Sync User

Check to see if there is a sync user exists on the computer you are on

Assuming that the sync user was created with the name “ngssync” you can check for it as follows:

id ngssync

Outputs either:

1. User does not exist

   id: ngssync: No such user
   

2. User exists

   uid=500(ngssync) gid=500(ngssync) groups=500(ngssync)
   

   Which tells you that the user exists and the user id is 500, primary group id is 500, and a full list of all the groups that user is in. In this case ngssync is only in the one group which is also the same as the primary group(ngssync)

Create the Sync User

1. You need to be root to create a new user

   su -
   

2. Setup some useful variables for later

   sync_username="ngssync" # Change this if you want
   ngs_data_path="/path/to/your/NGSData" # Set this to your path
   

3. Then create the user account

   useradd -s /bin/bash ${sync_username}
   passwd ${sync_username}
   

4. Setup the default umask for this account so files/directories are read only

   echo "umask 0022" >> ~/.bashrc
   

Ensure your sync user has read/write/execute to your data

Check access to files

You need to make sure that your sync user has rwx access to your NGS Data Structure

$> ls -l /path/to/NGSData
dr-xr-xr-x.    8 ngssync ngssync   4096 Jul 14 11:56 RawData
drwxr-xr-x.    7 ngssync ngssync   4096 Jul  9 08:07 ReadData
drwxr-xr-x. 3667 ngssync root 286720 Sep 15 16:22 ReadsBySample

Listing format:

permissions

ignore

owner

group

size

date

directory/file

The important thing is that the ngssync is the username listed for the owner(3rd column) and that the permissions start with

drwx

So in the example above you can see that the RawData is owned by ngssync but does not have w(write) permissions which is wrong. You may think that ReadsBySample is setup incorrectly since the root group is set as the group(4th column), but that really doesn’t matter since ngssync has rwx(read/write/execute) permissions.

If you see a directory that looks incorrect you can fix it with the following command:

su -c "chown -R ngssync /path/to/directory; chmod -R u=rwX,go=rX /path/to/directory"

Requires root privileges

Be patient as this can take a really long time if you have lots of data