Regarding the fastx-splitter:
This one is a perl+shell script, not a binary,
so try installing GNU sed (no need to override Mac's sed, the GNU sed will
probably be installed as "gsed"), and modify the shell script (from "sed" to
"gsed").
On Apr 27, 2011, at 19:15, "Pieter Neerincx" wrote:
>
I’m getting this same error and I’m running nginx as a proxy server. Is there
a specfic parameter we should be aware of to allow partial gets? I don’t see
anything in the wiki page for setting up the ProductionServer.
Thanks,
Dave
On 4/27/11 12:33 PM, "Daniel Blankenberg" wrote:
Hi Alex,
Hi Jeff,
On Apr 28, 2011, at 12:42 AM, Whyte, Jeffrey wrote:
> Hi Pieter,
>
> Thanks to both you and Florent for the suggestion of MacPorts. GnuPlot is
> now working well in Galaxy after I installed the port.
:)
> I also appreciate the information on specifying the custom environment.
> T
One more note on the FASTX barcode splitter error:
After a little searching, I believe the problem is with the options used for
sed utility, specifically the -r option
An error occurred running this job:sed: illegal option -- r
If I log in to my Linux server, and type "man sed", one of
Hi Pieter,
Thanks to both you and Florent for the suggestion of MacPorts. GnuPlot is now
working well in Galaxy after I installed the port. I also appreciate the
information on specifying the custom environment. That could be related to the
only other problem I am having: the FASTX toolkit b
Hi Branden,
Vipin, thanks for the tip. I was not aware of data tables at all.
>
> I checked bwa_wrapper.xml and it is still using the from_file attribute for
> the reference genome parameter, not from_data_table. It would appear then
> that BWA is not using data tables? Additionally, I have no
Hi Alex,
Displaying BAM files at external applications usually requires an http server
that supports partial gets. Unfortunately, the current lightweight http server
that is built into Galaxy does not support these advanced http options.
However, this limitation can be overcome by using a prox
Hi Pieter,
On Wed, Apr 27, 2011 at 4:14 PM, Pieter Neerincx
wrote:
> Hi Leandro,
>
> On Apr 27, 2011, at 3:50 PM, Leandro Hermida wrote:
>
> > Hi,
> >
> > Just wondering if I got my setup right, I have Galaxy front-ended by
> Apache doing the static caching, proxying and LDAP auth. What's nice i
Hi Leandro,
On Apr 27, 2011, at 3:50 PM, Leandro Hermida wrote:
> Hi,
>
> Just wondering if I got my setup right, I have Galaxy front-ended by Apache
> doing the static caching, proxying and LDAP auth. What's nice is that user's
> don't have to be created by an admin if the user authenticates
Hello all,
I just updated our local copy of Galaxy and just wanted to try the new IGV
display application.
When I try to display a BAM file with the local IGV or the web IGV I
encounter following error complaining about the Null content-length.
Has any of you encountered the same problem? Do I miss
Hi,
Just wondering if I got my setup right, I have Galaxy front-ended by Apache
doing the static caching, proxying and LDAP auth. What's nice is that
user's don't have to be created by an admin if the user authenticates and
authorizes properly against the LDAP config then Galaxy will automaticall
Hi everyone,
To answer my own question after testing various front-end auth setups it
looks like REMOTE_USER must be the email address, and what's nice about LDAP
is that you can have users authenticate with a username or other ID that is
not the email address and still return the email address to
Not currently, though the API is being continually extended with new features
as the need arises.
-Dannon
On Apr 27, 2011, at 9:40 AM, Leandro Hermida wrote:
> Hi Dannon,
>
> Thanks for your replies and advice, this leads me to a quesion... is it
> possible to execute a tool job via the Galaxy
On Thu, Apr 21, 2011 at 2:40 PM, Dannon Baker wrote:
> Leandro,
>
> I see what you mean, I misunderstood your original goal. There currently
> isn't a way to execute single tools in this fashion.
>
> It isn't exactly straightforward, but you could construct a workflow that
> consisted of two ste
Hi Jeff,
1. As Florent wrote, probably the easiest solution is to install the
dependencies with MacPorts. Only if stuff is not available via MacPorts or the
version available is too old / incompatible with other dependencies I install
things manually. MacPorts will add a line like this:
---
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