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(a)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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--
Alexandre Maucuer, Ph.D.,
INSERM,
laboratory: INSERM UMR1204, Structure-Activité des Biomolécules Normales
et Pathologiques,
Université d'Evry,
Batiment Maupertuis,
Rue du père Jarlan, Evry 91025,
France
http://sabnp.univ-evry.fr/?lang=en
tel: 01 69 47 01 87