= Transferring data =
----

Before anything read first about the storage and login. We will assume you are logged in potato.wurnet.nl server.

== Copy programs to use ==

This machine support several software to copy files but for users only 3 are recommended (rsync, scp, cp).

'''''Rsync''''' and '''''scp''''' can both be used by users to copy their data from a distant machine or from one partition to another one.

'''''Rsync''''' program is more versatile and has the ability to only copy files that are different or missing.

On the server itself the command '''''cp''''' can be used to copy files and folders.

The definition of those command is always the same:
cmd [options] source destination

== Data to analyze ==

Let's assume the following username '''''alberto''''' tries to copy sequenced data from micro4 server to this server to run an assembly.

We also assume that on '''''micro4''''' server files are located in /home/alberto/all_my_data/illumina/sample_1/

First create a folder for your run in the '''''/work''''' partition.

For example:

{{{#!highlight bash
mkdir -p /work/alberto/assembly #Folder for data and results
mkdir /work/alberto/assembly/raw_data #Folder where to send your raw data
}}}

The data can now be copied with the following command:

To copy only files do:

{{{#!highlight bash
rsync -avztP alberto@micro4:/home/alberto/all_my_data/illumina/sample_1/sample_1_R1.fastq.gz /work/alberto/assembly/raw_data/
}}}

To copy entre folder do (please notice that the trailing / in the source folder path has been removed):

{{{#!highlight bash
rsync -avztrP alberto@micro4:/home/alberto/all_my_data/illumina/sample_1 /work/alberto/assembly/raw_data/
}}}

You are now to run you analyses.

== Raw sequencing data ==

Data coming from sequencing company or machine (so called raw data) should be placed in a specific place '''''/seq/sequencing_runs'''''.
Only admins can/should add this data to avoid wrong manipulation of the data.
Please contact the local admin, felix.homa@wur.nl

This rule also applies to data received from collaborators, stored in '''''/seq/collaborators_seqs/'''''.

== WARNINGS ==

{{{#!wiki caution
'''Clean your data'''
To make sure the servers are running fine for everybody, take the habit of moving your data to a more appropriate place.
/work partition should only be reserved for running data.
}}}