1. Example Data Set
a. Create a directory - dapars - in your home directory and change to that directory
mkdir dapars
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
unzip DaPars_Test_Dataset.zip
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;
Output_directory=results
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;
./daparscripted.sh
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.