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 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:
---
Jeff,
I haven't tried GnuPlot specifically in Galaxy, but all the applications
that you install with MacPorts are installed under /opt/local/bin. I
think that MacPorts adds this folder to your $PATH. So yes, Galaxy
should be capable of finding any program that you installed through
MacPorts.
Hi Florent,
I installed MacPorts this afternoon, but that was after I installed gnuplot
(sudo make install). Have you found that gnuplot works in Galaxy if installed
through MacPorts? Thanks for the suggestion.
Jeff
On Apr 23, 2011, at 7:03 PM, Florent Angly wrote:
> Hi Jeff
> Some of thes
Hi Pieter,
Thanks very much for taking the time to provide the advice and explanations -
very helpful! As you suggested, my search path was not defined properly to
locate gnuplot. If I typed "gnuplot" in the Terminal, I would get the message,
"command not found". Now, Gnuplot is in /usr/loca
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 Gala
Hi Jeff,
This is indeed a dependency issue and I have seen those both on Linux and Mac
OS X. What happens if you type gnuplot in a Terminal window yourself? If you
also get "command not found". There is either still something missing or your
environment is not setup properly. If the tool works
