Hi Paul,
I have Galaxy running on a small Mac workstation. I have made a specific
user, 'galaxy', for it. It is cleaner, but probably overkill for 1 person.
Note also that you can install a daemon to start Galaxy automatically
when your computer starts:
Hi Amanda,
I would certainly be interested in using your helpful QIIME wrappers if
you put them on the Toolshed.
Best,
Florent
On 06/02/12 06:22, Amanda Zuzolo wrote:
Hello, all.
I have been working on getting the Qiime scripts into Galaxy as
mentioned before, and they are working with Qiime
Hi Bassam,
Try Grinder, which is available from the Galaxy Toolshed at
http://toolshed.g2.bx.psu.edu/.
Regards,
Florent
On 30/12/11 04:23, Bassam Tork wrote:
Dear All,
Is there a way to generate 454 simulated amplicon reads with errors
using galaxy.
Happy New Year,
Bassam Tork.
On 14/10/11 06:45, Greg Von Kuster wrote:
Hello Forent,
On Oct 13, 2011, at 2:48 AM, Florent Angly wrote:
But maybe I need a little bit of guidance with this because the example shown, the
user is given a _limited_ number of output datasets to choose from. The Grinder case
seems simple: give
additional problems.
Thanks for finding this!
Greg Von Kuster
On Oct 4, 2011, at 2:53 AM, Florent Angly wrote:
Hi all,
I tried the latest stable version of Galaxy:
http://wiki.g2.bx.psu.edu/News%20Briefs/2011_08_30. This page has links to how
to use the new tool shed including how
Thanks for the pointer Ross. It was really useful. I also found more
information about multiple output datasets on the wiki:
http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files?highlight=%28dataset%29
I plan on writing a script that renames the output of the Grinder tool I
am
Hi,
I too would be interested in knowing how to handle tools that might
generate multiple output files for the Grinder wrapper I am developing.
Any news on this? Has a ticket been recorded?
How about when the tool generate an number of files that cannot be
determined from the values the
tried this patch? Feedback would be appreciated.
Thanks,
K
On Fri, May 27, 2011 at 1:27 AM, Florent Angly
florent.an...@gmail.com mailto:florent.an...@gmail.com wrote:
Can anyone comment on my email please?
Florent
On 22/05/11 14:03, Florent Angly wrote:
Let me know if you
On 27/05/11 00:04, Peter Cock wrote:
I regard fixing issue 325 as one of the top priorities in Galaxy
Can't agree more with you Peter!
This bug and other tool wrapper related bugs make it harder and more
tedious to contribute tool wrappers. It's a big turn off for me.
Florent
Can anyone comment on my email please?
Florent
On 22/05/11 14:03, Florent Angly wrote:
Let me know if you have any questions about this.
Thanks,
Florent
Original Message
Subject:Request for pulling the updated FASTQ (de-)interlacer tool
Date: Tue, 17 May 2011 17:47
Let me know if you have any questions about this.
Thanks,
Florent
Original Message
Subject:Request for pulling the updated FASTQ (de-)interlacer tool
Date: Tue, 17 May 2011 17:47:13 +1000
From: Florent Angly florent.an...@gmail.com
To: galaxy-dev
Hi Jeroen,
The idea of having a tool to automatically generate Galaxy wrappers is
attractive, and in some cases, possible. For example, I know that the
tools in QIIME (http://qiime.sourceforge.net/) use some sort of argument
declaration and a Python module to read it and deal with the
Hi Jeff
Some of these tools can be installed easily on Mac OS using MacPorts
port search gnuplot
Of course, you have to install MacPorts first.
Florent
On 23/04/11 01:25, Whyte, Jeffrey wrote:
Hi Everyone,
I'm having trouble getting some of the tools to work on my local installation of
:03 PM, Florent Angly wrote:
Hi Jeff
Some of these tools can be installed easily on Mac OS using MacPorts
port search gnuplot
Of course, you have to install MacPorts first.
Florent
On 23/04/11 01:25, Whyte, Jeffrey wrote:
Hi Everyone,
I'm having trouble getting some of the tools to work
Hi Peter,
I get the same error here.
Florent
On 06/04/11 01:50, Peter Cock wrote:
Hi all,
I had wondered why none of the tools on the Galaxy Tool Shed had a
rating, and had assumed it was just that so far no-one had bothered. I
have a new theory, it doesn't work?
I just viewed Brad's BAM to
.
Florent Angly wrote:
Indeed, this workaround works! Thank you.
I added these lines to the beginning of my run.sh:
PATH=/opt/local/bin:/opt/local/sbin:$PATH
export $PATH
Now, Galaxy can find Grinder, Velvet, etc
Could Galaxy detect and use ~/.profile automatically if it exists
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