My notes...
awk: one line codes for fasta files
snpEff: Genetic variant annotation and functional effect prediction toolbox.
SOAPdenovo2: It is a very fast tool
- GNU documentation tree
- AWK Getting Started with awk, a complete guide
- AWK power for your command line. a short summary
- AWK GTF! How to Analyze a Transcriptome Like a Pro...
I suggest to use JupyterLab instead of PyCharm. Jupyter Notebook configuration for the virtual environments. ipython
jupyter_lab on graham.computecanada
There are several package managers such as pip, homebrew, apt-get, CRAN, CPAN and Bioconductor. Conda is a combination of other package managers. Bioconda is a channel for bioinformatics tools found in conda. Biopython can be installed via conda.
Bioconda compose of a collection of bioinformatics tools which can be installed easily.
Configure the local computer not to use password when connecting to graham.
Type ssh_keygen to the terminal. This will ask a name for the rsa key-pair. I am going to give it a name rsa_key.
This will produce a rsa key file called rsa_key on the working directory. One can move this key-pair to the ~/.ssh folder.
Now configure and resolve to access graham without password.
eval 'ssh-agent'
ssh-add ~/.ssh/rsa_key
Note that it is important to add the key file name after ssh-add command. Now we can log in cluster by typing
ssh -i ~/.ssh/rsa_key username@graham.computecanada The first time of login it will ask passphrase which is the password but it won't ask a password for later logins. Adding an alias to the ~/.bash_profile file is also handy so that we can log in to clusters by just typing graham.
nano ~/.bash_profile
#add the following line to the end of the file
alias graham="ssh -i ~/.ssh/rsa_key username@graham.computecanada.ca"
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