GotCloud: Versions

For information on installing the releases, see: Install GotCloud Software

Version 1.06 (Full Release on 4/17/2013)

Variant Calling

• Update to always require REF
  • this fixes bug that ldrefine was not checking REF or adding the optional prefix to it.

Version 1.05 (Full Release on 4/17/2013)

Aligner & Variant Calling'

• Cleanup handling of BASE_PREFIX & added REF_PREFIX.
  • Allows user to specify --base_prefix or --baseprefix on command-line
  • Now used for index files & reference files in addition to fastqs (aligner) and bams (variant calling)

Version 1.04 (Full Release on 4/16/2013)

Aligner & Variant Calling

• Update relative paths to be relative to the current working directory
  • Aligner effects:
    • INDEX_FILE as specified in the aligner configuration
    • fastq paths specified in the INDEX_FILE
  • Variant Calling effects:
  • BAM_INDEX as specified in the configuration
  • bam paths specified in the BAM_INDEX
• Add getAbsPath() method for determining the absolute path with the additional capability of prepending an optional PREFIX (as specified in configuration) to the directory:
  • BASE_PREFIX
  • FASTQ_PREFIX (for aligner reading the fastq index file)
    • renamed from FASTQ/FASTQ_REF
  • BAM_PREFIX (for variant calling reading bam index file)
• Improve Error detection
  • With --test option, check that the testdir exists before running the test

Cluster Support

• Update the mosix option to run mosbatch instead of mosrun
• Only attempt to "fix" the CWD for mosix/mosbatch
  • Remove the warning if this "fix" fails
  • This "fix" is specific for running at UM, but should not cause a failure when running elsewhere

Includes all updates from previous Internal Only Releases.

Version 1.03a6 (Internal Only Release on 4/10/2013)

• Cleanup the cluster support code
  • Also add support for fixing the problem with UMich directories when using Mosix
• Update the default Reference directory to be as expected for UM
• Variant Calling changes:
  • SVM
    • Add option to merge all chromosome sites prior to running SVM (to better support targeted sequencing)
  • Cleanup some of the Makefile dependencies to depend on files rather than phony targets (this prevents it from always rerunning those steps)

Version 1.03a5 (Internal Only Release on 4/5/2013)

• Add pre-checks for required files & reference files prior to running
• Add checks for deprecated configuration settings
• Merge aligner & variant calling default configurations into a single file (bin/gotcloudDefaults.conf)
• Aligner
  • Update to put actual values into the Makefile recipes rather than using variables
• Variant Calling
  • Fix vcf-summary to handle chromosomes that have string names (like X,Y)

Version 1.03a4 (Internal Only Release on 4/2/2013)

• Variant Calling:
  • Update to by default run as local
  • Target Loci file updates:
    • When WRITE_TARGET_LOCI is set to true: only generate the .loci file if the specified bed is newer than the loci file
    • When WRITE_TARGET_LOCI is set to ALWAYS, generate the .loci file regardless of the timestamps
  • Only create the glf index file for a region if it does not exist or is older than the bam index file

Version 1.03a3 (Internal Only Release on 3/29/2013)

• Attempted to Fix bug that it wasn't properly running batching
  • This version was not good (fixed in 1.034a.

Version 1.03a2 (Internal Only Release on 3/27/2013)

• Add the qplot source code

Version 1.03a1 (Internal Only Release on 3/26/2013)

• Variant Calling
  • Add FILTER_MIN_NS to add the option of filtering based on the number of samples
  • Add FILTER_ADDITIONAL to add the option of adding additional filters.

Version 1.03a (Full Release on 3/22/2913)

• Cleanup README & INSTALL instructions
• Variant Calling
  • Fix dependency bug/error in SVM
  • Fix commands that run locally to check for pipe failures
  • Improve file open error detection in SVM logic
• Add option to obtain the version number

Version 1.03 (Full Release on 3/15/2013)

• Add SVM Filtering
  • there was a bug in this, please do not use this version.
  • Version 1.03a fixes this bug.

Version 1.02 (Full Release on 3/13/2013)

• Cleanup cluster scripts
• Rename alinger to align.pl & umake to snp
• Add VerifyBamID source
• MANY Updates, please use a newer version.