Hello Flavia,
It sounds like the results are in a compressed format, and this can be
fine in many cases. What server are you using? The admin there can
likely help to determine if this is a problem. There is usually contact
information on the center home page - a link to the lab or help. A lis
Toni,
As a quick work-around until set up natively, you may be able to use the
Extract DNA tool with a custom reference genome:
http://wiki.galaxyproject.org/Support#Custom_reference_genome
See the example in: "Tools on the Main server", should work on any
Galaxy set up as a production server
Hello,
Thanks for your response. I can almost never get anything done on the
public instance of Galaxy. It can take an entire day to even load a.bed
file. When I was encountering the error I was on the Broad Instance.
Marco, I tried following the instructions above to ensure that genome was
avail
Hi Toni,
Bjoern is correct - if you are using a local Galaxy that does not have
this reference genome available, it needs to be added. The "Extract DNA"
tool requires a .2bit version of the genome available and the
alignseq.loc file configured. More is here, section " LASTZ and EXTRACT
Genomi
Hi Toni,
to convert a bed file to a fasta file you need the genomic sequence. You
can specify a genome-build for every bed file in your history. You
probably don't have a genome build specified or its specified as
sacCer2. sacCer2 is not configured I would guess, so no genome is
available. Try to
Hello Delong ZHOU,
On 6/7/13 8:23 AM, Delong, Zhou wrote:
Hello,
I'm using the main galaxy server to analyse some data and then I got
this messege:
An error occurred while getting updates from the server. Please
contact a Galaxy administrator if the problem persists.
This message indicates t
Hi Kenneth,
It is likely that the path is wrong in the .loc file. It has to point to
the actual files, not just the directory. Inside here
/9720/genome_references/ncbi/nr-protein-db
is where all the nr.* files are? In that case, the path should be
/9720/genome_references/ncbi/nr-protein-db/n
Hi Kenneth,
Yes, target databases require indexes and *.loc file set-up. Please see
this wiki for details. For Genbank data such as NR, FTP the pre-built
indexes and use those (generating them with formatdb is not necessary).
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
See the second
Hello Kenneth,
Are you using BLAST+ in a local install or cloud instance? The problem
may be that the query dataset needs to have the datatype assigned as
"fasta". To do this, click on the pencil icon for the dataset to reach
the Edit Attributes form. Then either scroll down to (or click on th
9 matches
Mail list logo
