Question: Operating On, And Getting At, Large Files In Galaxy...
0
Nick Schurch • 50 wrote:
Hi all,
I've recently encountered a few problems when trying to use Galaxy
which are
really driving me away from using it as a bioinformatics platform for
NGS. I
was wonderinf if there are any simple solutions that I've missed...
Firstly, It seems that while there are a few solutions for getting
large
files (a few GB) into a local install of galaxy without going through
HTTP,
many tools that operate on these files produces multiple, uncompressed
large
files which quickly eat up the disk allocation. This is particularly
significant in a workflow that has multiple processing steps which
each
leave behind a large file. With no way to compress or archive files
produced
by intermediate steps in a workflow, and no desire to delete them
since I
may need to go back to them and they can take hours to re-run, the
only two
remaining options seem to be to save them and then delete them.
And this brings me to the second problem. Getting large files out of
Galaxy.
The only way to save large files from Galaxy (that I can see) is the
save
icon, which downloads the file via http. This take *ages* for a large
file
and also causes big headaches for my firefox browser. I've taken a
quick
peek at the Galaxy file system to see if I could just copy a file, but
its
almost completely indecipherable if you want to find out what file in
the
file system corresponds to a file saved from a tool. Is there some way
to
get the location of a particular file on the galaxy file system, that
I can
just copy?
--
Cheers,
Nick Schurch
Data Analysis Group (The Barton Group),
School of Life Sciences,
University of Dundee,
Dow St,
Dundee,
DD1 5EH,
Scotland,
UK
Tel: +44 1382 388707
Fax: +44 1382 345 893
--
Cheers,
Nick Schurch
Data Analysis Group (The Barton Group),
School of Life Sciences,
University of Dundee,
Dow St,
Dundee,
DD1 5EH,
Scotland,
UK
Tel: +44 1382 388707
Fax: +44 1382 345 893