Linux and macOS
Support for checking if sequencing machine is done writing sample file to disk
If files-per-sample detection is used for analysis automation (see Definition of sample completion), the connector must be able to check if a sample file has been completely written to disk before submitting it for analysis. The ability to perform this check on Linux® and macOS® depends on the following:
- Permissions to execute check:
The check is performed using
lsof. The system user must have permissions to execute the commandsudo lsofon the filesystem where the sequencing machine outputs the sample files.On many systems, sudo privileges can be granted by editing the sudoers file using
sudo visudo, and adding a line like the one below:<username> ALL=(root) NOPASSWD: /usr/bin/lsofPlease check your OS documentation for details on how to do this on your system.
- Filesystem type:
- The use of
lsofmeans that FUSE filesystems will generally not be appropriate. - The location in which the sequencing machine outputs results must be on a locally mounted disk (i.e. not a mounted network drive, e.g. NFS or Samba/CIFS).
- The use of