got it,  I didn't pick up that the align.conf was being read in as vars


On Mon, Apr 28, 2014 at 2:26 PM, Kyle Ellrott <notifications@github.com>wrote:

> In job_upload.sh:
>
> > @@ -2,6 +2,9 @@
> >
> >  BASEDIR="$(cd `dirname $0`; pwd)"
> >
> > +#PYTHON=/pod/opt/bin/python
> > +UPLOAD_KEY=/pod/home/cwilks/UCSC_PAWG.key
>
> I moved this into $BASEDIR/align.conf
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/kellrott/tcga_realign/pull/2/files#r12068754>
> .
>