Some words on how to work with MIB servers
Contents
Space management
Space usage
Every users should bear in mind that space management is tricky, on one hand it is hard to know how much is needed and on the other hand, it is never enough. The amount of space cannot be infinite (for the time being). However, with a good management it is possible to extend the life span of the available storage and make sure everyone can work. We distinguish 2 types of storage, the administrative storage and the working storage.
Administrative storage
The seq and home folders are administrative partitions and their access is limited. seq is where all the sequencing runs are saved. Only admins can modify the folders in this partition. Which means that only admins can save the sequencing run there. User can see all sequencing runs unless decided otherwise. In the home partition, users have access to their personal folders. These folders should not be used to store any sequencing runs or any output files related to sequencing run analysis or big files in general. Another administrative partition is tools, this folder is only meant to host tools, no data and no databases. Users can install tools via 'conda'. Please address a message to admins to install a tool which is not present on conda.
Working storage
The working storage are projects and work, these two folders are meant to store users projects files. To start working in the work partition, make a personal folder with the same name as your login name. By default, other users can see in that folder but not modify it, feel free to adjust the permissions on your folders. That personal folder will host your analyses. After running your analyses, all users are expected to clean their work space, remove any files/folders that are not useful for the future steps of analyses (intermediate files). After being done with all your analyses, delete any file/folder that is not worth keeping for publications and request a project folder to bioinfo.mib@wur.nl. For those who wants to keep intermediate output files until publication several options are available,
WUR YODA offers to have some significant amount of space for free.
- You can buy an extra hard drive of 2TB or 4TB or more
- It is also possible to rent space from many providers, WUR, amazon,...
projects partition is meant to host after publication files, the files you have to keep for 10 years and those folder should be kept clean. Make sure to compress all text files using either gzip or bzip2. Gzip is faster and more suitable for non redundant files, you can also use the multithreaded version '''pigz''' to speed up the compression. bzip2 offers a better compression level and takes a bit more time, compression can be accelerated using the multithreaded version '''pbzip2'''. Use bzip2 by default. DO NOT STORE RAW SEQUENCING FILES HERE!
Documentation
Documentation is a very important part of data management, it helps your supervisor and anyone interested in your data knowing what you have already done, what is left to do, where to find the data. Many platforms provide a wiki allowing users to document their work, here are a few options:
gitlab, this is managed by FB-IT @WUR. There is a MIB repository that could also be used jupyter notebook redmine, ask bioinfo.mib@wur.nl for questions galaxy with galaxy pages And many external ones... It is recommended to use internal tools for documentation as they are easily accessible to all and are not subject to external rules.
Databases
Bioinformatics databases can be of very significant size, therefore it is recommended to manipulate them with care. A database partition exist, admins will store database of common interest there. More specific databases can be stored in the work partition and removed afterward.
Working with sequence files
Leaving MIB
Think about tidying up
End of contract is always a tricky period for everyone because there are numerous of things to do and cleaning up your workspace on the server is yet another task that is expected from you. Before leaving all important files (publication related files) should be stored in a project folder under the projects partition. Your folder in the work partition should be left empty. Make sure all files are documented somewhere. Your home folder should also be emptied before you leave.
Student files
Student working with the server are not responsible of the files they create, their supervisors are. Supervisors are expected to assess the quality of their students work and make sure important files are saved to the correct place in the correct way. Students folders should be empty before they leave. A documentation of the student work will be much appreciated by their supervisor.
Other IT related actions to take
In addition,
- your laptop must be returned back to IT.
Docking station and adapters should be handled to admins (bioinfo.mib@wur.nl).