It looks like if I set 'retry_metadata_internally = False' it stops trying
to index them on the queue node. The datasets get added into the library,
without a BAM index file, but without error.
I guess the index files can be generated on demand later on.
Kyle
On Mon, Jan 28, 2013 at 12:42 PM, Gr
On Mon, Jan 28, 2013 at 5:29 PM, Greg Von Kuster wrote:
> And that did the trick. Is this the expected way of handling these cases?.
>
>
> Yes, however, if your install the repository from the Galaxy administrator
> interface, this should all happen automatically for you. If you download
> the re
Hello Carlos,
On Jan 28, 2013, at 5:13 PM, Carlos Borroto wrote:
> Hi,
>
> I'm trying to get lastz to show a locally cached reference. As I'm
> used to do I went ahead and copy tool-data/lastz_seqs.loc.sample(still
> included with galaxy-dist) to tool-data/lastz_seqs.loc and added my
> local ref
Hi,
I'm trying to get lastz to show a locally cached reference. As I'm
used to do I went ahead and copy tool-data/lastz_seqs.loc.sample(still
included with galaxy-dist) to tool-data/lastz_seqs.loc and added my
local references. Nothing happened. I get:
galaxy.tools.parameters.dynamic_options WARNI
On Mon, Jan 28, 2013 at 1:59 PM, Carl Eberhard wrote:
> If you go to your galaxy root in a terminal and then cd to eggs, what is the
> version listed for SQLAlchemy?
>
SQLAlchemy-0.5.6_dev_r6498-py2.7.egg
> Do you have SQLAlchemy installed already on that machine (apart from the one
> in Galaxy
If you go to your galaxy root in a terminal and then cd to eggs, what is
the version listed for SQLAlchemy?
Do you have SQLAlchemy installed already on that machine (apart from the
one in Galaxy's eggs)?
On Mon, Jan 28, 2013 at 4:50 PM, Dan Tenenbaum wrote:
> On Mon, Jan 28, 2013 at 1:40 PM,
On Mon, Jan 28, 2013 at 1:40 PM, Carl Eberhard wrote:
> I was incorrect in stating that the changes in the next galaxy-dist will
> help in this case, unfortunately. From the stack trace you posted, there is
> a deeper error with your instance that the client-side changes won't help.
>
> Can you po
I was incorrect in stating that the changes in the next galaxy-dist will
help in this case, unfortunately. From the stack trace you posted, there is
a deeper error with your instance that the client-side changes won't help.
Can you post the size, type, and name of the file you're trying to upload?
> You're right -- the EMBOSS version supported by the Galaxy wrappers is
> currently EMBOSS 5. We do have a Tool Dependency page here:
> http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies, but
> unfortunately while it lists versions for many tools it doesn't cover them
> all. I'll upda
Hey Simon,
You're right -- the EMBOSS version supported by the Galaxy wrappers is
currently EMBOSS 5. We do have a Tool Dependency page here:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies, but
unfortunately while it lists versions for many tools it doesn't cover them all.
I'l
Hi Kyle,
I'm hoping I can help you a bit on this, although i am not very familiar with
the code that is producing this behavior. Your previous reply mentions the
following:
During job cleanup,
galaxy.jobs.__init__.py:412, because
external_metadata_set_successfully returns false.
An external se
> There is a mismatch between the options Galaxy is passing to infoseq (-
> version), and what infoseq wants (-seqversion). This breaks the tool.
Clarification: I see the -version/-seqversion change to infoseq was made in
EMBOSS 6.2.0. I'm still wondering which version I should be using with G
Dear Galaxians,
I am troubleshooting a problem with running EMBOSS infoseq on our local galaxy
installation. We are running EMBOSS 6.5.
There is a mismatch between the options Galaxy is passing to infoseq
(-version), and what infoseq wants (-seqversion). This breaks the tool.
While this woul
Nate:
I used the config from the wiki directly…
…
RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e
...
but I also had a section like this below it...
#
I've opened a Trello card, but it's in the Galaxy development project, so not
sure if you can see it or not. Here's the link to the card just in case...
https://trello.com/card/nice-citable-urls-for-galaxy-tool-shed-repositories/506338ce32ae458f6d15e4b3/182
On Jan 28, 2013, at 2:28 PM, Peter C
Hi Brad and Sajoscha,
Is there any chance that your proxy configurations are not passing the username
in the REMOTE_USER header when the request is to an /api path? Could you
provide the relevant portions of your proxy server configs?
Thanks,
--nate
On Jan 28, 2013, at 7:12 AM, Langhorst, Bra
On Mon, Jan 28, 2013 at 6:49 PM, Greg Von Kuster wrote:
> Hi Peter,
>
> Thanks for your request, having citable tool shed URLs is definitely
> important. I've got this on my list (which is maxed out as usual).
> I will look into this in a timely manner and keep you posted appropriately.
>
> Greg
Hi Peter,
Thanks for your request, having citable tool shed URLs is definitely important.
I've got this on my list (which is maxed out as usual). I will look into this
in a timely manner and keep you posted appropriately.
Greg Von Kuster
On Jan 28, 2013, at 8:41 AM, Peter Cock wrote:
> Dea
Dear Galaxy DevTeam,
I have made a few updates to the bowtie_wrappers tool from the Tool
Shed, may someone please pull from:
https://bitbucket.org/nsoranzo/bowtie_wrappers/
for the following changes:
- Add fields for --nofw and --norc options also for single-end reads
- Remove field for --cutoff
Hi All
On my local install of galaxy I'm having problems executing workflows. I will
upload data into a new history and then select to run a saved workflow. This
initiates fine but, after the completion of a variable number of steps, the
workflow just stops after the successful completion of
The client side of the workflow editor is in javascript, using a mix
of HTML5 Canvas and DOM elements. It communicates with the server
using JSON. The server side is written in Python. The editor could be
decoupled and reused, however there are some details that are fairly
Galaxy specific right now
On Sun, Jan 27, 2013 at 10:04 AM, Jeremy Goecks wrote:
>
> Actually, there an easier way to fix this without patching your Galaxy
> installation. Builds will show up in the library dbkey box if there's a
> chromosome length file associated with the build. Chromosome length files are
> used in s
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 wrote:
> On Sun, Jan 27, 2013 at 10:26 PM, Kolby Chien wrote:
>> Hello,
>>
>> I've been working with a local
Sorry. I got it O the drop down menu.
Thanks again.
J
On 2013-01-28 9:30 AM, "Dannon Baker" wrote:
>What probably happened here is that due to the filesize, the browser
>upload failed but this went undetected.
>
>The good news is that you *can* tell galaxy to copy directly, or you
>could even
Thanks.
I now have the option to upload via directory path. How do I create the
ability to use files in their current location without a copy into Galaxy
database ?
Thanks,
J
On 2013-01-28 9:30 AM, "Dannon Baker" wrote:
>What probably happened here is that due to the filesize, the browser
Dear all,
Something I am conscious of every time I have directed someone
to a tool or wrapper on the Galaxy Tool Shed is the lack of nice
stable URLs. The current frame based design hinders this - and
as a result I usually just have to give the ToolShed URL and tell
them what to search for. This p
What probably happened here is that due to the filesize, the browser upload
failed but this went undetected.
The good news is that you *can* tell galaxy to copy directly, or you could even
use the files exactly where they are without any copy.
What you want to do is enable this section in you
Hi,
I am trying to upload 2x 2.5GB files to my data libraries (in Admin on a
local instance) but it has so far been running over night and not completed.
How can I speed this up?
Can I upload compressed files?
Can I not just copy these files directly in to
$galaxy-dist/database/files/000 ?
Thank
Hi Sajoscha:
I have exactly the same problem… it started about a month ago.
Also with external ldap auth.
I have not yet investigated in detail, since it's not crippling - just annoying.
Brad
On Jan 28, 2013, at 6:38 AM, Sajoscha Sauer
wrote:
> Hi list,
>
> I have a weird problem after u
Hi list,
I have a weird problem after updating to the latest version.
After doing the update as usual, the history panel is not updating
automatically anymore. And when I press refresh, I get an javascript popup
saying:
Error getting history updates from the server.
Forbidden
Also, in the
Hi,
I want to know about workflow editor and how it works internally? what
type of canvas editor are you using ? doest it support only python
environment ?
if you have any documents related with ,can i get it .
Regards
shashi
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