Go to your system’s incoming directory, e.g.:

          $ cd /home/helicos/data/incoming

Create a directory for the run under incoming and go to it. This is typically named for the date of the run. Substitute the appropriate date.

          $ mkdir 2009-07-22
          $ cd 2009-07-22

Create a midrun directory and go to it.

          $ mkdir midrun
          $ cd midrun

Invoke the download_srf command, as follows, substituting the appropriate values for the example values in the {}'. (There should not be any {}'s in the final command.) The \ at the end of each line tells LINUX that the command is being continued across multiple lines; you can combine lines and eliminate the \'s if you prefer.

          download_srf --instrument_name={e.g. heliscope4} \
               --instrument_domain_name={e.g. 10.0.1.13 or heliscope4.xxx.edu} \
               --run_integer_id={e.g. 10048} \
               --run_id={e.g. 2009-07-22} \
               --flow_cell_1 _barcode={e.g. 0226491251007} \
               --flow_cell_2_barcode={e.g. 0226491251008}
               --intermediate=1 > download.log 2>&1 &

You can use the top command to see a list of jobs running. There should be a download_srf job near the top until the job completes. You can exit top at any time by typing Q. You can also monitor the download with the ls command:

          $ ls -l
          total 2.0G
          -rw-rw-r-- 1 helicos bioinf 1.8G Jul 22 20:22 Heliscope4.2009-07-22.intermediate.srf

Copy the sample midrun config file to the midrun directory. (Since you it should be your current directory at this point you can refer to it with ".", meaning the current directory.)

          $ cp $HELICOS_ANALYSIS_HOME/sample/run.midrun.conf .

Edit the file run.midrun.conf in the working directory using a text editor as follows. Where it says

          run = 2009-09-04

change the date to the name you used for the run folder. If you need to change the channels list to fewer than all of the channels, you can do that as well. E.g., you could do 1:3-5,7,9-15,2:1-4,6,18. This would analyze flow cell 1 channels 3,4,5,7,9,10,11,12,13,14,15, as well as flow cell 2 channels 1,2,3,4,6,18. The sample conf file specifies that the output should be written to the current directory, so output directories created by the pipeline will be placed directly in the current directory. You can change that to another path if you want them to be placed in a subdirectory, or somewhere else entirely.

Enter this command to run the midrun pipeline. You may be able to cut & paste it.

          pypeline -p midrun -c run.midrun.conf -j 4

The -j value should be chosen as described in Section 4.4, “Parallel Processing”.