[ensembl-dev] VEP options - everything cell_type selection

Will McLaren wm2 at ebi.ac.uk
Thu May 10 15:28:07 BST 2012


Hi Duarte,

Thanks for spotting this; I changed the behaviour of the cell_type
flag half way through development and forgot to remove it from the
everything flag.

It's fixed on CVS now.

Will

On 10 May 2012 15:17, Duarte Molha <Duarte.Molha at ogt.co.uk> wrote:
> I see that you have added a “everything” command line option that selects
> the most common options instead having to put them all one by one.
>
>
>
> This is very useful but I believe the cell_type activation on line 425 might
> be wrong. Cell_type expects a string, it is not a on/off parameter.
>
> Am I correct in this assumption?
>
>
>
> When you use the everything opton the script dies!
>
>
>
> Here is the output:
>
> ERROR: cell type 1 not recognised; available cell types are:
>
> HeLa-S3,GM06990,U2OS,CD4,IMR90,HL-60,HepG2,Lymphoblastoid,CD133,CD36,K562,GM12878,HUVEC,NHEK,H1ESC,MultiCell,K562b,NH-A,HSMM,HMEC
>
>
>
>
>
> Best regards,
>
>
>
> Duarte Molha
>
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe):
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>




More information about the Dev mailing list