Hi, I would like to autofill cycles for next-gen sequencing. Most of our
submitters probably don't even know what that means actually and so we want
to simplify it. Same goes with paired end reads. How would I fill out the
nglims yaml file so that they could skip over that section? Or maybe
I am running a local instance of galaxy, which has been functioning fine until
2 weeks ago.
However, now when I go to the Admin section, then to ‘Search and browse tool
sheds’ and click ‘Galaxy main tool shed’ the browser waits for a while then I
get a ‘Connection was reset’ error instead of
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
Hi guys,
we are currently trying to integrate CLC Bios short read assembler into our
local Galaxy version. So far everything went smoothly. However, the command
line tool allows for specifying the number of CPU that should be used for
computation. We are wondering, whether it is also possible
Hi guys,
when building workflows we can choose for each parameter whether to 'set at
runtime' or to 'set in advance' (when creating or editing the workflow). We are
looking for a possiblity to set a default value that is used (only) for the
workflow, i.e., we like to specify a value that might
Peter and Dan,
I like the idea of replacing all open() with galaxy_open() in all tools. You
can tell the format by looking at the first 4 byes (see C code below from the
UCSC browser team). Is there some pythonic way of overriding open?
You need to read the first four bytes of the file to see
On Tue, Jul 9, 2013 at 4:29 PM, Keilwagen, Jens
jens.keilwa...@jki.bund.de wrote:
Hi guys,
we are currently trying to integrate CLC Bios short read assembler into
our local Galaxy version. So far everything went smoothly. However, the
command line tool allows for specifying the number of CPU
May you make your question more specific? Have you read the online
docs: http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information
On Tue, Jul 9, 2013 at 5:53 PM, Robert Baertsch rbaer...@ucsc.edu wrote:
On Jul 8, 2013, at 3:33 PM, Peter Cock wrote:
The tools available in Galaxy are written in a range
of languages including C, Perl, R, etc. Yes, some are in Python,
but of those most are independent of Galaxy and can be
Hi Ricardo,
You might want to take a look at this[1] page in the wiki. The short
answer is there is no way to configure purging datasets in Galaxy
itself. It would be nice to do so. Galaxy does provide an external
script that can be easily put in a cron job to do this. The script is
great. Let's put the bx-python calls in a galaxy_open helper function.
On Jul 8, 2013, at 3:20 PM, James Taylor wrote:
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,
great. Let's put the bx-python calls in a galaxy_open helper function.
On Jul 8, 2013, at 3:20 PM, James Taylor wrote:
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,
I will implement this if the galaxy team likes the approach.
We did this in ucsc genome browser code years ago: a single open_helper call
handles, gzip, http, ftp and pipes. No need to care about how the data is
compressed or where it data resides.
wouldn't it be great to be able to pipe
I haven't been able to find a way to make the drmaa runner work in this
situation. I'm going to move on to trying this with a pbs runner instead.
I will post to this thread if this works for me.
- Bart
___
Please keep all replies on the
Hi, I get an internal server error when clicking sequencing results under
the lab menu. I'm hoping for an easy fix :)
This is in my server log file (and I'm removing some data and IP addresses
found in the log):
10.xx.xx.xx - - [09/Jul/2013:15:45:21 -0400] GET
/chapman/nglims/list_sqn_results
Basically the same thing happens on a few different menus actually
including most recently Review tool migration stages so I don't think
it's a nglims thing anymore.
On Tue, Jul 9, 2013 at 3:54 PM, Lee Katz lsk...@gmail.com wrote:
Hi, I get an internal server error when clicking sequencing
Dear all,
As I was trying to do visualize my data set in trackster, I get the following
error:
/bin/sh: 1: bedtools: not found
sort: fflush failed: standard output: Broken pipe
sort: write error
needLargeMem: trying to allocate 0 bytes (limit: 1000)
When doing a sudo find / -name
Lee;
Hi, I get an internal server error when clicking sequencing results
under the lab menu. I'm hoping for an easy fix :)
Basically the same thing happens on a few different menus actually
including most recently Review tool migration stages so I don't think
it's a nglims thing anymore.
Lee;
Hi, I would like to autofill cycles for next-gen sequencing. Most of our
submitters probably don't even know what that means actually and so we want
to simplify it. Same goes with paired end reads. How would I fill out the
nglims yaml file so that they could skip over that section?
You'll need to make sure that bedtools is in your Galaxy user's path.
Best,
J.
On Jul 9, 2013, at 6:40 PM, Perez, Ricardo wrote:
Dear all,
As I was trying to do visualize my data set in trackster, I get the following
error:
/bin/sh: 1: bedtools: not found
sort: fflush failed: standard
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