Difference between revisions of "GotCloud: Versions"
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For information on installing the releases, see: [[GotCloud#Install_GotCloud_Software|Install GotCloud Software]] | For information on installing the releases, see: [[GotCloud#Install_GotCloud_Software|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) == | == Version 1.05 (Full Release on 4/17/2013) == | ||
− | ''Aligner & | + | ''Aligner & Variant Calling''' |
* Cleanup handling of BASE_PREFIX & added REF_PREFIX. | * Cleanup handling of BASE_PREFIX & added REF_PREFIX. | ||
** Allows user to specify --base_prefix or --baseprefix on command-line | ** 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 ( | + | ** 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) == | == Version 1.04 (Full Release on 4/16/2013) == | ||
− | '''Aligner & | + | '''Aligner & Variant Calling''' |
* Update relative paths to be relative to the current working directory | * Update relative paths to be relative to the current working directory | ||
** Aligner effects: | ** Aligner effects: | ||
*** INDEX_FILE as specified in the aligner configuration | *** INDEX_FILE as specified in the aligner configuration | ||
*** fastq paths specified in the INDEX_FILE | *** fastq paths specified in the INDEX_FILE | ||
− | ** | + | ** Variant Calling effects: |
** BAM_INDEX as specified in the configuration | ** BAM_INDEX as specified in the configuration | ||
** bam paths specified in the BAM_INDEX | ** bam paths specified in the BAM_INDEX | ||
Line 23: | Line 29: | ||
** FASTQ_PREFIX (for aligner reading the fastq index file) | ** FASTQ_PREFIX (for aligner reading the fastq index file) | ||
*** renamed from FASTQ/FASTQ_REF | *** renamed from FASTQ/FASTQ_REF | ||
− | ** BAM_PREFIX (for | + | ** BAM_PREFIX (for variant calling reading bam index file) |
* Improve Error detection | * Improve Error detection | ||
** With --test option, check that the testdir exists before running the test | ** With --test option, check that the testdir exists before running the test | ||
Line 39: | Line 45: | ||
** Also add support for fixing the problem with UMich directories when using Mosix | ** Also add support for fixing the problem with UMich directories when using Mosix | ||
* Update the default Reference directory to be as expected for UM | * Update the default Reference directory to be as expected for UM | ||
− | * | + | * Variant Calling changes: |
** SVM | ** SVM | ||
*** Add option to merge all chromosome sites prior to running SVM (to better support targeted sequencing) | *** Add option to merge all chromosome sites prior to running SVM (to better support targeted sequencing) | ||
Line 47: | Line 53: | ||
* Add pre-checks for required files & reference files prior to running | * Add pre-checks for required files & reference files prior to running | ||
* Add checks for deprecated configuration settings | * Add checks for deprecated configuration settings | ||
− | * Merge aligner & | + | * Merge aligner & variant calling default configurations into a single file (bin/gotcloudDefaults.conf) |
* Aligner | * Aligner | ||
** Update to put actual values into the Makefile recipes rather than using variables | ** 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) | ** Fix vcf-summary to handle chromosomes that have string names (like X,Y) | ||
== Version 1.03a4 (Internal Only Release on 4/2/2013) == | == Version 1.03a4 (Internal Only Release on 4/2/2013) == | ||
− | * | + | * Variant Calling: |
** Update to by default run as local | ** Update to by default run as local | ||
** Target Loci file updates: | ** Target Loci file updates: | ||
Line 69: | Line 75: | ||
== Version 1.03a1 (Internal Only Release on 3/26/2013) == | == 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_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. | ** Add FILTER_ADDITIONAL to add the option of adding additional filters. | ||
Line 75: | Line 81: | ||
== Version 1.03a (Full Release on 3/22/2913) == | == Version 1.03a (Full Release on 3/22/2913) == | ||
* Cleanup README & INSTALL instructions | * Cleanup README & INSTALL instructions | ||
− | * | + | * Variant Calling |
** Fix dependency bug/error in SVM | ** Fix dependency bug/error in SVM | ||
** Fix commands that run locally to check for pipe failures | ** Fix commands that run locally to check for pipe failures |
Revision as of 14:11, 17 April 2013
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
- 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 3/22/2913)
- 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.