GotCloud: Versions

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

Version 1.08 (Full Release on 7/31/2013)

Aligner

• no aligner only changes

Variant Calling

• Add the ability to copy a glf to a different directory prior to running glfExtract or glfMultiples
• Remove chromosome Y from the default CHRS. Also allow CHRS to be set on the commandline via a comma separated list specified in --chrs
• Update glfMerge to skip glf files that only have a header.
• Change default FILTER_MAX_SAMPLE_DP to 1000 (from 20)
• Some SVM updates

Aligner & Variant Calling

• Fix bug in Conf.pm that caused a failure in some versions of perl
• Add the ability to set the GOTCLOUD_ROOT so you can test with an alternate align.pl/umake.pl script and still be able to access everything else from the standard gotcloud path.
• Cleanup the perldoc for align/snpcall
• Output all configuration settings into a file when running.
• Upgrade to most current libStatGen
• Compile as optimized

Version 1.07 (Full Release on 7/3/2013)

Aligner

• DEPRECATED configuration settings:
  • 'BWA_MAX_MEM' is now 'SORT_MAX_MEM'
  • 'VERIFY_BAM_ID_OPTIONS' is now 'verifyBamID_USER_PARAMS'
• ALN_TMP now defaults to $(TMP_DIR)/alignment.aln rather than $(TMP_DIR)/alignment.bwa
• Upgrade to latest QPLOT
  • GC Content file has been renamed to have the extension: .winsize100.gc
• Automatically generates the bam index file if BAM_INDEX is specified
• Run DEDUP & RECAB as 1 step instead of 2
• Update dedup, recab, qplot, & verifyBamID steps to be specified via configuration
  • Easier to insert steps between/before/after these
  • Use PER_MERGE_STEPS to disable any of these steps (see gotcloudDefaults.conf for its default setting)
    • RUN_QPLOT and RUN_VERIFY_BAM_ID are only used for validating executable/reference existence and will be deprecated completely soon
• Fixed bug where the merge failed if there was only 1 fastq pair
• Improve informational messages
• Update to BWA version 0.6.1-r104
• Bring in mergeBam updates from latest bamUtil
  • ignore PG lines with duplicate ids
• General code cleanup
• Add some Mosaik support
  • Added support to align.pl and a way to enable it, but the code doesn't compile
• Calculate approximate storage needed for GotCloud so user can have an idea what is coming
• Makefile now uses bash and pipefail to catch errors that occur within piped commands
• Removed the md5sum calculation

Variant Calling

• Update to always require REF
  • this fixes bug that ldrefine was not checking REF or adding the optional prefix to it.
• SVM - fix bug on qual check in run_libsvm.pl
• Update defaults for filtering
• Fixed bug in libVcf/VcfFile that had FamID instead of FatID
• Fixed bug in samtools-hybrid that caused it to fail when checking for BAI files if bam was elsewhere in the filename
• Fix vcfPielup to accept .bam.bai or .bai in bam index filenames.
• Fix the split logic to work if a VCF file had no PASS records

Aligner & Variant Calling

• Add checks for required executables prior to running
• Limit the number of jobs that can run locally (there is a flag to override this)
• Extract configuration routines from the 2 .pl's to a common Conf.pm
• Add FLUX support
• 1st attempt at checking for new versions
  • Doesn't quite always work yet, but shouldn't cause a problem

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 3/22/2013)

• 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.