Hello,
I tried to download several times the several egg on these following
mirrors but the download is always blocked near 50%...I asked several
different people and they all have the same problem :
http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg
Dear galaxy members,
I have a question on the databases used in megablast module from galaxy. There
are four db options to blast against with -
1. htgs 28-Jan-2013
2. nt 28-Jan-2013
3. wgs 28-Jan-2013
4. phiX174
Is there any further information to guide which database
Hi,
I noticed that the version of cuffdiff used in main.g2.bx.psu.edu is really
obsolete (0.0.5) whereas the most recent version is 2.1.1.
Is there a chance that a more up-to-date version will be ever installed on
the main galaxy instance?
many thanks,
Nikolay
Please, I have been unable to use any of the tools under FASTQ Tools
for the last 4 days. I keep getting an error message with codes, for
instance GURU MEDITATION: #376b73ae417d41f3a7c2088770e13b8f.
Is this part of the platform down for some reason?
Best wishes and thanks,
E. Fox
Hi, could you be more specific. Name one or two specific tools that
are not working. Also, when does the error occur, after submitting the
job or before loading the tool?
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, May 24, 2013 at 10:31 AM, Eduardo Fox
Hi Eduardo,
I've committed some code that should fix the issue that you are experiencing,
and it will be available on the main server after the next update (some time
next week).
Until then, if you change the name of e.g. your history item 34 to not have a
'í' or other non-ascii characters
Hi,
Two related issues:
We tried to run BWA for Illumina on two groomed files (fastqsanger) and
got the following error message.
* *
*24: Map with BWA for Illumina on data 6 and data 5: mapped reads*
error
An error occurred with this dataset: *BWA Version: 0.5.9-r16 The alignment
Hi,
When you say uploaded the files for hg19 indexed for bwa, do you mean
that these indexes were loaded into the history as datasets? If so, that
won't work. Instead, for a local install, adding the data as a buillt-in
index is better. Instructions are here:
Hi Kathryn,
These first three are three different types of sequence databases
available from GenBank The last is a genome assembly for the phiX174 genome.
Information about all can be found here:
http://www.ncbi.nlm.nih.gov/genbank/
There are many uses, one example is covered in our
Hello Nikolay,
There are two version numbers associated with tools - the wrapper
version and the underlying tool/binary version. For Cuffdiff, the binary
on the pubilc Galaxy server is at 2.1.1, and this can be seen in a
dataset's result info field once a job is complete. (The wrapper is
Jen,
Thank you very much for the information. They are very informative.
I found the htgs and wgs databases information there. What does nt 28-Jan-2013
stand for?
Meantime, if I am looking for virus containing database, I found wgs is one.
Can anyone confirm or advice further if there is
Hello,
nt refers to the nucleotide database. It is also linked from the
link below, to here:
http://www.ncbi.nlm.nih.gov/nuccore
The Quick start guide can answer many questions about it:
http://www.ncbi.nlm.nih.gov/books/NBK44863/
A good technical content description is here:
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