Maybe too obvious but something we have encountered before with other scripts.
Check that galaxy can find the requirements to run your script. Shell settings
like PATH.
What we do when starting galaxy is to source the /etc/profile
Since galaxy is not using the ENV of for instance bash.
Hope this
Dear all,
Would it be possible somehow to not only export a single history of a user (to
file) but also all histories of a user in one go. Or even all user-bound
histories/settings and such?
I would like to import them into another galaxy instance (basically from our
internal development
Phil,
we also have a MiSeq and currently experienced the same phenomenon how to
demultiplex.
We have our local galaxy instance and wrote some scripts to efficiently
demultiplex the sample. However, you FIRST need to convert on the MiSeq the
primary fastq into a (in their view) multiplex
Matthew,
yes we have seen such kind of long runs before (depending on server load).
Happy most of our reads are now in 1.8+ format.
You can parallelise the process by splitting the file in 4 or 6 and submit for
grooming and afterwards merge them again...
Alex
Are you sure the fastq's are in older format? Otherwise you won't need to groom
the files anymore (as far as I understood) since the newer format is comparable
Sanger quality score already Saves huge resources!
Alex
-Oorspronkelijk bericht-
Van: galaxy-user-boun...@lists.bx.psu.edu
Edward,
If you just want to conacatenate the fastq files (I assume that is what you
mean) you can do that using the text manipulation tools: concatenate datasets
tail-to-head.
Good luck.
Alex
Van: galaxy-user-boun...@lists.bx.psu.edu
Joseph
We are already quite a while up and running the central and dist version on
Ubuntu 10.10 x64 server without any problem. I didn't like the new desktop of
11 but it seemed to work without any trouble there as well...
Please note the version of python in combination with R (if you want to
Aaron,
As far as I remember MIRAisn't MIRA taking into account the low/high
quality bases anyway? So no need to filter there right?
Only filtering needed is for contaminating sequences.(incl adapters and
such). You can/have to check the MIRA website to be sure though.
The high qual
Surya,
have a look at the galaxy wiki and quickies/video's. A nice metagenomics
example is the windshield splatter analaysis.
Screencasts section: http://main.g2.bx.psu.edu/screencast
Meta genomics example:
http://screencast.g2.bx.psu.edu/galaxy/flash/mg_screencast_1.html and
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