Running and Verifying PASA

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to add the GMAP environment variable:

   export PATH=/path/to/GMAP/Install/bin:$PATH

3. Run the following commands to modify the configuration file:
   1. Open the configuration file.

      cp /path/to/PASA/PASApipeline-pasa-v2.4.1/pasa_conf/pasa.CONFIG.template /path/to/PASA/PASApipeline-pasa-v2.4.1/pasa_conf/conf.txt
      vim /path/to/PASA/PASApipeline-pasa-v2.4.1/pasa_conf/conf.txt

   2. Press i to enter the insert mode and modify the file as follows:

      MYSQLSERVER=localhost
      MYSQL_RO_USER=test
      MYSQL_RO_PASSWORD=123456
      MYSQL_RW_USER=pasa
      MYSQL_RW_PASSWORD=123456

   3. Press Esc, type :wq!, and press Enter to save the file and exit.
4. Run the following command to go to the directory where the test case is stored:

   cd /path/to/PASA/PASApipeline-pasa-v2.4.1/sample_data

5. Run the following commands to modify the configuration file:

   cp /path/to/PASA/PASApipeline-pasa-v2.4.1/pasa_conf/pasa.alignAssembly.Template.txt alignAssembly.config
   vi alignAssembly.config
   DATABASE=sample_data

   Enter :wq! to save the change and exit.

6. Run the following commands to run the test case:

   gzip -d genome_sample.fasta.gz
   { time Launch_PASA_pipeline.pl -c  alignAssembly.config -C -R -g genome_sample.fasta -t all_transcripts.fasta.clean -T -u all_transcripts.fasta -f FL_accs.txt --ALIGNERS blat,gmap --CPU 96; } 2>&1 |tee PASA.log

   View the PASA.log file. If Finished is recorded in the log file, the PASA process ends properly.

   Figure 1 shows an example of the running result.

   Figure 1 Result example