### Support - Frequently Asked Questions

Running jobs on deva in the queue

The CBRG servers use the GridEngine batch-queuing system for distributed resource management. If you intend to running any jobs using NGS data, or any other long running job, you should submit your job to the queue.

In brief, to submit a job you need to use a shell script. First copy the default script to the directory from which you want to run the job:
cp /package/cbrg/templates/qsub.sh .

Edit this file:

• add in the command you want to run

To submit your job to the queue type:
qsub qsub.sh

To see the status of the queue, type:
qstat

Click for a full explanation of how to run jobs in the queue (pdf).

How do I load applications to use in my account? [using the module utility...]

Many common programs are pre-loaded in deva but some need to be loaded before you use them. You can use the module utility to do this.

module is a utility, which is used to manage the working environment in preparation for running applications. By loading the module for a certain installed application, the environment variables that are relevant for that application are automatically defined or modified.

Display the modules available on CBRG by typing:
module avail

You should see (something like) the following:

module add module-name
For example...
module add bowtie

The above command will load the default version of an application. To load a particular version of an application use:
module add module-name/version
For example...
module add bowtie2/2.0.0

Modules that are already loaded by users can be displayed with the command:
module list

A module can be "unloaded" with the commands: unload or rm, for example:
module unload bowtie
module rm bowtie

You can display the help for module by typing:
module help
You should see the following:

If you have any queries on how to use this utility please email genmail.

Share data externally

Option 1. - OxFile
OxFile is an easy way for members of Oxford University to share files with other members, and with people outside the University. Individual files up to 25Gb in size may be uploaded and kept on OxFile for up to 30 days.
OxFile can be found at: https://oxfile.ox.ac.uk/oxfile/

Option 2. - public space at CBRG
We have public directories that are available on the web, so any file placed in:
/public/username/
...will be available online, at: http://userweb.molbiol.ox.ac.uk/public/username/

For example, if the user, "manager" wanted to share a file called example.txt, it could be placed on the system at:
/public/manager/example.txt
...and be available online at:
http://userweb.molbiol.ox.ac.uk/public/manager/example.txt

Important - rather than copying files into the public directory, we generally recommend making symbolic links to avoid duplicating the file contents. This is particularly useful for large files, such as BAM and BigWig files, when used to display tracks in the UCSC genome browser

Public directories are not made automatically when your account is created - if you need access to a public directory, please email CBRG to request the creation of a public directory for your account.

We do not have directory indexing enabled so you cannot automatically see a list of available files on the web. If you want people to be able to download multiple files they will need a list of them all, perhaps as an extra file in your public space.

Data quota

To find information concerning your quota, type
getquota.

You should see something resembling:

       user/group     ||           size          ||    chunk files
name     |  id  ||    used    |    hard    ||  used   |  hard
--------------|------||------------|------------||---------|---------
jbsmith|  0001||   1.69 TiB |   3.00 TiB ||     8268| 31876689


The key information is contained in the middle two columns - this indicates a 3TB total quota, of which the user has so far used 1.69TB.

iGenomes - a collection of reference sequences and annotation files for commonly analyzed organisms

iGenomes is a collection of reference sequences and annotation files for commonly analyzed organisms. The files were originally generated by Illumina

The files have been downloaded from Ensembl, NCBI, or UCSC, and chromosome names have been changed to be simple and consistent with their download source.

On the CBRG servers these files can be found at:
/databank/igenomes/

The Ensembl and UCSC annotation and sequence files for the following organisms are available under these directories:

 Human /databank/igenomes/Homo_sapiens/ Mouse /databank/igenomes/Mus_musculus/ Rat /databank/igenomes/Rattus_norvegicus/ Zebrafish /databank/igenomes/Danio_rerio/ Drosophila /databank/igenomes/Drosophila_melanogaster/ Chicken /databank/igenomes/Gallus_gallus/ Pig /databank/igenomes/Sus_scrofa/ Chimpanzee /databank/igenomes/Pan_troglodytes/

In these directories you will find sub-directories for Ensembl and UCSC annotation and sequence for different builds, for example
/databank/igenomes/Homo_sapiens/UCSC/hg19/Annotation
/databank/igenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa

Indices for Bowtie, Bowtie2 & BWA, and fastq format files of sequence are all in the Sequence directory:
/databank/igenomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index
/databank/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex
/databank/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex

Annotation files eg gtf files can be found in the Annotation directory:
/databank/igenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf

If you have any queries on how to use this utility please email genmail

BaseSpace - How do I get my files from my BaseSpace account to my CBRG account?

Using BaseMount it is possible to mount your BaseSpace account on the CBRG file system. You can find full details how to do this at the BaseSpace HelpCenter.

The BaseMount application is installed on the CBRG servers so watch the tutorial videos from Step 3. First Time Launch and onwards or go straight to Mounting Your BaseSpace Account on the same page.

Once mounted, you can copy the files you want to the directory of your choice. Since you only have 1TB space in BaseSpace available, it is recommended you do this after each run to free up space otherwise you may be charged for excessive BaseSpace usage.

The Gene Expression Omnibus (GEO) is a public functional genomics data repository supporting MIAME-compliant data submissions.

Click for illustrated instructions on how to download fastq format data from GEO (pdf) using a GEO accession code.

Unix Commands

Unix is a command line environment, which means that primarily you have to enter commands on the keyboard instead of using point-and-click mouse.

Unix will only do something if you tell it to by giving it a command.

The basic structure of a Unix command is:

command [options...] [arguments...]
What are Unix options (flags)

options (also called flags) are generally single characters which in some way modify the action of the command. There may be no options or there may be several acting on the same command.

Options are preceded by a hyphen character ( - ) but there is no consistent rule among Unix commands as to how options should be grouped. Some commands allow a list of options with just a single hyphen at the beginning of the list (e.g. -apfg). Other commands require that each option is introduced by its own hyphen (e.g. -a -p -f -g)

Some options allow a value, often a filename, to be given following the option. Again, there is no consistent manner in which this is allowed, with some options requiring the value to be placed immediately following the option letter, while others expecting a space between the option letter and the value.

Unix is case-sensitive throughout. The exact combination of upper and lower case letters used in a command, option or filename is important.
For example, the options -p and -P in the same command will have different meanings.

How do I know what command to use

There are a few core Unix commands that are used routinely - after a while you find that these come as second nature and you no longer have to think "What's the command for that?". These common commands involve moving around your account, creating, copying and deleting files and directories. It is a good idea for the novice Unix user to keep a list of common commands at hand until you have learnt them.

How do I find out what a command does

There are man pages associated with (almost) every Unix command (man stands for manual)

To read a man page simply type man command e.g. to learn about the Unix command "ls", we could type:
man ls

This will bring up all sorts of information associated with that command. Much of it may not be of any interest to you but it will tell you what the command does, what flags are available and will give an example (ususally near the bottom)

If you find that the man pages scroll up so you cannot read them then remember to use the pipe symbol ("|") and "pipe through less" - this will allow you to scroll with the up-down arrows keys e.g.
man ls | less

Saving time on the command line

There are many tricks to saving time on the command line and cutting down the number of keystrokes. Here are just a few.

#### Moving around:

 cd move to home directory cd .. move up one directory cd ../.. move up two directories cd - move back to the directory I was just in cd ../another_dir move up one directory and then down to another_dir cd ~/another_dir move to home directory and the down to another_dir

#### Use the Tab button to fill in filenames

When typing on the command line you can use the keyboard tab button to fill in the rest of a filename for you. Examples:

1. If I had a file called humamph1.tfa and I had no other file beginning with "hum" in the directory I am in presently, I can type:
less hum
and then press the tab button. As there are no other files beginning with "hum" the machine knows the name of the rest of the filename and fills it in... giving me:
less humamph1.tfa
2. If I have two files called humamph1.tfa and humamph2.tfa. If I type:
less hum
and press the tab button, the machine will fill in up to the point that it knows e.g.
less humamph
It then stops because it does not know whether I want 1 or 2.
If I then type 2 and press tab again it will finish off the file name for me....
less humamph2.tfa
Files and Filenames

Unix does not understand spaces, dots or slashes in filenames! If you have filenames with spaces in them, then you are advised to change the name of the file to something without spaces. To do this, you need to use the mv command, and surround your filename containing spaces with quotation marks. e.g.

mv "a filename with spaces" a_filename_without_spaces

These files are usually special files and are hidden, i.e. they are not listed when you use the ls command. To see hidden files in your directory use the -a flag with the ls command (ls -a). These files are usually important and it is a good idea to leave these files alone unless you are sure of what you are doing. If you have any doubt please contact CBRG before editing or deleting any of these dot files. Examples of dot files include:

• .forward
• .profile
• .procmailrc
• .gaprc

#### Paths and Pathnames

You can imagine a Unix machine as a large file folder containing other folders and documents. Analogous to real filing systems, these folders can contain both documents and other folders. The Unix word for folder is "directory" and the term for document is "file".

A diagram of they way files are stored on a Unix system looks like a tree. The bottom of the tree is called root and is represented by a forward slash (/)

For the machine to be able to find different documents (files) or directories (file folders), it sometimes has to be told explicitly where they are with reference to the bottom of the tree. i.e. root.

So, for example, the full path to the directory called "sue" is

/    usr     users    user1    sue

That is, first you start at root (/), then go through the directory usr, then the directory users, then the directory user1, and then you find the directory sue.

Unix doesn't like spaces though, so to describe this full path on a Unix machine, you separate each term with a forward slash (/). So, the full path to "sue" becomes:
/usr/users/user1/sue

If you don't know the full path to where you are in your account, just type pwd (Present Working Directory) on the command line. This returns the full path to the directory from which you typed the command.

#### What's inside a file? How do I see it?

There are various ways to view a text file. To view the file contents page by page, use the command less e.g.
less filename.txt

To view graphical files, except for postscript files, try using the command display e.g.
display file.jpeg

To view a postscript file, try the command ghostview e.g.
ghostview filename.ps

#### Removing files

To remove a file, you need to use the rm (Remove) command. For example:
rm filename

You will then be prompted to see if you really want to delete this file.

To delete a number of files that all have something in common, you can employ "wildcards". For example, to delete all files that end in the letters "seq", you could type:
rm *seq

You will then be prompted for each file individually to see if you really want to delete it.

If you have a large number of files to delete, and you are SURE you want to delete them, you can use a backslash before the rm command. This removes the safety feature of being prompted about each file to be deleted (be careful using this option!!). e.g.
\rm *seq

#### Removing directories

If you wish to remove a directory that contains no files in it, you can use the rmdir command e.g.
rmdir directoryname

If you wish to remove a directory containing files, and remove all files within that directory, you must use the -rf flag with the rm command e.g.
rm -rf directoryname

You will then be presented with the name of each file inside the directory, and asked to confirm you wish to delete it.

This can be quite tedious. So if you are really SURE you wish to delete this directory and its contents, you can forgo this safetly mechanism by preceding the command with a backslash (be VERY careful using this option!!). e.g.
\rm -rf directoryname

#### Renaming files and directories

This is done using the command mv (Move):
mv old_filename new_filename
mv old_directoryname new_directoryname

If the file called "new_filename" already exists, you will be asked whether you really want to overwrite it.

#### Editing text files

If you need to edit a text file, there are a number of text editors on our system. A user friendly, GraphicalUserInterface-based editor is nedit. Type:
nedit
...and type some text in the window that appears. You can cut and paste this text and you can save it in whichever folder you like (under your account space) by using the save as option from the file drop down menu.

This editor also lets you open any other plain text files for editing. It does not open word documents, as these are full of binary code. We also have other text editors, such as pico (simple GUI with commands), vi (entirly command line driven), and xemacs (probably best left to programmers).