Bioinformatics Support Team Helpdesk

Before you start, if you are working on a Windows pc, download and install the Ubuntu subsystem. Instructions can be found here:

https://docs.microsoft.com/en-us/windows/wsl/install-win10

Also check if the server you are transferring data to has a specific data transfer node. At UCT, if you are using hex, transfer data using hexdata.

The basic command to transfer files from one computer to another is as follows:

rsync -vr -P -e ssh <location of files you would like to send> <destination>

An example is sending a fastq file from your computer to the cluster:

rsync -vr -P -e ssh /documents/data/reads.fq Rincewind@hexdata.uct.ac.za:/scratch/Rincewind/data/

You can send all the files in a directory by using the wildcard character " * "

rsync -vr -P -e ssh /documents/data/* Rincewind@hexdata.uct.ac.za:/scratch/Rincewind/data/

If you are copying large files, it is important to check if they are not truncated (missing the end bit). You can check by using a checksum.

Go into the directory containing your file on your computer and type:

md5sum * > checklist.chk

Then copy the checklist.chk file to the server, into the directory where you transferred your files and type this:

md5sum -c checklist.chk

This will give you a result that looks like this:

sample_1.fastq: OK

sample_2.fastq: OK

etc...

Solution provided here: (https://askubuntu.com/questions/318530/generate-md5-checksum-for-all-files-in-a-directory)