New Version (1.07) is now available

[GotCloud]

A new version of gotcloud, 1.07 is now available.  

Sorry for the delay in releasing a new version.  I plan to release more frequently in the future.

There is also a wiki page that describes the changes in each version:

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

Summary of changes since the last release (1.06) on 4/19/2013:

• 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

Note for those at the University of Michigan: This version is already installed on the cluster and should be in your path, just type "gotcloud" to run it.

Please let me know if you have any questions.

Mary Kate Wing