
--
James Taylor, Associate Professor, Biology/CS, Emory University
On Fri, Oct 11, 2013 at 8:36 AM, Renato Alves rjal
So I have used Galaxy to convert 50 different FASTQ files into FASTA with no
problems before over the past year. The sequencer and FASTQ file format have
been identical, however, yesterday when I tired to use the the FASTQ to FASTA
converter I couldn't get it to recognise my files.
The drop
on, onto a future
stable database version.
Yes, this should not be a problem, eventually the revision you are
running will be an ancestor of stable and from there you can just
upgrade to the new stable.
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James Taylor, Associate Professor, Biology/CS, Emory University
Make the precedence a config option. Otherwise I agree.
In addition, I still like the idea I suggested earlier of dependency provider
plugins. Then you could (for example) have one that uses 'modules' and skips
env.sh entirely.
On Sep 26, 2013, at 9:15 PM, John Chilton chil...@msi.umn.edu
This should happen automatically at startup though, indicating a bug,
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James Taylor, Associate Professor, Biology/CS, Emory University
On Tue, Sep 24, 2013 at 12:08 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
We recently upgraded the Fabric egg, which now depends on paramiko. You
Sqlite is absolutely not intended for production use. With multiple users or
complex components you will definitely see database locked. Use Postgres.
On Sep 16, 2013, at 9:48 PM, Nikhil Joshi najo...@ucdavis.edu wrote:
I am not using CloudMan, but we do use a sqlite database. It seems to
env.shs.
And yes, we would definitely accept something like this as long as it
is a plugin that is not enabled by default.
--
James Taylor, Associate Professor, Biology/CS, Emory University
On Thu, Sep 12, 2013 at 7:03 PM, Guest, Simon
simon.gu...@agresearch.co.nz wrote:
Another vote
Another vote for the excellent modules system from us at AgResearch. I think
it's the only sane way to manage PATH, etc, when you have multiple versions
of tools installed.
http://modules.sourceforge.net/
I know I've said this before here. Tell all your friends. ;-)
Galaxy's dependency
dependencies.
The idea of standard recipe templates (e.g. typical Python
install) James outlined here might help:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016273.html
I (as always) think a lot can be solved through abstraction. I'm
envisioning a very high level description of what
All,
I've been seeing some examples of tool_depedencies.xml come across of
the list, and I'm wondering if there are ways that it can be
simplified. When we were first defining these features, we talked
about having high level recipes for certain types of installs. This
could greatly simplify
if the PyPI URL no longer works we still
have it stored.
I think we all value reproduciblity here, but we make different
calculations on what is reproducible. I think in terms of implementing
the ideas James has laid out or similar things I have proposed, it
might be beneficial to have some
It should be as simple as adding use_pbkdf2=False to the
universe_wsgi.ini file.
This commit made it configurable:
https://bitbucket.org/galaxy/galaxy-central/commits/a6f688dade808b0e16903fbb50186ad9656c0d1c
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Mon, Aug 19
For the moment, the best solution is to disable PBKDF2 in Galaxy if
you are also using FTP. That is how Galaxy main is currently
configured.
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James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Aug 9, 2013 at 10:01 AM, Nate Coraor n...@bx.psu.edu wrote:
On Aug 9, 2013
I would actually prefer we use $GALAXY_SLOTS.
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James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jul 30, 2013 at 11:18 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hello all,
Re:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010153.html
http
What format are the files you are trying to process with MACS in?
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jul 23, 2013 at 3:05 PM, Jianxin Wang jianxin.w...@oicr.on.ca wrote:
Hi Galaxy dev team,
I'm trying to the you galaxy server to do NGS peak calling
use_threadpool and threadpool_workers specify the number of threads
for handling web requests and have nothing to do with job running.
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James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, Jul 24, 2013 at 11:02 AM, Ido Tamir ta...@imp.ac.at wrote:
Hi,
what
of the corresponding tool. So far, we did not find any
possiblity.
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Rather than adding additional increments to add/remove, what about
allowing the user to directly set the number of elements in the
repeat?
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On Tue, Jul 16, 2013 at 7:34 AM, Berner, Thomas
thomas.ber...@jki.bund.de wrote:
Hey
Michael,
Galaxy is all about plugins! Tools, datatypes, batch systems,
visualizations, et cetera.
Additional ways to extend Galaxy through plugins are very welcome. We
just need to make sure that whatever solution is chosen is extremely
general.
--
James Taylor, Assistant Professor, Biology/CS
On Mon, Jul 15, 2013 at 7:27 PM, John Chilton chil...@msi.umn.edu wrote:
One of my goals for the GCC was to sell the idea that tool shed
repositories need to be installable without a database present. I
John, as I've mentioned in the past I'm very strongly in favor of
this. There is
On Fri, Jul 12, 2013 at 2:42 PM, Saliya Ekanayake esal...@gmail.com wrote:
Hi,
I see in documentation that Galaxy tools may be configured to run on a
cluster (http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster).
This is something our research group is interested in, but it's not
Can you be more specific about what resources Galaxy is consuming and
how you are measuring them? Galaxy should consume very few resources
when idle (other than perhaps memory).
On Fri, Jul 12, 2013 at 3:20 PM, Auerbach, Kenneth R.
kauerb...@research.bwh.harvard.edu wrote:
Hello,
Can you tell
You can use the minwidth attribute in the tool config for this
purpose, it will hide the history if the main panel is less than a
certain width. See the UCSC Get Data tool as an example.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, Jul 11, 2013 at 12:00 AM, Peng Li
open_compressed in bx-python does this already (for bz2 as well).
On Jul 8, 2013, at 5:58 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Jul 8, 2013 at 10:24 PM, Robert Baertsch
robert.baert...@gmail.com wrote:
Peter and Dan,
I like the idea of replacing all open() with
('X11_INCLUDE_DIR', False):
./configure --prefix=$env.INSTALL_DIR
--x-includes=$env.X11_INCLUDE_DIR --x-libraries=$env.X11_LIB_DIR
#else:
./configure --prefix=$env.INSTALL_DIR
#end if
/action
--
James Taylor, Assistant Professor, Biology/CS, Emory University
liftOver files come from the UCSC genome browser, derived from
pairwise alignments.
A variety of tools can create nib files from fasta, however we prefer
the use of the twoBit format now, which can be created using
faToTwoBit from the UCSC utilities.
--
James Taylor, Assistant Professor, Biology
1) Is there any kind of existing functionality that is close to what I want?
Depending on whether you are using stock Galaxy or nglims, and how you
are getting data into Galaxy, there are various ways to do it. For
Galaxy's stock sample tracking, you can setup workflows to trigger
automatically
.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Jun 21, 2013 at 11:11 AM, graham etherington (TSL)
graham.ethering...@sainsbury-laboratory.ac.uk wrote:
Hi,
I'm trying to see if I can style Galaxy tools, so instead of all the input
fields being a long list one after
Tightly integrated interactive visualizations like Trackster need to be web
based (implemented in Javascript). See our paper that just came out in BMC
genomics. Note there is already a phylogenetic tree visualization tool
(phyloviz) that was built by Tomithy Too. Extensions to that for
the upload tool, then run your tool on the
resulting dataset.
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James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jun 18, 2013 at 11:48 AM, vijayalakshmi v...@buffalo.edu wrote:
Hi all,
I have a tool written in java for which I want to upload a file as a
parameter. I
sample.xml
tool id=sample name=Compute correlation
commandjava -jar sample.jar/command
/tool
Your tool config does not define any output elements, so no dataset is
created. You need to define at least one output, and then use it's
name in the command line.
This message should be associated with a particular step in the
workflow. If you can tell us what tool it is that will help to
diagnose. The message means that a parameter that could not be checked
until the workflow ran had an invalid value.
--
James Taylor, Assistant Professor, Biology/CS
[galaxy@q ~]$ /bin/cuffdiff
/bin/cuffdiff: /usr/lib64/libz.so.1: no version information available
(required by /bin/cuffdiff)
cuffdiff v2.0.2 (3522)
This definitely indicates a problem with your cuffdiff install. Did
you build cuffdiff on that system or install in some other way? (very
odd to
You might find it instructive to look at the existing bedtools wrappers here:
http://toolshed.g2.bx.psu.edu/view/aaronquinlan/bedtools
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, May 22, 2013 at 12:21 PM, vijayalakshmi v...@buffalo.edu wrote:
Hi all,
I
user or does not allow ident authentication for that
user.
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It is a debugging feature that dumps an enormous amount of information
about memory usage. Unless you are debugging a memory leak there is
absolutely no reason you would want to use this.
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James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, May 16, 2013 at 8:51 AM, Nikos
be a
warning and the tool might still work -- but in the second case, Error in
library(cummeRbund), is definitely fatal.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Sun, May 12, 2013 at 12:34 AM, Panzer, Adam panze...@kids.wustl.eduwrote:
Hello All,
I have
How is your Galaxy configured? Are you using any kind of proxy server
in front of it?
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Mon, May 13, 2013 at 2:53 AM, sridhar srinivasan
sridhar2bioi...@gmail.com wrote:
Dear Developers,
After configuring the galaxy.. i
. Specifically, calling
buildapp for the web application which starts all of the other Galaxy
components.
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James Taylor, Assistant Professor, Biology/CS, Emory University
On Sun, May 12, 2013 at 3:11 AM, 王聃Don wangdanburn...@163.com wrote:
Hello, Galaxy developers:
I'm a galaxy user and have
there is any good javascript editor for
reStructuredText which is used in the tool help.
For non-html readable markup these days I'd prefer markdown since
there seems to be so much consensus around it. Or a fairly minimal
subset of HTML.
--
James Taylor, Assistant Professor, Biology/CS, Emory
a comparison on the hashed part.
I have this working in a backward compatible way, and I think it is a
good idea so I will be committing it to central shortly.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, May 2, 2013 at 2:34 PM, Vipin TS vipin...@gmail.com wrote
, but a sanity check
is appreciated.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Sun, May 5, 2013 at 12:12 PM, James Taylor ja...@jamestaylor.org wrote:
Vipin, I think the main problem here is that you cannot treat PBKDF2
as a hash in this way. Every time you hash
The only other relevant place is the User object in model/__init__.py
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, May 2, 2013 at 6:46 PM, Vipin TS vipin...@gmail.com wrote:
I have updated the table schema from the script to adjust the column length
from
into
security.validate_user_input since it is really specific to user
passwords, especially with those changes.
I'd be happy to see this go into main with sha256 or something
similar. Also, we could consider adding a random per-user salt field
if you are really concerned about this.
--
James Taylor, Assistant
I regard this as a bug or limitation of the test framework, but if not,
things are confusingly inconsistent. If you think parameter names
should be unique, it would make the Cheetah commands a bit
shorter as the wouldn't need the conditional-name-dot prefixes.
Definitely a Bug/Limitation of
No it does not have root, and it is very important that we not install
anything at the system level since we need to maintain version
isolation. We should always be able to inject things into the
environment so that Python/Perl/R look in the right place.
--
James Taylor, Assistant Professor
On Tue, Apr 16, 2013 at 5:34 AM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
In the table 'galaxy_user' you will find your mail and password.
Importantly, you will find a hash of the password, Galaxy does not
store user's plaintext passwords.
--
James Taylor, Assistant
The default value for static_enabled is True, and I don't think this
has changed recently, so I'm not sure how your config ever worked.
Uncommenting static_enabled and changing it to False *should* solve
the problem.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Apr
This looks like just a configuration file problem. What is the value
of the various static_ options (like static_dir =) in your
universe_wsgi.ini?
On Mon, Apr 15, 2013 at 7:25 PM, Christophe Antoniewski
christophe.antoniew...@snv.jussieu.fr wrote:
webapp = wrap_in_static( webapp,
I haven't looked at this directly, but it should be using None, in
which case the correct comparison is library_type is None and
library_type is not None.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, Mar 28, 2013 at 6:35 AM, Peter Cock p.j.a.c...@googlemail.com
I think if you save your trackster visualization first then switching
over to circster should work fine.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, Mar 27, 2013 at 10:04 AM, Merella Stefania
merella.stefa...@hsr.it wrote:
Hi Jeremy,
thanks for replying.
When
:
Is it my imagination or has the history panel become much slower in the
latest release?
Maybe I have something misconfigured?
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Greg, I don't think there is currently any support for variable
substitution of this sort in job runner configuration, but it could
definitely be added. Worth filing as an issue.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, Mar 13, 2013 at 8:12 AM, greg margeem
integration.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Mar 12, 2013 at 8:11 AM, Fingerman, Ian (NIH/NLM/NCBI) [E]
ian.finger...@nih.gov wrote:
I have a question regarding data sources currently available on the main
instance of Galaxy (https://main.g2.bx.psu.edu
On Wed, Mar 6, 2013 at 12:22 PM, John Chilton chil...@msi.umn.edu wrote:
This whole concept puts a lot of onus on the tool developer. A
biologist who has taken a two week course on perl could probably write
a Galaxy tool, they probably couldn't write a secure tool for a public
LWR. I think
I understand that instead of having one dataset with multiple files you are
planning to use existing datasets and combine them in a ‘collection’. My
concerns are:
This needs to be fleshed out much more, but this is not exactly what
we are thinking. The main change is to make it possible for a
How about some kind of captcha support?
-- jt
(composed on my phone)
On Mar 1, 2013, at 10:39 AM, Vipin TS vipin...@gmail.com wrote:
Hello members,
I believe currently there is no process to validate email address provided
during user account creation. We are experiencing a huge fake
repoze.who would seem like the best candidate these days, it would be great
to see that integrated, but I worry it would also cause lots of
unintentional breakage in the corner cases.
On Mar 5, 2013 12:27 PM, Paul Boddie paul.bod...@biotek.uio.no wrote:
On 05/03/13 17:09, James Taylor wrote
Broken pipe normally occurs when the browser drops the connection
(e.g. if you quit your browser while downloading a dataset you might
see this). Can you describe in more detail how the frequent hiccups
manifest?
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Mon, Mar 4
indicating
warning vs error.
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James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, Feb 20, 2013 at 11:08 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
Hello all,
I was wondering if anyone else writing Galaxy tools has
wanted to be able to show warning messages conditional
for blast, et cetera.
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On Tue, Feb 19, 2013 at 3:39 AM, Pierre Pericard
pierre.peric...@sb-roscoff.fr wrote:
Is there a Galaxy XML tool wrapper XSD ?
No, but if anyone would like to make such a schema we would be happy
to include it.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
The wrapper you are using is for MACS 1.3, there is a wrapper that is
compatible with 1.4 in the toolshed.
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James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Feb 15, 2013 at 9:26 AM, greg margeem...@gmail.com wrote:
Hi guys,
I'm trying to run MACS in my local galaxy
On Fri, Feb 15, 2013 at 9:30 AM, James Taylor ja...@jamestaylor.org
wrote:
The wrapper you are using is for MACS 1.3, there is a wrapper that is
compatible with 1.4 in the toolshed.
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James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Feb 15, 2013 at 9:26 AM
to toolform.mako.
Could i parse them
to my module using javascript.
Although I feel the best approach would be to add these options to the
job model and then they would remain tracked in the database.
Cheers James.
On 2/14/2013 4:20 AM, Nate Coraor wrote:
On Feb 4, 2013, at 6:03 PM, James Boocock
together on this.
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I don't believe you can, although it should be possible to extend
upload to provide that information. However, is there no header you
can use in your filetype to detect it?
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James Taylor, Assistant Professor, Biology/CS, Emory University
On Mon, Feb 11, 2013 at 10:51 PM, David Angot dav
a Galaxy frontend.
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James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, Feb 6, 2013 at 9:51 AM, lukeyoyo lukey...@gmail.com wrote:
Hi,
I am a computer engineer and have to deploy a cloud computing system, like
Hadoop. I want to deploy a local Galaxy system on the Hadoop
preparation in each tool runner if the
job has come from my clustering module
or is there a better way to do this. Will the job runners
wrapper.prepare() overwrite any of my changes to the command-line
when the job makes its way to the runner say local.py.
Cheers James
Command lines inside tool configs are assumed to be 'sh' (posix bourne
shell). If you are extending one of the runners, definitely stick to
pure 'sh'.
However, once your command is run, there is no reason you can't use
any shell of your choice.
--
James Taylor, Assistant Professor, Biology/CS
It seems strange not to be able to share workflows with groups if you can
share them with individual users..
The group/role system for data libraries and the sharing system for
other assets were developed concurrently. It would be reasonable (and
probably not that difficult) to add groups to
I have a patch to replace the searchable select implementation with
select2 which seems to work well, but still needs comprehensive
testing. I think it may address this problem. If anyone is interested
in trying it:
https://bitbucket.org/james_taylor/james-galaxy-central-patches/src
people
ar actively working on that code it might be best to wait, merging
lots of code on top of renames can get messy.
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You may want to be careful with this solution because it allows script
injection, any HTML including javascript in the uploaded tabular file
will be executed by the .html call, with complete access to everything
in the Galaxy browser window (like your session cookies).
--
James Taylor, Assistant
Not currently, however we are planning to implement this in the future.
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James Taylor, Assistant Professor, Biology/CS, Emory University
On Sun, Jan 27, 2013 at 10:20 AM, Hagai Cohen hag...@cs.huji.ac.il wrote:
Hi,
is it possible that when I rerun a tool it will also rerun the tools
Can you send some additional lines of the error? The important part is
to see what part of the stack is repeating. Based on what you have it
suggests recursion in trying to do a datatype conversion. Have you
modified datatypes_conf.xml and is it possible there is a problem
there? Thanks!
--
James
Can you send the output of hg heads after having run the pull -u ?
Thanks!
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jan 29, 2013 at 9:57 AM, Waldron, Michael H
mwald...@email.unc.edu wrote:
To be honest, I barely understand this enough to just follow the wiki
Wasn't sure of the order, those are definitely after running the
update. Dannon's advice makes a good point, upgrading to the latest
mercurial should help.
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James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jan 29, 2013 at 11:10 AM, Waldron, Michael H
mwald
You can work around this using the from_work_dir attribute when specifying the
output file in your tool config.
-- jt
(composed on my phone)
On Jan 27, 2013, at 6:13 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Sun, Jan 27, 2013 at 10:26 PM, Kolby Chien kc...@nau.edu wrote:
Hello,
now (particularly how tool states -- the values
of the various input parameters -- are encoded).
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James Taylor, Assistant Professor, Biology/CS, Emory University
On Mon, Jan 28, 2013 at 5:17 AM, ssha...@cdac.in wrote:
Hi,
I want to know about workflow editor and how it works internally
is using 8 bit character codes in the stdout and
galaxy is failing on adding to the database. Has anyone experienced
this problem and could help me.
Cheers James
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is using 8 bit character codes in the stdout and
galaxy is failing on adding to the database. Has anyone experienced
this problem and could help me.
Cheers James
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This is great. For the Galaxy tools, will you be able to submit
wrappers to the toolshed? This should make it easier for users to
install into their local Galaxy instances. Thanks!
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James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, Jan 16, 2013 at 8:38 AM, Quang Trinh
are looking for.
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James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jan 15, 2013 at 8:52 PM, neil.burd...@csiro.au wrote:
Hi
Sorry if these questions are obvious but I just don’t know how to find
the answers.
I’m trying to get one of the API examples to work
Even for a small change a pull request is preferred since they allow the
origin of the change to be tracked.
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and other
Do you see the same problem if you access main.g2.bx.psu.edu? What browser
are you using? You may need to clear your browser cache.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Mon, Jan 14, 2013 at 11:03 PM, Anthonius deBoer thondeb...@me.comwrote:
Hi,
I just
Ted, have you considered if you can do what you need with the 'allowed'
method of GridOperation? It let's you define a callable condition that
determines if that operation is allowed on a given item. It does not have
access to trans but it would be reasonable to add that.
--
James Taylor
The fix is in this changeset, applied conditionally on iOS devices:
https://bitbucket.org/galaxy/galaxy-central/commits/312ba8a948a1c678bea807f4a0d3320a
On Fri, Jan 4, 2013 at 2:08 PM, James Taylor ja...@jamestaylor.org wrote:
Carrie,
Thank you so much for bringing this new webkit CSS
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