Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
(howto) Test your Queue installation
Test that Queue is correctly installed, and that the supporting tools like Java are in your path.
- Basic familiarity with the command-line environment
- Understand what is a PATH variable
- GATK installed
- Queue downloaded and placed on path
- Invoke the Queue usage/help message
1. Invoke the Queue usage/help message
The command we're going to run is a very simple command that asks Queue to print out a list of available command-line arguments and options. It is so simple that it will ALWAYS work if your Queue package is installed correctly.
Note that this command is also helpful when you're trying to remember something like the right spelling or short name for an argument and for whatever reason you don't have access to the web-based documentation.
Type the following command:
java -jar <path to Queue.jar> --help
<path to Queue.jar> bit with the path you have set up in your command-line environment.
You should see usage output similar to the following:
usage: java -jar Queue.jar -S <script> [-jobPrefix <job_name_prefix>] [-jobQueue <job_queue>] [-jobProject <job_project>] [-jobSGDir <job_scatter_gather_directory>] [-memLimit <default_memory_limit>] [-runDir <run_directory>] [-tempDir <temp_directory>] [-emailHost <emailSmtpHost>] [-emailPort <emailSmtpPort>] [-emailTLS] [-emailSSL] [-emailUser <emailUsername>] [-emailPass <emailPassword>] [-emailPassFile <emailPasswordFile>] [-bsub] [-run] [-dot <dot_graph>] [-expandedDot <expanded_dot_graph>] [-startFromScratch] [-status] [-statusFrom <status_email_from>] [-statusTo <status_email_to>] [-keepIntermediates] [-retry <retry_failed>] [-l <logging_level>] [-log <log_to_file>] [-quiet] [-debug] [-h] -S,--script <script> QScript scala file -jobPrefix,--job_name_prefix <job_name_prefix> Default name prefix for compute farm jobs. -jobQueue,--job_queue <job_queue> Default queue for compute farm jobs. -jobProject,--job_project <job_project> Default project for compute farm jobs. -jobSGDir,--job_scatter_gather_directory <job_scatter_gather_directory> Default directory to place scatter gather output for compute farm jobs. -memLimit,--default_memory_limit <default_memory_limit> Default memory limit for jobs, in gigabytes. -runDir,--run_directory <run_directory> Root directory to run functions from. -tempDir,--temp_directory <temp_directory> Temp directory to pass to functions. -emailHost,--emailSmtpHost <emailSmtpHost> Email SMTP host. Defaults to localhost. -emailPort,--emailSmtpPort <emailSmtpPort> Email SMTP port. Defaults to 465 for ssl, otherwise 25. -emailTLS,--emailUseTLS Email should use TLS. Defaults to false. -emailSSL,--emailUseSSL Email should use SSL. Defaults to false. -emailUser,--emailUsername <emailUsername> Email SMTP username. Defaults to none. -emailPass,--emailPassword <emailPassword> Email SMTP password. Defaults to none. Not secure! See emailPassFile. -emailPassFile,--emailPasswordFile <emailPasswordFile> Email SMTP password file. Defaults to none. -bsub,--bsub_all_jobs Use bsub to submit jobs -run,--run_scripts Run QScripts. Without this flag set only performs a dry run. -dot,--dot_graph <dot_graph> Outputs the queue graph to a .dot file. See: http://en.wikipedia.org/wiki/DOT_language -expandedDot,--expanded_dot_graph <expanded_dot_graph> Outputs the queue graph of scatter gather to a .dot file. Otherwise overwrites the dot_graph -startFromScratch,--start_from_scratch Runs all command line functions even if the outputs were previously output successfully. -status,--status Get status of jobs for the qscript -statusFrom,--status_email_from <status_email_from> Email address to send emails from upon completion or on error. -statusTo,--status_email_to <status_email_to> Email address to send emails to upon completion or on error. -keepIntermediates,--keep_intermediate_outputs After a successful run keep the outputs of any Function marked as intermediate. -retry,--retry_failed <retry_failed> Retry the specified number of times after a command fails. Defaults to no retries. -l,--logging_level <logging_level> Set the minimum level of logging, i.e. setting INFO get's you INFO up to FATAL, setting ERROR gets you ERROR and FATAL level logging. -log,--log_to_file <log_to_file> Set the logging location -quiet,--quiet_output_mode Set the logging to quiet mode, no output to stdout -debug,--debug_mode Set the logging file string to include a lot of debugging information (SLOW!) -h,--help Generate this help message
If you see this message, your Queue installation is ok. You're good to go! If you don't see this message, and instead get an error message, proceed to the next section on troubleshooting.
Let's try to figure out what's not working.
First, make sure that your Java version is at least 1.6, by typing the following command:
You should see something similar to the following text:
java version "1.6.0_12" Java(TM) SE Runtime Environment (build 1.6.0_12-b04) Java HotSpot(TM) 64-Bit Server VM (build 11.2-b01, mixed mode)
If the version is less then 1.6, install the newest version of Java onto the system. If you instead see something like
java: Command not found
make sure that java is installed on your machine, and that your PATH variable contains the path to the java executables.
On a Mac running OS X 10.5+, you may need to run /Applications/Utilities/Java Preferences.app and drag Java SE 6 to the top to make your machine run version 1.6, even if it has been installed.