System dependancies:
To install graphviz follow package manager on your unix/linux system.
In Ubuntu, do this on a linux terminal as root user, if you are not super user, ask your system admin to install it.
sudo apt-get install graphviz
In Red Hat flavor linux such as CentOs:
sudo yum install graphviz
Note: Make sure the pip and virtualenv packages are installed on your system.
which pip
which virtualenv
If not installed,
curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
python get-pip.py --user
Then, if there is no virtualenv package
pip install virtualenv
To install puticr, run this command in your terminal:
git clone https://github.com/demis001/puticr.git ; cd puticr ; make install
This is the preferred method to install puticr, as it will always install the most recent stable release.
Download test data from this site https://www.ddjima.com/software/ and extract the result in the same directory. The directory contains an example fastq files and indexed genome and test data.
wget https://ddjima.com/wp-content/uploads/2019/02/testData.zip
To extract …
unzip testData.zip
The application has to run in Python virtual envirnoment. First, activate the virtual environment to use the application after installation.
source puticr/bin/activate
Then, run the following line to test the application … This is also the way to run germ layer tissue samples (50% methylation)
puticr_cli -o outdir2 -f testData/raw -l 6 -c 12 -L 0.3 -U 0.7 --indexed=no --refGenome=hs_chr6.fa --refGenomeDir=testData/genome2/
To index your own reference genome and run your own data, create the directory to hold the reference genome, merge all chromosome and store your genome as a single fasta file. Example, mm10.fa, hs.fa etc.
Then do this, indexed=yes telling the application to index before it uses it. Assumming you saved mm10.fa genome under mm10ref directory…
puticr_cli -o outdir2 -f testData/raw -l 6 -c 12 -L 0.3 -U 0.7 --indexed=yes --refGenome=mm10.fa --refGenomeDir=YOURPATH/mm10ref/
To run gamet cells samples (oocytes and sperm) that expected (100% methylation call). We haven’t provided the oocytes and sperm test data. The files are similar to the test data provided. Please rename the files as oocyte.*.fastq.gz and sperm.*.fastq.gz in its separate directory.
puticr_cli -o outdir2 -f testData/raw -l 6 -c 12 -L 0.8 -U 1.0 --indexed=no --refGenome=hs_chr6.fa --refGenomeDir=testData/genome2/
Note: The Germ layer tisse samples and the gamet cells samples must be called separetlly.
Once you have installed the document, don’t forget to activate before each use.
source puticr/bin/activate
To deactivate virtual envirnoment. Type the following command on Linux commmand line
deactivate
This will exit the virtual envirnoment