-Running the GATK with the -et NO_ET or -et STDOUT options now
requires a key issued by us. Our reasons for doing this, and the
procedure for our users to request keys, are documented here:
http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home
-A GATK user key is an email address plus a cryptographic signature
signed using our private key, all wrapped in a GZIP container.
User keys are validated using the public key we now distribute with
the GATK. Our private key is kept in a secure location.
-Keys are cryptographically secure in that valid keys definitely
came from us and keys cannot be fabricated, however keys are not
"copy-protected" in any way.
-Includes private, standalone utilities to create a new GATK user key
(GenerateGATKUserKey) and to create a new master public/private key
pair (GenerateKeyPair). Usage of these tools will be documented on
the internal wiki shortly.
-Comprehensive unit/integration tests, including tests to ensure the
continued integrity of the GATK master public/private key pair.
-Generation of new user keys and the new unit/integration tests both
require access to the GATK private key, which can only be read by
members of the group "gsagit".
Moved gsalib and queueJobReport.R to embeddable namespaced locations.
Updated packager dependencies/dir to add an @includes which filters the embedded fileset.
RScriptExecutor can now JIT compiles the gsalib.
RScriptExecutor uses ProcessController and sends the Rscript output to java's stdout when run under -l DEBUG.
Refactored ProcessController and IOUtils from Queue to Sting Utils.
Added more unit tests to ProcessController along with a utility class to hard stop OutputStreams at a specified byte count.
Replaced uses of some IOUtils with Apache Commons IO.
ShellJobRunner refactored to use direct ProcessController and now kills jobs on shutdown.
Better QGraph responsiveness on shutdown by using Object.wait() instead of Thread.sleep().
-Added targets to run unit and integration tests on the fully-packaged GATK jar,
and pipeline tests on the fully-packaged Queue jar. Once enabled in Bamboo,
these will provide greatly-enhanced protection against breakage in the binary
release.
-Unconditionally include all of the subset of org.broadinstitute.sting
included in the intermediate jars GenomeAnalysisTK.jar, StingUtils.jar,
etc. in the final, fully-packaged jar. This:
* is necessary to get tests to run on the fully-packaged jar
* decreases the chances of a class that is a runtime-only
dependency getting left out of the binary release
* only slightly increases the size of the binary release
(before: 9352465 bytes, after: 10985482 bytes)
David Roazen
Khalid Shakir
Matt Hanna
Eric Banks
Ryan Poplin