GotCloud: Versions
From Genome Analysis Wiki
Revision as of 15:24, 3 July 2013 by Mktrost (talk | contribs) (→Version 1.07 (Full Release on 7/3/2013))
For information on installing the releases, see: Install GotCloud Software
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
- 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 - fib 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
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
- Aligner effects:
- 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)
- SVM
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.