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Commits : Listings

Analyzed about 3 hours ago. based on code collected about 18 hours ago.
May 21, 2023 — May 21, 2024
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
Generalize ipython cluster creation to allow heterogenous engines with multiple cores. Remove separate configuration step for clusters moving details into commandline arguments to ipcluster
chapmanb
More... over 11 years ago
Finalize initial version of installation script. Update documentation
chapmanb
More... over 11 years ago
Initial version of automated script to install bcbio-nextgen, tool dependencies and data files
chapmanb
More... over 11 years ago
Provide documentation on seting up data requirements for pipeline
chapmanb
More... over 11 years ago
Provide additional documentation on configuration parameters including resources section and ensemble calling
chapmanb
More... over 11 years ago
Fixes for tophat2 pipeline: correctly handle keyword options and use bowtie2/tophat2 by default. Thanks to Warren Emmett for report.
chapmanb
More... over 11 years ago
Support specifying the blast and blast database command in input YAML to work on windows systems
chapmanb
More... over 11 years ago
Move fastq utilities into bam namespace to avoid conflict with bcbio-hiv pipeline. Update for #66
chapmanb
More... over 11 years ago
Merge pull request #66 from roryk/memoize_refactor
Brad Chapman
More... over 11 years ago
Add documentation to example ensemble script and re-order to emphasize replicates
chapmanb
More... over 11 years ago
Include example of ensemble calling for NA12878
chapmanb
More... over 11 years ago
Revert back to piped splitting from BAM plus correct options for JVM tuning
chapmanb
More... over 11 years ago
More robust approach to handling safe multi-process mkdirs. Default to non-piped sort/split to work on gluster filesystems having trouble with pipe
chapmanb
More... over 11 years ago
Allow usage of a local scratch temporary filesystem for temporary directories based on system configuration
chapmanb
More... over 11 years ago
More cleanly catch and avoid intermittent pipe failures for sorting and splitting from BAM inputs
chapmanb
More... over 11 years ago
Increase delays for ipcluster startup and piping sorting results to handle larger input sizes
chapmanb
More... over 11 years ago
Nest alignment and alignment split directories to avoid large directories with large sample numbers
chapmanb
More... over 11 years ago
Updated to use the new memoization.
roryk
More... over 11 years ago
Added a fastq groomer to play with the updated memoization.
roryk
More... over 11 years ago
Refactor of memoize output to take either ext or stem as an argument and do the right thing.
roryk
More... over 11 years ago
Inclusive varscan p-value that still includes calculation of p-values
chapmanb
More... over 11 years ago
Added unit tests for the updated decorators.
roryk
More... over 11 years ago
Memoize returns the output from the function it decorates if the function runs.
roryk
More... over 11 years ago
Changed decorator signatures to more closely match the originals.
roryk
More... over 11 years ago
Refactor @memoize_outfile to not also transform the filename.
roryk
More... over 11 years ago
Include multiple batching target in ipython tasks
chapmanb
More... over 11 years ago
Increase input counts for recalibration on whole genomes to include additional data and keep recal/re-write times in sync
chapmanb
More... over 11 years ago
Avoid additional filtering for VarScan calls since calls are filtered as part of calling process
chapmanb
More... over 11 years ago
Convert VarScan indel format into VCF compatible representation. Use local temporary directories by default for GATK runs
chapmanb
More... over 11 years ago
Merge pull request #65 from roryk/master
Brad Chapman
More... over 11 years ago