Hi John, Sorry I forgot the repply to all stuff, so once again:
I checked that I have a tab not a space. I am using gedit as an editor. Maybe my problem with extract is linked to the fact that bx-python is not installed correctly because: I could install bx-python (0.7.1) from IUC but not devteam from the toolshed. Then when I run the extract_genomic_dna.py from the command I get the following error:
Traceback (most recent call last): File "extract_genomic_dna.py", line 17, in <module> import bx.seq.nib ImportError: No module named bx.seq.nib
Thanks for your help. Alexandre
On 25-07-2016 15:10, John Chilton wrote:
- It needs to be a tab not spaces between the fields in that loc file
- can you confirm that it is a tab? (Many editors will implicitly
replace tabs with spaces.)
- You need to restart Galaxy after updating that file - can you
confirm it has been restarted?
-John
On Fri, Jul 22, 2016 at 11:34 AM, Alexandre Maucuer alexandre.maucuer@inserm.fr wrote:
Hi, I've installed a Galaxy instance on a local machine under ubuntu 16.04. I am trying to fetch sequences from hg19.2bit I downloaded from ucsc as ~/galaxy/depot/data2/galaxy/hg19$hg19.bit I added: hg19 /depot/data2/galaxy/hg19/hg19.2bit to my twobit.loc file in tool-data directory
When running the extract genomic dna, I get the error: "No sequences are available for 'hg19', request them by reporting this error." see also attached screenshot Thanks in advance for your help
-- Alexandre Maucuer, Ph.D., INSERM, France
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