Hi,
we recently activated the feature for non admin users which allows them to
upload a directory of files:
...
# Add an option to the library upload form which allows authorized
# non-administrators to upload a directory of files. The configured directory
# must contain sub-directories named
Hi John,
thanks for your reply, I'll give it a try.
Thomas
Von: John Chilton [jmchil...@gmail.com]
Gesendet: Montag, 7. April 2014 16:15
An: Berner, Thomas
Cc: galaxy-dev@lists.bx.psu.edu
Betreff: Re: [galaxy-dev] authorize non admin user to only link
Hi,
I've seen there is a new version (3.1-1) of GATK available at
http://www.broadinstitute.org/gatk/download .
Are there any plans of getting this version into Galaxy in the nearer future?
Greetings, Thomas
---
Thomas Berner
Julius Kühn-Institut (JKI)
- Federal Research Centre for
Hey guys,
we have a problem in our local galaxy instance (10392:1ae95b3aa98d
release_2013.08.12) using bcftools (Version: 0.1.19-44428cd) from the tool shed
to convert our bcf files into vcf.
With bcf files less than ~ 3 GB everything works fine, but above that (we have
a 13gb bcf file), the
Hey guys,
we know that we can use a variable to rename output files after their input
e.g. #{input}, by using the rename dataset action in the workflow editor.
However, we would like to use these variable as a workflow parameter too, e.g.
for the Add or Replace Groups tool as the ID tag, so
Hey guys,
we want to use trackster in our local galaxy instance (rev. 10392:1ae95b3aa98d
release_2013.08.12) and followed the instructions at
http://wiki.g2.bx.psu.edu/Learn/Visualization .
We tested it with a custom Build of 96 sequences in a fasta file, where all
bams were mapped against
. August 2013 00:41
An: Bjoern Gruening
Cc: Berner, Thomas; galaxy-dev@lists.bx.psu.edu
Betreff: Re: [galaxy-dev] Manhattan/qq plots
Hi, Thomas.
There are no resources available to support that now 3 year old rgenetics code
so I'm sad but not surprised to hear of this new problem.
The grant ended
: Dienstag, 27. August 2013 16:12
An: Berner, Thomas
Cc: galaxy-dev@lists.bx.psu.edu
Betreff: RE: tool not runing in workflow
Thomas,
Did you generate the work flow from scratch or did you make a simple analysis
in the history and extracted a work flow from that? The latter we usually do
without
Hey guys,
we installed and used a tool of the mothur_toolsuite in our local galaxy
instance named get.otulist, but if we want to integrate it into a workflow
(extract from history) we get the following error for the next step:
Error due to input mapping of 'Join two datasets' in
Hey guys,
we are running a local galaxy instance (10200:fd4113962c32)with R version 3.0.1
and want to use Manhattan/qq, but we are missing the pval manhatan.pdf, only
pval qqplot.pdf is generated and we are getting the following error:
Nonzero exit code = 1
[1] ### 11008 values read from
Hey guys,
we found a curios bug, but it is a little bit tricky to explain.
Here is an example:
- Click on Concatenate datasets tail-to-head
- add a new data set
- click on the first data field and select your data set of choice
- press tab to get to the next data set an select the second
. Juli 2013 17:42
An: Berner, Thomas
Cc: galaxy-dev@lists.bx.psu.edu
Betreff: Re: [galaxy-dev] repeat tag enhancement?
Rather than adding additional increments to add/remove, what about allowing the
user to directly set the number of elements in the repeat?
--
James Taylor, Assistant Professor
Hey guys,
i was searching the mailing list and wiki for some hints if there is a
possibility to enhance the repeat tag.
We want to give the option to our users to add more than one additional set of
the contained parameters at one go e.g. 10 or 20 or 50, because it can be very
frustrating to
Hi guys,
we are currently establishing our own local Galaxy instance. However, after we
tried to install the mothur toolsuite we could not enter the admin pages
anymore. Every time we try we we obtain the following error:
Internal Server Error
Galaxy was unable to successfully complete your
-down-menu like it is in the edit
Attributes menu if it is possible...
Regards,
Thomas
-Ursprüngliche Nachricht-
Von: Peter Cock [mailto:p.j.a.c...@googlemail.com]
Gesendet: Donnerstag, 13. Juni 2013 11:59
An: Berner, Thomas
Cc: galaxy-dev@lists.bx.psu.edu
Betreff: Re: [galaxy-dev] Blast
Hi guys,
another error appeared after we installed NCBI BLAST + to our local Galaxy
instance and wanted to test it.
After uploading some testdata to our history we tried to run blastn on it and
got the following error:
Fatal error: Matched on Error:
Error: NCBI C++ Exception:
Hi guys,
We recently installed NCBI BLAST + to our local Galaxy instance and now we need
to provide the possibility to filter/mask ... by taxon id (taxid) using the
command line option (-window_masker_taxid) of BLAST (cf.
http://www.ncbi.nlm.nih.gov/books/NBK1763/) before the job will be
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