On Mon, Apr 29, 2013 at 3:27 AM, Mike Dyall-Smith
mike.dyallsm...@gmail.com wrote:
Dear Peter Cock, thanks for your advice. Just to be clear, do I leave the
files within their decompressed folders or do I put all the individual files
into one folder? I assume the former, but want to be sure.
Thanks again, Mike DS
Hi Mike,
Unless you're using a Graphical decompression tool which is trying
to be too helpful, each tar-ball does *not* decompress into its own
folder. The files should all be in the *same* folder.
I use this to verify the checksums,
$ md5sum --check nr.00.tar.gz.md5
nr.00.tar.gz: OK
Then I use this to decompress the tar-balls,
$ tar -zxvf nr.00.tar.gz
etc
(Actually I don't do this personally any more - it has been setup
to happen automatically when the NCBI update the databases.)
We keep all our NCBI databases in the same folder,
$ ls /data/blastdb/ncbi/nr.*
/data/blastdb/ncbi/nr.00.phd
/data/blastdb/ncbi/nr.00.phi
/data/blastdb/ncbi/nr.00.phr
/data/blastdb/ncbi/nr.00.pin
/data/blastdb/ncbi/nr.00.pnd
/data/blastdb/ncbi/nr.00.pni
/data/blastdb/ncbi/nr.00.pog
/data/blastdb/ncbi/nr.00.ppd
/data/blastdb/ncbi/nr.00.ppi
/data/blastdb/ncbi/nr.00.psd
/data/blastdb/ncbi/nr.00.psi
/data/blastdb/ncbi/nr.00.psq
/data/blastdb/ncbi/nr.00.tar.gz
/data/blastdb/ncbi/nr.00.tar.gz.md5
...
/data/blastdb/ncbi/nr.10.phd
/data/blastdb/ncbi/nr.10.phi
/data/blastdb/ncbi/nr.10.phr
/data/blastdb/ncbi/nr.10.pin
/data/blastdb/ncbi/nr.10.pnd
/data/blastdb/ncbi/nr.10.pni
/data/blastdb/ncbi/nr.10.pog
/data/blastdb/ncbi/nr.10.ppd
/data/blastdb/ncbi/nr.10.ppi
/data/blastdb/ncbi/nr.10.psd
/data/blastdb/ncbi/nr.10.psi
/data/blastdb/ncbi/nr.10.psq
/data/blastdb/ncbi/nr.10.tar.gz
/data/blastdb/ncbi/nr.10.tar.gz.md5
/data/blastdb/ncbi/nr.pal
We can then refer to the NR database at the command line
as /data/blastdb/ncbi/nr or as just nr if the BLAST database
path is configured to check this folder.
In this folder we also have other NCBI database, like NT:
$ ls /data/blastdb/ncbi/nt.*
/data/blastdb/ncbi/nt.00.nhd
/data/blastdb/ncbi/nt.00.nhi
/data/blastdb/ncbi/nt.00.nhr
/data/blastdb/ncbi/nt.00.nin
/data/blastdb/ncbi/nt.00.nnd
/data/blastdb/ncbi/nt.00.nni
/data/blastdb/ncbi/nt.00.nog
/data/blastdb/ncbi/nt.00.nsd
/data/blastdb/ncbi/nt.00.nsi
/data/blastdb/ncbi/nt.00.nsq
/data/blastdb/ncbi/nt.00.tar.gz
/data/blastdb/ncbi/nt.00.tar.gz.md5
...
/data/blastdb/ncbi/nt.13.nhd
/data/blastdb/ncbi/nt.13.nhi
/data/blastdb/ncbi/nt.13.nhr
/data/blastdb/ncbi/nt.13.nin
/data/blastdb/ncbi/nt.13.nnd
/data/blastdb/ncbi/nt.13.nni
/data/blastdb/ncbi/nt.13.nog
/data/blastdb/ncbi/nt.13.nsd
/data/blastdb/ncbi/nt.13.nsi
/data/blastdb/ncbi/nt.13.nsq
/data/blastdb/ncbi/nt.13.tar.gz
/data/blastdb/ncbi/nt.13.tar.gz.md5
/data/blastdb/ncbi/nt.nal
Note you don't need to keep the *.tar.gz and the *.md5 files
once you've verified the checksum (using md5sum to detect
any data corruption during download) and decompressed the
tar-ball.
Peter
P.S. This galaxy-users list is meant for discussion of using the
tools within Galaxy from an end user perspective. Although
there is talk about creating a new Galaxy mailing list specifically
for deployment questions like this, currently galaxy-devel is
preferred for this kind of discussion.
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