ssh -X btw000@login.hpc.qmul.ac.uk
Have a look around, remember this is a Linux command line.
Apocrita has a large number of tools and software packages installed. However, because many of these tools conflict with each other you need to manually load the tools you want to use into your environment. This is done with the module command
module avail
module load R/3.2.5
~/.bash_profile
qsub my_submission_script.sh
qlogin
qlogin -l h_vmem=100G
/data/scratch/btw000
/data/home/btw000
/data/SBCS-BloggsLab
Hive
Ultimately it depends on your style of working and the space requirements of the project. Here is one suggestion on what to keep where:
For big files the best option is gzip, when it is done zipping it will append the .gz extension and delete the original filegzip data/lane1.fastq
gzip data/lane1.fastq
you can use gzipped file without uncompressing them with some programs. There are also versions of for example less (to read the file), cat (to print it to the console or concatenate with other files) and grep (searching a file). These are called zless, zcat and zgrep.zless data/lane1.fastq.gzzcat data/lane1.fastq.gz | fastx_clipper ...zgrep "search-term" data/lane1.fastq.gz
zless data/lane1.fastq.gz
zcat data/lane1.fastq.gz | fastx_clipper ...
zgrep "search-term" data/lane1.fastq.gz
To compress a directory of many small files it is better to use a tar archive instead of compressing all individual files one by one. It will create a new file which contains the directory and can automatically gzip the file if you supply the -z option to the tar program.tar -czvf my_directory.tar.gz my_directoryYou can also use zip which may be more familiar to windows userszip -r ~/archive/2012-02-21-my-analysis.zip ~/work-weekly/2012-02-21-my-analysis/
tar -czvf my_directory.tar.gz my_directory
zip -r ~/archive/2012-02-21-my-analysis.zip ~/work-weekly/2012-02-21-my-analysis/
You need to know your target (which folder or file you want your link to go to) and what name you wish to give the link.The command is $ ln -s target_name link_name
$ ln -s target_name link_name
$ ln -s /home/btw123/target_file link_file
link_file
/home/btw123/target_file
You can use "scp" top copy the files onto the server:scp my.fastq.gz btw000@login.hpc.qmul.ac.uk:~/btw000/temp/my.fastq.gz
scp
scp my.fastq.gz btw000@login.hpc.qmul.ac.uk:~/btw000/temp/my.fastq.gz
Alternatively, use a program with a graphical user interface such as CyberDuck or Filezilla.
You should see a your home directory on Apocrita and you can now drag and drop files to and from your desktop
$TMPDIR
$TMPDIR/my_file
$PATH
.bashrc
.profile