New Version (1.11) is now available

[GotCloud]

A new version of gotcloud, 1.11 is now available.  

Reminder, there is also a wiki page that describes the changes in each version:

http://genome.sph.umich.edu/wiki/GotCloud:_Versions

I have copied below the information on changes for this version.

There is also a wiki page with FAQ and issues/resolutions for specific versions:

http://genome.sph.umich.edu/wiki/GotCloud:_FAQs#Version_Problems

Sorry, it looks like I missed sending notices for 1.09 & 1.10, so I have included the updates for those versions here as well.

Please let me know if you have any questions.

Mary Kate Wing

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 gotcloud beagle and gotcloud thunder commands so that beagle/thunder can be called independently rather than just through ldrefine.
• Add command-line options to gotcloud vc 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:
    • --index (or RUN_INDEX = true in the configuration file)
    • --pileup (or RUN_PILEUP = true in the configuration file)
    • --glfMultiples (or RUN_GLFMULTIPLES = true in the configuration file)
    • --vcfPileup (or RUN_VCFPILEUP = true in the configuration file)
    • --filter (or RUN_FILTER = true in the configuration file)
    • --svm (or RUN_SVM = true in the configuration file)
    • --split (or RUN_SPLIT = true 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)

Aligner

• Update gccalcstorage for better align estimates

Variant Calling

• Add additional comments to umake.pl
• Update vcf-summary to print the skipped counts
• Add option to specify the REF_FAI file used by the umake (gotcloud) script for determining CHRs and their lengths.

Aligner & Variant Calling

• Only print Configuration settings to a file if the file doesn't exist

Version 1.09a (Full Release on 8/08/2013)

Aligner

• Fix relative paths
• Upgrade to newest samtools (and add source)
• Update gcrunsummary.pl - summary stats for the run.
• Upgrade to newer Mosaik

Variant Calling

• Fix minNS filter for odd number of samples. It used to give a fraction and then would be ignored.

Aligner & Variant Calling

• Cleanup phonehome script
• Cleanup gotcloud script and add ability to run perf/audria for dev purposes.