Hi Björn,
It should be fixed, the problem was with tools with uppercase characters in
the guid:
https://bitbucket.org/galaxy/galaxy-central/commits/0b955e54451c/
--nate
On Thu, Feb 13, 2014 at 2:38 AM, Björn Grüning bjoern.gruen...@gmail.comwrote:
Hi Nate Simon,
was that solved? I
I've gone ahead and made the change in the datatypes registry to use log.debu
instead of log.warning, so hopefully this issue is resolved. The changeset in
central is 12497:0b0018fa5d20, which has also be grafted to stable.
Greg Von Kuster
On Feb 13, 2014, at 11:51 AM, Jim Johnson
Hello All,
I recently was gifted an ioFusion ioFX acceleration card to help speed
my bioinformatics work along and I am wondering how best to integrate it
into my instance to make Galaxy more efficient. Is it sufficient to
merely ensure that the datasets being operated on are on the flash
storage
Dear,
Is it possible to use SnpEff with genomes of other species (e.g. Drosophila)
other than C.elegan on galaxy website (not local)? It seems the only option for
the genome menu (Caenorhabditis elegants : WS220.64).
In fact, I am trying to use CloudMap (the EMS Variant Density Mapping
Last time I checked the EMS Variant Density Mapping tool, specifically, had
an unnecessary restriction to chromosome names as in WS220.64 (chrI, chrII,
chrIII, chrIV, chrV, chrX). So maybe before putting too much effort into the
SnpEff side of the workflow, maybe try the Mapping tool individually
Hi Sam,
thank you for the quick reply but I can't seem to find the revision, or
maybe don't know how to pull it.
I tried to check galaxy-dist on BitBucket but couldn't find any updates
related to Galaxy Reports.
Bests,
Nikos
2014-02-13 17:35 GMT+01:00 sam guerler aysam.guer...@gmail.com:
Hi
Hi all,
I'm writing a tool in Galaxy and I need to parse the input file's format
(bam, bed, etc) to pass it as a variable to the command.
Something like:
command.sh $input ${input.format} $output
Is there a way to get it?
Bests,
Nikos
Hi,
this has been resolved in galaxy-central repo (not dist). You can apply the
patch manualy, it is less than one-liner.
https://bitbucket.org/galaxy/galaxy-central/commits/3691fd3e12ef8160ae993cef5ebd51ddeee95da1
Martin
On Fri, Feb 14, 2014 at 1:28 PM, Nikos Sidiropoulos
Thanks so much Martin!
2014-02-14 19:32 GMT+01:00 Martin Čech mar...@bx.psu.edu:
Hi,
this has been resolved in galaxy-central repo (not dist). You can apply
the patch manualy, it is less than one-liner.
Thank you so much for your reply! But, may I double check what do you mean by
try the Mapping tool individually?
maybe try the Mapping tool individually first with some test data to see
whether you are getting any result at all.
You mean I should try the tools individually (like BWA for map,
Worked.
Thanks Björn!
2014-02-14 19:41 GMT+01:00 Björn Grüning bjoern.gruen...@gmail.com:
Hi Nikos,
try $input.ext ...
Cheers,
Bjoern
Hi all,
I'm writing a tool in Galaxy and I need to parse the input file's
format (bam, bed, etc) to pass it as a variable to the command.
Hi Nikos,
try $input.ext ...
Cheers,
Bjoern
Hi all,
I'm writing a tool in Galaxy and I need to parse the input file's
format (bam, bed, etc) to pass it as a variable to the command.
Something like:
command.sh $input ${input.format} $output
Is there a way to get it?
Hello all,
*We are pleased to announce that Early Registration
https://wiki.galaxyproject.org/Events/GCC2014/Register and Talk and
Poster Abstract Submission
https://wiki.galaxyproject.org/Events/GCC2014/Abstracts are now open for
the 2014 Galaxy Community Conference (GCC2014)
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