Ok, I found some tape I can put on it. Here:
http://misc.feedfury.com/content/45712644-anton-bobrov-bad-servers-chunked-encoding-and-incompleteread.html
In scripts/api/common.py I put this piece of code at the beginning of
the file, after the imports:
import httplib
def patch_http_response_re
Hi Chaolin,
Although I haven't tested this, the following changes should probably work.
In the datatypes_conf.xml change on this line:
the max_optional_metadata_filesize to the desired size or remove tag like so:
Furthermore in the file lib/galaxy/datatypes/data.py at function
set_peek() s
Hi, I've noticed a bug in sam2interval.py.
There are a few indentation errors in the final lines of code. I think
there should be an indent after:
if not ref_name == '*':
And this whole if statement should be included in the for loop above.
Also, would you be able to add read_
Dannon,
"Extract Genomic DNA" tool demands that intervals had set genome build.
In my case interval dataset is not persistent, I generate this in
"meantime", so after generating this I set genome build to dataset by
hand. It's not a problem if you do this in "history pane mode" but in
workf
Dear all,
I've just uploaded my Galaxy wrapper for command line NoD (clinod) to
the Galaxy tool shed (under the Sequence Analysis category):
http://usegalaxy.org/community
NoD is from the Barton group at the University of Dundee, and does
Nucleolar localization sequence (NoLS) prediction. There i
Hi all,
I've been investigating use of Galaxy for our lab and it has many
attractive aspects -- a big thank you to all involved.
We still have a couple of related sticking points, however, that I would
like to get the Galaxy developers' feedback on. Basically, I want to use
Galaxy to run Map/Redu
Hi all,
I am trying to set up httpd to serve galaxy from the root url and to
serve static content as described on
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy. I will not serve
Galaxy under a subdirectory.
I have added to /etc/httpd/conf.d/ a file galaxy.conf with contents
(CentOS
On Tue, Aug 2, 2011 at 3:12 PM, Andrew Straw wrote:
> ...
>
> My proposal for a general solution, and what I'd be interested in
> feedback on, is an idea of a "dataset container" (this is just a working
> name). It would look and act much like a dataset in the history, but
> would in fact be a log
Dear Alex,
Thanks a lot for your useful information.
--Bo
On Mon, Aug 1, 2011 at 5:18 AM, Bossers, Alex wrote:
> You can also directly link the R script in the galaxy-tool.
> We have many of those. For testing (NOT SAFE!) we also have a tool that
> allows the upload of an R script for testing p
Hi
I really like this proposal. We faced some of the similar issues you talk about
below when we tried to use galaxy to use High Throughput computing techniques
(using Condor) for sequencing close to 500 genomes (embarrassingly parallel
problem). We leveraged (hacked) the dataset construct but i
On Aug 2, 2011, at 10:12 AM, Andrew Straw wrote:
> 1) My first specific problem is that loading many datasets (e.g. 250)
> into history causes the javascript running locally withing a browser to
> be extremely slow.
What browser are you using?
> 2) My second specific problem is that applying a
On 08/02/2011 06:43 PM, James Taylor wrote:
> On Aug 2, 2011, at 10:12 AM, Andrew Straw wrote:
>
>> 1) My first specific problem is that loading many datasets (e.g. 250)
>> into history causes the javascript running locally withing a browser to
>> be extremely slow.
> What browser are you using?
Pr
I did something similar, but implemented as an evolution of the original
"basic" parallelism (see BWA), that:
- Moved the splitting of input files into the datatype classes
- Allowed any number of inputs to be split, as long as they were the same
datatype (so they were mutually consistent - think
Hi Joachim,
I'm not sure what's wrong with your setup, but for what it's worth I
could not get the provided instructions to work properly either, when I
combined the proxy with a step to authenticate against our University's
single-sign service (CAS). Not sure if you're going to do
authentic
I'd like to have an external program that registers a file by absolute path
(link, not upload) in a data library, then immediately starts a workflow on it.
My question is to whether or not that will work in the general case where:
- The system is configured to set metadata externally
-
This should not lock. The job(s) for the workflow will be queued until they're
able to execute, but the call will return.
-Dannon
On Aug 2, 2011, at 4:17 PM, Duddy, John wrote:
> I’d like to have an external program that registers a file by absolute path
> (link, not upload) in a data library
Hi all,
I have been using Galaxy for a few years now and I am about to start
creating my own repositories for the new Tool Shed. However, I can't seem
to find any good documentation on how to do that exactly. Can someone point
me in the right direction? I need to figure out the best way to orga
John, I took a look at this and it's definitely a defect, not something you're
missing. Thanks for the report, I can let you know when a fix is available.
-Dannon
On Jul 28, 2011, at 2:30 PM, John Chilton wrote:
> Hello Galaxy Developers,
>
>I have a user who noticed a potential bug when
Alex,
This method of hiding datasets isn't exposed to tool wrappers, it's only used
within the workflow framework.
-Dannon
On Jul 6, 2011, at 3:27 PM, Bossers, Alex wrote:
> Hi all,
>
> by default I let my tools produce ("the old way") a logfile of the console
> and additional running stati
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