mirror.rst

Fetching existing sequence repositories

A public instance of seqrepo with dated snapshots is available at on dl.biocommons.org.

Fetching using the seqrepo command line tool

The easiest way to get a new seqrepo repository is with the command line tool:

$ seqrepo pull

The first invocation will download a complete repository. Subsequent invocations will pull the most recent instance, pulling only incremental sequences.

Fetching using rsync manually

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 2016-08-28

You 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 sequences

For 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.