1. Example Data Set
a. Create a directory - dapars - in your home directory and change to that directory
b. Copy the test dataset folder to your dapars folder
cp /usr/local/bioinf/dapars/DaPars_Test_Dataset.zip dapars
c. Change directory to your dapars folder and make sure you have the .zip file
cd dapars ls
d. Unzip the test directory folder
e. Change directory to the unzipped folder - DaPars_Test_Dataset and look what we have there
cd DaPars_Test_Dataset ls
2. DaPars Configuration
DaPars requires a configuration file to run. The configuration file has everything DaPars need. DaPars needs two sample files (RNA-Seq alignment data and the gene model). Look at the contents of the wig files, UTR file, refseq id file, gene bed file.
a. Open the “DaPars_test_data_configure.txt” in text editor, set the output directory line like below;
3. Run DaPars
...using the below command;
python /usr/local/bin/DaPars_main.py DaPars_test_data_configure.txt
4. Scripting the run
Lets write a script to automate steps 1 to 8.
a. Open the text editor from Applications, Accessories, gedit or pluma
b. Turn on the highlight mode, by choosing; View - Highlight mode - sh
c. Type the below commands (these are the ones that you typed from 1 to 3 above);
mkdir daparscripted cp /usr/local/bioinf/dapars/DaPars_Test_Dataset.zip daparscripted cd daparscripted unzip DaPars_Test_Dataset.zip cd DaPars_Test_Dataset mv DaPars_Test_data DaPars_Test_data_old #this line is a comment about the below line - the below line runs dapars python /usr/local/bin/DaPars_main.py DaPars_test_data_configure.txt echo "Congratulations on creating and successfully running your script/program/software"
d. Save the file, with the name ‘daparscripted’
e. In the terminal, navigate to the folder where you save the script and run the script with the following command;
f. Make the script executable, using the below command;
chmod 755 daparscripted.sh ls -lh
g. Now run the script as done in #4e above and see if your script worked.