3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems|FAQ: Version Problems]]
For information on issues/resolutions for specific versions, see: [[GotCloud:_FAQs#Version_Problems|FAQ: Version Problems]]
== Version 1.11 (Full Release on 9/6/2013) ==
'''Aligner'''
* Remove an extra space from the Makefile for the dedup command.
* Brought in latest bwa source, but it is not yet being used.
'''Variant Calling'''
* Rename OUT_PREFIX to MAKE_BASE_NAME to specify the base filename for snpcall, ldrefine (beagle & thunder), & vc Makefiles. The typeOfRun.Makefile is appended to MAKE_BASE_NAME.
** These Makefiles all used to have the same name and would overwrite each other
** --makebasename/--make_basename/--make_base_name can be specified on the command-line
** Default value for MAKE_BASE_NAME is umake
*** snpcall is now: $(MAKE_BASE_NAME).snpcall.Makefile (default umake.snpcall.Makefile)
*** ldrefine beagle step is now: $(MAKE_BASE_NAME).beagle.Makefile (default umake.beagle.Makefile)
*** ldrefine thunder step is now: $(MAKE_BASE_NAME).thunder.Makefile (default umake.thunder.Makefile)
*** vc is now: $(MAKE_BASE_NAME).vc.Makefile (default umake.vc.Makefile)
* Added <code>gotcloud beagle</code> and <code>gotcloud thunder</code> commands so that beagle/thunder can be called independently rather than just through <code>ldrefine</code>.
* Add command-line options to <code>gotcloud vc</code> for running just certain steps rather than having to set RUN...=true in the configuration
** More than one --commandToRun can be specified at once
** New commands-line options:
*** <code>--index</code> (or <code>RUN_INDEX = true</code> in the configuration file)
*** <code>--pileup</code> (or <code>RUN_PILEUP = true</code> in the configuration file)
*** <code>--glfMultiples</code> (or <code>RUN_GLFMULTIPLES = true</code> in the configuration file)
*** <code>--vcfPileup</code> (or <code>RUN_VCFPILEUP = true</code> in the configuration file)
*** <code>--filter</code> (or <code>RUN_FILTER = true</code> in the configuration file)
*** <code>--svm</code> (or <code>RUN_SVM = true</code> in the configuration file)
*** <code>--split</code> (or <code>RUN_SPLIT = true</code> in the configuration file)
* Cleaned up the snpcall Makefile entries for pileup. It used to print targets/commands that were never executed. These unused targets have now been removed
'''Aligner & Variant Calling'''
* Remove trailing spaces from configuration values
* Add MAKE_OPTS configuration value that allows users to add Makefile options to the make calls that run the pipelines.
* Update gccalcstorage for better estimates and to have option to print estimates from a starting size rather than from actually input files
== Version 1.10 (Full Release on 8/22/2013) ==
== Version 1.10 (Full Release on 8/22/2013) ==
