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
wr
probably to move workflow creation into a background
process. Starting the workflow would just save the initial state, and a
background process would actually create all the datasets and jobs and get it
running. The downside is that the history would not be completely populated by
the time th
John, the prefixes like "22|" are added to the inputs associated with each
step, so that they can be separated back out. In this case, the chunk of HTML
you have pasted likely corresponds to the 22nd step of the workflow.
53 on the other hand should be a dataset id from the current history (une
Hey John, are you sure you don't want to use a "converted dataset" rather than
a metadata element for this. This is how we handle most types of secondary
indexes for visualization.
If you do it this way, the converter that creates the offset index is just
another tool (but registered in dataty
Not currently, but since a converted dataset is just a dataset, you could reuse
all of the existing upload mechanism, and just add the converted dataset
connection between the two after the fact.
On Aug 26, 2011, at 11:54 AM, Duddy, John wrote:
> Is there a way to upload that converted datas
On Aug 26, 2011, at 7:23 PM, Duddy, John wrote:
> I'm looking into these, and it seems that the spirit is to store a version of
> the data that is converted, like a FASTQ -> BAM or some such use case, where
> one file can be extracted from the other.
It was originally built for that (hence the
Coding standards have been discussed before, but perhaps never written down.
So, here is my interpretation:
We follow PEP-8, with particular emphasis on the parts about knowing when to be
inconsistent, and readability being the ultimate goal. In addition, we make the
following specific exceptio
't know they are being
invoked by a web application). What are you trying to achieve with this?
Is this for a tool generating an HTML report?
--
James Taylor, Assistant Professor, Biology / Computer Science, Emory University
___
Please ke
like it should be decoupled from the actual tool
config since the translators are usually not the tool authors. Best case
would probably be to have many translation files which a given Galaxy
instance compiles together.
--
James Taylor, Assistant Professor, Biology / Computer Science, Emory Un
as why?
There is currently no support for upload tool parameters in workflows.
What behavior are you looking for in this case? The upload tool is very
special, and the parameters are quite interdependent. Are you trying to
create a new dataset from the uploaded file or something else?
--
James
ated so that all data used by tools is
captured within immutable datasets to ensure reproducibility.
You could implement this, but unless you still create a dataset for the
uploaded file, I think it would break other things (like re-running
tools).
--
James Taylor, Assistant Professor, Biology /
ou provide the specific error you get from url_for? There is no
single variable that stores the app url, it is constructed from the
routing system which url_for is connected to. If you look in
form_builder.py for example you can see the use of url_for from non
template code.
--
James Taylor, Assis
lize
route's mapper in the job runner, but I think this would be a big
mistake. Instead you probably want to capture the URL somehow when the
job is created. I need to think about it some more.
--
James Taylor, Assistant Professor, Biology / Computer Science, Emory University
_
at occurs within that
scope. For tools/__init__.py there are some methods that have access and
some that don't, it depends on how they are called (all the user
interface generation related code has access to trans for example).
--
James Taylor, Assistant Professor, Biology / Computer
t references that type. Is there other
information that should go in the requirement tag?
--
James Taylor, Assistant Professor, Biology / Computer Science, Emory University
___
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in yo
ng command
lines / config files.
This could be implemented however. You would need to update the context
used by Tool.update_state to be able to lookup these special variables,
and perform substitution on values -- probably only the first time you
get_initial_value for a ToolParameter.
--
James T
154478)*
> Can anyone help me in this?
I believe this question is for the Rätsch labs Galaxy instance and
should be directed to gal...@tuebingen.mpg.de, which I have copied here.
--
James Taylor, Assistant Professor, Biology / Computer Science,
9 02 26439140
> Mail: cittaro.dav...@hsr.it<mailto:cittaro.dav...@hsr.it>
> Skype: daweonline
> */
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James Taylor, Assistant Professor, Biology / Computer Science, Emory University
___
Please keep all replies on the list by
ou keep your existing database you will need to move
files to the new location.
The safest thing is to start with a clean Galaxy on the external drive.
--
James Taylor, Assistant Professor, Biology / Computer Science, Emory University
___
Plea
Dean, nginx integration works by proxying to the Paste server, but offloading
some data intensive parts. So you still need that configuration as it is.
Thanks!
-- jt
(composed on my phone)
On Nov 2, 2011, at 12:35 PM, Dean Snyder wrote:
> I switched from using the default Python Paste web s
James, do you have an entry for the "fasta_to_len" convertor in your
datatypes_conf.xml? If not, you might want to update your config to include
those entries from the sample. Thanks!
-- jt
(composed on my phone)
On Nov 2, 2011, at 11:58 AM, James Vincent wrote:
> Hello Devs,
>
> I can con
On Nov 15, 2011, at 9:59 PM, Clare Sloggett wrote:
> If this is the case, what is the best way to install and maintain two
> versions of the same tool? I can write code into the wrapper to find
> the correct version of the tool in a given case, but I was wondering
> if there is a more standard 'ga
On Nov 15, 2011, at 7:40 PM, Duddy, John wrote:
> Currently, the schema is created the first time Galaxy is run. I did not see
> a way to cause that to happen via the manage_db.sh script. Have I missed
> something? If not, any pointers on how I might go about adding that (i.e.
> what stuff to c
r
>> variable isn't in there at all at the moment, at least in the
>> galaxy-dist I have. It would also be useful to have a brief mention or
>> link to it on http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup to
>> save time for people like me who had tools installed in a no
the interface at:
>
> http://lists.bx.psu.edu/
-- jt
James Taylor, Assistant Professor, Biology / Computer Science, Emory University
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in your mail clie
To:
From: James Taylor
Subject: Re: [galaxy-dev] List of browsers which supports galaxy
Quoting Nate Coraor (2012-07-13 17:22:22)
> We don't maintain an official list except with Internet Explorer, for which
> support was dropped recently, as Peter noted above.
We do attempt to
Quoting Rodrigo Faccioli (2012-07-26 00:08:23)
>I'd like to create a web-interface to run a C program. It is necessary a
>config file which is used as input to this program. Therefore, the values
You probably want to look at the element for the tool
configs:
http://wiki.g2.bx.psu.edu
Quoting romain desprat (2012-07-26 13:49:02)
>galaxy ( on the linux partition). Unfortunately, galaxy doesn t have
>enough memory to work with this file.
Exactly what error is Galaxy reporting?
___
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Quoting Peter Cock (2012-07-25 20:40:42)
> On Wed, Jul 25, 2012 at 9:35 PM, David Hoover wrote:
> > dataset from a history, all the delete icons disappear from the
> > datasets. They come back if I refresh the page. Has anyone else
My fault, should be fixed in 6d23049609a9.
___
Galaxy developers,
There is an upcoming workshop on accessible HPC that might be of interest to
many of you. It would be great to see the Galaxy community perspective included
in these discussions. Details follow.
Thanks,
James
--
http://www.psc.edu/index.php/escience-2012-workshop
Extending
Quoting Kenneth Auerbach (2012-08-07 01:19:56)
> Modification to universe_wsgi.ini file:
>
> #database_connection =
> sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
>
> database_connection =
> mysql:///galaxy?unix_socket=/var/run/mysqld/mys
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 wrote:
> Hi Galaxy dev team,
>
> I'm trying to the you galaxy server to do NGS peak calling: Tools
use_threadpool and threadpool_workers specify the number of threads
for handling web requests and have nothing to do with job running.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, Jul 24, 2013 at 11:02 AM, Ido Tamir wrote:
> Hi,
>
> what is the rel
I would actually prefer we use $GALAXY_SLOTS.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jul 30, 2013 at 11:18 AM, Peter Cock wrote:
> Hello all,
>
> Re:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010153.html
> http://lists.bx.ps
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.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Aug 9, 2013 at 10:01 AM, Nate Coraor wrote:
> On Aug 9, 2013, at 2:38 AM, L
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
O
On Mon, Aug 19, 2013 at 1:35 PM, Peter Cock wrote:
>> Additionally, it is not recommended to run functional tests on a production
>> instance, since the test suite alters a number of configuration settings on
>> the fly, with the result being that it is not a reliable test of the exact
>> producti
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 thing
On Mon, Aug 26, 2013 at 11:48 AM, John Chilton wrote:
> I think it is interesting that there was push back on providing
> infrastructure (tool actions) for obtaining CBL from github and
> performing installs based on it because it was not in the tool shed
> and therefore less reproducible, but th
description of what it takes to install
a package, and then have different adapters to take that and install
it for a given OS.
--
James Taylor, Associate Professor, Biology/CS, Emory University
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> 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 dependen
stead of source 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
wrote:
>> > Another vote for the excel
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 wrote:
> I am not using CloudMan, but we do use a sqlite database. It seems to have
> that behavior
This should happen automatically at startup though, indicating a bug,
--
James Taylor, Associate Professor, Biology/CS, Emory University
On Tue, Sep 24, 2013 at 12:08 PM, Dave Bouvier wrote:
> Peter,
>
> We recently upgraded the Fabric egg, which now depends on paramiko. You
> sh
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 wrote:
> I was not even
> 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.
--
James Taylor, Associate Professor, Biolog
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 wrote:
> Hi every
They are already running a local instance.
I didn't realize that bowtie required a different index for colorspace
alignment. So Lei, you will have to build the index using bowtie-build
-C.
--
James Taylor, Associate Professor, Biology/CS, Emory University
On Wed, Oct 16, 2013 at 3:
ow 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
--
James Taylor, Associate Profes
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
th
> So far $GALAXY_SLOTS seems to be working nicely for me.
>
> However, I am wondering if it would be possible to use it inside
> the section? Is that run at the time of job creation
> on the Galaxy server (where determining the number of threads
> may be hard) or as part of job execution (e.g. on
I have not tested the patch, just read it, but won't this result in
dataset names like:
"Some operation on data 27 (Some operation on data 26 (Some other
operation on data 25 (...(...(..."
(avoiding this is why we came up with HIDs in the first place).
--
James Taylor, Asso
rner? Is there realistically a system that Galaxy
> should support that will not have /bin/bash available?
--
James Taylor, Associate Professor, Biology/CS, Emory University
___
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in y
VisiGene only sends gif and jpeg over the wire.
--
James Taylor, Associate Professor, Biology/CS, Emory University
On Tue, Dec 3, 2013 at 12:59 PM, Robert Baertsch wrote:
> I was planning to use server code to tile the large images and then use one
> of a number of JavaScript librar
Would something as simple as showing the input parameter name in a tooltip
inside the workflow editor accomplish what you need?
--
James Taylor
On Fri, Dec 27, 2013 at 4:24 PM, Thon deBoer wrote:
> Hi,
>
> In order to make Galaxy workflows even more useful, it is going to be
&g
> 'PBKDF2$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 i
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 wrote:
> Hello Galaxy People!
>
> (it's been a while since I've last been here... a pleasure to be back).
>
> I intend t
Eric, I'm very much in favor of this feature, and particularly the
idea of generating a list of citations from a history or workflow. I
imagine the only thing to quibble about will be the syntax. There are
already some efforts to represent bibtex in xml (e.g.
https://github.com/Zearin/BibTeXML), ho
David, because of the restrictive licensing terms of GATK2 the main
Galaxy Team will not continue to develop any GATK tools except for
those which remain under the open source license (basically, GATK
1.6).
We will be very happy to have wrappers for these and other
non-open-source tools contribute
On Sunday, September 16, 2012, Fields, Christopher J wrote:
> This seems to correspond with what I have tried; I attempter setting
> log_destination in the config file (as James suggested) and the server
> wouldn't start
What was the error? This should work.
> , but changing run.sh to point t
Interesting. If I'm reading this correctly the problem is happening
inside pkg_resources? (galaxy.eggs unzips eggs, but I think it does so
on install [fetch_eggs] time not run time which would avoid this). If
so this would seem to be a locking bug in pkg_resources. Dannon, we
could put a guard arou
Dan, I may not be following, but why not make the serialized R object
a dataset (of its own datatype). Then the user can just pass it to the
downstream tools just by specifying one parameter.
-- jt
On Tue, Sep 18, 2012 at 3:00 PM, Dan Tenenbaum wrote:
> I want the user to upload a text file, th
No, but this is a good idea that can be implemented as a new type of
workflow module (fixed data set, like input dataset but specified at
workflow build time). Can you file an issue in bitbucket describing how you
would like this feature to work? Thanks!
On Wednesday, September 19, 2012, Marc Logg
If the two different Galaxy instances are different *versions* of
Galaxy, this is unlikely to work out well.
-- jt
On Fri, Sep 21, 2012 at 11:59 AM, Chebbi Mohamed Amine
wrote:
> Hello Galaxy-team!
>
> I installed recently two differents versions of Galaxy and I would like to
> use the same dat
Definitely not. And please keep replies on the list.
-- jt
On Fri, Sep 21, 2012 at 1:50 PM, Chebbi Mohamed Amine
wrote:
> Yes the two instances are of two different versions. So if I understand well
> there is no mean to do it like this ?
> Thanks
>
>
> 2012/9/21 James Taylor
Galaxy should probably be shutdown with --stop-daemon (depending on
how you are running it).
In the future we can look at making the logging handle the HUP signal.
-- jt
On Tue, Sep 25, 2012 at 11:40 AM, Scott McManus wrote:
>
> Lukasz-
>
> How are you stopping the process? It's possible that
It is definitely intended to be general (I believe there is a column
data provider intended for scatterplot visualizations that should land
soon). We definitely want this to be general enough to use for any
visualization, so please consider this API and help us to make it as
general as appropriate.
The Galaxy Web API is documented here: http://wiki.g2.bx.psu.edu/Learn/API
-- jt
On Tue, Oct 9, 2012 at 6:30 AM, harry humphries wrote:
> We are trying to develop a plugin for drupal CMS that interacts with the
> galaxy api, basically we want to create a control panel for the S3 server
> from
Mark, how are you running your Galaxy instance, and have you changed
the value of log_level in your universe_wsgi.ini? By default Galaxy
should be provide quite verbose logging on stdout.
-- jt
On Wed, Oct 10, 2012 at 2:21 PM, Mark Johnson wrote:
> I'm trying to add CSRA (NCBI Compressed Sequen
You can get to the captured stdout/stderr in the UI by clicking the
info (i) button for the dataset. The way I would normally debug
outside of the Galaxy UI is to take the command line generated by
Galaxy (which should be logged) and run it outside Galaxy.
-- jt
On Fri, Oct 12, 2012 at 9:35 AM,
Be aware that this may not work in future versions of Galaxy, and
probably won't work in some places already (e.g. trackster).
If this is a common need, one option would be to create a new type of
grouping construct that would simply be a labeled group. In the config
this would be:
...
...
Todd, this is definitely unusual. Can you post (or send directly)
relevant sections from the Galaxy log?
-- jt
On Tue, Oct 16, 2012 at 8:15 PM, Todd Oakley
wrote:
> Hello,
> We just did a few tweaks to improve Galaxy performance, and a new issue
> popped up that I would like advice on troub
On Tue, Oct 23, 2012 at 12:55 PM, Anthonius deBoer wrote:
> I had sent James Taylor the schema as he requested, but I never heard
> anything so I guess he must not have found anything weird
Yes, it appears to have all the right indexes
The Galaxy application does store quite a bit in memory (not as
globals though). This doesn't preclude running under mod_wsgi, but it
will work best in a configuration that uses a small number of long
running processes with multiple threads.
Basically, we run nginx proxying paste on the main Galax
FYI, trackster supports BigWig directly (no conversion or additional
indexing) and quite efficiently, so you will likely have the most luck
with that.
-- jt
On Wed, Oct 24, 2012 at 3:09 PM, Jeremy Goecks wrote:
> bigwig file.
___
Please ke
On Fri, Oct 26, 2012 at 3:47 PM, Peter Cock wrote:
> i.e. This isn't something each tool author should be doing,
> but something general that should be in Galaxy itself.
Yes, we would very much like a visual/graphical indicator of dataset
ancestry, and possibly an alternative history view that wa
Ann,
I think you may be able to do this by generating another nexus file
using "configfiles" in the Galaxy tool config which just contains a
command block, similar to the example here:
http://mrbayes.sourceforge.net/wiki/index.php/FAQ#How_do_I_run_MrBayes_in_batch_mode.3F
-- jt
On Mon, Oct
This is a bug that is fixed in revision ecd131b. Sorry for the inconvenience.
-- jt
On Sat, Oct 27, 2012 at 6:12 PM, Luciano Cosme wrote:
> Howdy,
>I installed galaxy in a new server that I build and I am getting the
> following error when I try to upload the files from a local directory.
>
On Mon, Oct 29, 2012 at 9:23 PM, Todd Oakley
wrote:
> We've developed a large number of tools to allow my lab to conduct
> phylogenetic analyses in Galaxy. Inspired by the mothur package in Galaxy,
> which is all in one repo, I made the decision to add all our related tools
> to 1 repo on the tool
Arlin, this sounds great. There have been a few discussions on the
list over the last two weeks about Phylogenetic tools, it would be
great if the groups responsible could send representatives to the
hackathon to coordinate. My group would definitely like to send at
least one Galaxy core team membe
If you want to keep your tools separated by name and version
(recommended) see the section "Managed Tool Dependencies" at
http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Mon, Nov 5, 2012 at 12:44 PM,
You can determine what revision you have by running "hg tip" in the
galaxy checkout. Are you checking out from galaxy-dist or
galaxy-central?
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, Nov 8, 2012 at 10:41 AM, John Clayton
wrote:
> How can I determ
On Mon, Nov 12, 2012 at 9:43 AM, John Chilton wrote:
> >From IRC (weeks ago):
> (03:15:01 PM) jmchilton: Ideally, what would the API uri for assigning
> a tag to a histories dataset be? POST to
> api/tags// HistoryDatasetAssociation)>/ or POST to
> api/histories//contents//tags/ or
I personally p
On Sun, Nov 18, 2012 at 1:13 PM, Christophe Antoniewski
wrote:
> but the second script output is empty. I suspect that the second script is
> launched when the output of the first script is not available yet.
I'm pretty sure we do not currently support multiple "command" tags.
However whatever is
NCODE/integrativeAnalysis/VM/
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Sun, Nov 18, 2012 at 10:29 AM, Scooter Willis wrote:
> I found out about Galaxy based on the ENCODE project making a big deal about
> packaging the software they used on a CD and available f
On Fri, Nov 16, 2012 at 2:35 PM, Joshua Orvis wrote:
> If I removed that line how is it still part of the call? Is Galaxy caching
> the xml tool files?
Did you restart Galaxy? Tool configuration files are read at startup.
You can also force a tool to be reloaded in the admin interface.
> Also, i
there is a
way for xgrid to support the DRMAA API, in which case you can use the
DRMAA runner.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, Nov 22, 2012 at 9:47 PM, James Boocock wrote:
> Hi Galaxy Dev Team.
>
> We are looking to put xgrid into the galaxy ap
.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Nov 30, 2012 at 6:30 AM, Bossers, Alex wrote:
> Philippe,
>
> As far as I know most of the styling is in
> galaxydir/static/june_2007_style/blue/base.css or the other stylesheets
> present in that location.
&g
On Wed, Apr 4, 2012 at 7:38 AM, Peter Cock wrote:
> It would be quite a popular feature I think - perhaps replacing the
> current "auto hide" feature in workflows with "auto delete" or is that
> too drastic?
I think a workflow level option to set whether non-output datasets are
hidden or deleted
Rpy is only used by a handful of tools (should be listed on the tool
dependencies page). Everything else in Galaxy should work fine without
it.
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s come from
the tool associated with the workflow_step.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Tue, Jan 1, 2013 at 6:21 AM, Sachit Adhikari
wrote:
> Dear all,
>
>
> This is the content of m
This pattern is used to implement versioning. Every time a workflow is
saved a new entry in the "workflow" table is created. The
"stored_workflow" table keeps a pointer ("latest_workflow_id") to the
most recent.
___
Please keep all replies on
I assume you are using the mgtaxa Galaxy instance at JCVI. I've copied
the mgtaxa maintainer on this message.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Dec 28, 2012 at 11:56 AM, Edlund, Anna wrote:
> Hello.
>
>
>
> My name is Anna Edlu
To the "workflow_step" table.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, Jan 2, 2013 at 10:48 AM, Sachit Adhikari
wrote:
> Ok. So they are the foreign key from which table? Or the same table
> workflow_step_connection?
>
>
> On Wed, Jan
Carrie,
Thank you so much for bringing this new webkit CSS attribute to our
attention! This iOS bug has plagued us for years. I think what you
want to do however is add this to the div containing the iframe.
Specifically in templates/root/index.mako there is a
unified-panel-body div that contains
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 wrote:
> Carrie,
>
> Thank you so much for bringing this new webkit CSS attribu
It is working for me on a real ipad (3rd gen). It isn't perfect,
sometimes it scrolls the whole page and other times the frame, but it
does seem to mostly work.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Jan 4, 2013 at 3:55 PM, Ganote, Carrie L wrote:
>
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.
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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James Taylor, Assistant Professor, Biology/CS, Emory University
On Mon, Jan 14, 2013 at 11:03 PM, Anthonius deBoer wrote:
> Hi,
>
> I just updat
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