A public instance of seqrepo with dated snapshots is available at on dl.biocommons.org.
The easiest way to get a new seqrepo repository is with the command line tool:
$ seqrepo pullThe first invocation will download a complete repository. Subsequent invocations will pull the most recent instance, pulling only incremental sequences.
You can list available snapshots like so:
$ rsync dl.biocommons.org::seqrepo
This is the rsync service for tools and data from biocommons.org
This service is hosted by Invitae (https://invitae.com/).
drwxr-xr-x 4,096 2016/08/31 01:25:54 .
dr-xr-xr-x 4,096 2016/08/28 03:25:40 2016-08-27
dr-xr-xr-x 4,096 2016/08/28 15:52:54 2016-08-28You may mirror the entire seqrepo archive or a specific snapshot, as shown below:
$ rsync -HavP dl.biocommons.org::seqrepo/2016-08-28/ /tmp/seqrepo/2016-08-28/
This is the rsync service for tools and data from biocommons.org
This service is hosted by Invitae (https://invitae.com/).
receiving incremental file list
2016-08-28/
2016-08-28/aliases.sqlite3
...If you have a previous snapshot, you should invoke rsync like this in order to hard link unchanged files:
$ rsync -HavP --link-dest=/tmp/seqrepo/2016-08-27/ dl.biocommons.org::seqrepo/2016-08-28/ /tmp/seqrepo/2016-08-28/If seqrepo is already installed, you may check the repo status with:
$ seqrepo -d /usr/local/share/seqrepo/2016-08-27 show-status
seqrepo 0.2.2
root directory: /home/reece/dl.biocommons.org/seqrepo/2016-08-27/, 7.9 GB
backends: fastadir (schema 1), seqaliasdb (schema 1)
sequences: 773494 sequences, 93002629585 residues, 188 files
aliases: 5572583 aliases, 5473096 current, 9 namespaces, 773494 sequencesFor other commands, see the command line documentation.
Note
seqrepo snapshot directories may be moved, renamed, or symlinked as needed. All paths are stored relative to the snapshot root.