CIPRES Perl Demo

This is a perl script that shows how to use the CIPRES REST API to submit jobs and retrieve results.

1. The demo requires libwww-perl. Please make sure it's installed.
2. If you're reading this on your computer, you have probably already downloaded the demo code and documentation, but if not, get it now by following the instructions in the Sample Code section of the User Guide. Once you've retrieved all the examples, you'll find this perl example in the "perl_demo" directory.
3. Put your username, password, application name and application ID in the supplied pycipres.conf file.
4. Copy pycipres.conf to your home directory. (Alternatively, put pycipres.conf anywhere you want and set the environment variable PYCIPRES to the full, absolute pathname of the file).

Windows:

The demo runs on windows under Cygwin. If using Windows, install Cygwin. Run the appropriate installer, and choose the packages to install. The package that this demo uses is called LWP (Library for WWW in Perl). Thus, you should make sure that along with all the other Perl packages (which are necesary for compilation and execution of Perl scripts), these three LWP packages are installed as well: perl-LWP: Perl WWW Modules, perl-LWP-Media Types: MME type detection module for Perl, and perl-LWP-Protocol-https: :UserAgent.

Mac:

You may encounter difficulties with certificate authority validation. To fix this, you can use the LWP library version 6.00 or above. Or look into Net::SSL and how to set the environment variables HTTPS_CA_DIR and HTPPS_CA_FILE. Otherwise, you can take the simple but insecure route that we have used in the demo by putting the following bit of code: $browser->ssl_opts(verify_hostname => 0); prior to the code that sets the user's credentials: $browser->credentials(..)

Linux:

Use apt-get or cpan to install libwww-perl if it isn't already installed.

Go to the "Code" directory containing "cipres_perl.pl" and run "perl cipres_perl.pl"

The output should look like:

Now checking the directory /Users/anthony/cipres_data/sdk_versions/testdata/pycipres.conf for pycipres.conf 
Now checking the directory /Users/anthony/pycipres.conf for pycipres.conf 
Now checking the directory  for pycipres.conf 
Hostname: www.phylo.org
What would you like to do? Valid commands are: 
List Jobs (LJ); Submit Job (S); Delete Job (D); List Results (LR); 
Download Results (DR); Get Tools (GT); Exit (E) 
		

• List Jobs (LJ): List all jobs you have submitted (minus those you've deleted) along with their status information.
• Submit Job(S): Builds and submits a job. You will first be prompted to enter the name of the tool, the input file, etc. An example for the Submit Job (SJ) command can be found here.
• Delete Job (D): Deletes a specified job whether completed or not. Some example output is here.
• List Results (LR): Shows results for a specific job. Some example output is here.
• Download Results (DR): Downloads a result file from a specific job. Some example output is here.
• Get Tools (GT): Retrieves a list of the tools that can be run and stores the list in a file in the current directory. Some example output is:
• here.
• Exit(E) will simply exit the program normally. Otherwise the user can use Ctrl+C or Ctrl+D.