MiModD Activity
Mutation Identification in Model Organism Genomes using Desktop PCs
Brought to you by:
wm75
Activity for MiModD
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Wolfgang Maier committed [5b7f2b]
Merge rebase EFF allele and build fixes into stable
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Wolfgang Maier committed [cbaec6]
Include cached Galaxy test-data in distribution
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Fix symlinks by specifying relative targets
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Add more tests for variant_annotation module
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fix wrong alleles in variant reports
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fixed by [2482ec]
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Reverse-complement EFF allele when reverting ALT during rebase
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mimodd reheader bug with renaming ref sequences in BAM
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correction to the correction: the real cause of the issue is that the SnpEff effect allele (which SnpEff writes correctly in every case) can get out of sync with the ALT column during rebasing (which may rv-complement ALT alleles, but doesn't know about SnpEff effects fields).
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fix wrong alleles in variant reports
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variant call tool should expose more samtools/bcftools options
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Merge Snap and vcf-filter fixes into stable
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allow unspecified start or stop in vcf-filter region filters
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Fix vcf-filter Galaxy wrapper region filter handling
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First-class sanitize tool
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enable variant filtering based on REF and ALT sequences and on snpEff annotations
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batch-level command line options for snap-batch
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variant filtering mini-language to allow for OR-based filters
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remove snap-batch tool
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Clean up SNAPLib source
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Fix two SNAP compile warnings and snap index crash on modern OSes
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Merge updated info tool docs into stable
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Document info tool enhancements
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Merge v0.2 info tool and wrapper enhancements into stable
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Adjust docs version to match package version exactly
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Include full Galaxy data assets in package install
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Bump package version
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Pull in Galaxy toolshed-related assets from wrapper repo
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Improve file info Galaxy tool wrapper
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Start work on Galaxy wrapper updates
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Support new BED output format of mimodd info
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Replace redundant copy of Galaxy tool_config with symlink
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Titles of datasets created with File Information tool
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fixed by https://github.com/wm75/mimodd_galaxy_wrappers/commit/d78d5783eea5d3cc7ccdb16d6ae3a11864beef2c
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Add BED as fileinfo output format
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MiModD on public Galaxy servers
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prepare for ssl certificate expiration
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could not reproduce, plus updated bundled certificate together with pip/setuptools
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bundled pip is incompatible with python3.8
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resolved by upgrade of the bundled versions of pip and setuptools in changeset [a36bcf]
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Wolfgang Maier committed [9d9d80]
Merge default into stable
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Wolfgang Maier committed [6b11e0]
Update testall script to test against all supported Python versions
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Wolfgang Maier committed [dc2845]
Adjust and simplify import hierarchy
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Wolfgang Maier committed [75c321]
Add .hgignore files
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Wolfgang Maier committed [5ffbb6]
Limit version downgrades to sane choices
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Wolfgang Maier committed [1c813d]
Fix newly introduced typo
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Wolfgang Maier committed [35e098]
Revert premature version bump
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Wolfgang Maier committed [a36bcf]
Update bundled pip and setuptools
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Wolfgang Maier committed [15d97c]
Update Galaxy installation instructions to make use of Python 3
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Wolfgang Maier committed [e6194c]
Merge documentation into default
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Wolfgang Maier committed [a398f0]
Update Galaxy installation instructions to make use of Python 3
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Wolfgang Maier committed [da68be]
Removed tag doc0.1.9
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Wolfgang Maier committed [7c80a8]
Added tag doc0.1.9 for changeset da68be06c8f0
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Wolfgang Maier committed [d7e669]
Update docs to reflect new dependency requirements
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Anonymous created ticket #116
bundled pip is incompatible with python3.8
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Wolfgang Maier committed [806dc6]
Drop support for Python 3.3/3.4, make compatible with Python 3.7+
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Wolfgang Maier committed [2babd1]
Update ChangeLog and copyright
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Wolfgang Maier committed [4f170c]
Handle "Operation not supported" as hardlink failure reason
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Wolfgang Maier committed [8a2fbe]
Document current incompatibility with Python3.7.5 and beyond
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Wolfgang Maier committed [237719]
Update macOS version information
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Fix for rpy2 3.x series
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addressed by [a4c951], which also restores R warnings output suppression for the 3.x series of rpy2
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Anonymous created ticket #115
Fix for rpy2 3.x series
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Wolfgang Maier committed [a4c951]
Make compatible with 3.x series of rpy2
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Welcome
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Titles of datasets created with File Information tool
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Anonymous created ticket #113
Report Variants Galaxy wrapper should generate plain html datasets
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fix remap rv strand bug
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handle freebayes-generated vcfs
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offer mapped reads postprocessing
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make annotate tool robust against very verbose snpEff output
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prepare for ssl certificate expiration
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teach tool wrappers about GALAXY_MEMORY_MB
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sample dropdown select menus
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tool-specific temporary file directories
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internal htslib/samtools/bcftools update
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rethink behaviour of pysamtools.header on empty output
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enable autocompletion of mimodd subcommands in shell
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Support for SNAP v1.0
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keep custom rginfo lines in vcf headers in synchrony with sample names
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keep custom rginfo lines in vcf headers in synchrony with sample names
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clean up code base after 0.1.6.1 pyvcf changes
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new RVD (relative variant density) mode for map tool
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handle uninstall/reinstall
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handle uninstall/reinstall
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FDR filter for delcall
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dealing with ANN format remains to be implemented, but should be part of v0.2
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enable deletion calling for only some of the samples in a BCF file
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scaffold-independent parallelization of variant calling
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add anno_links to vectorbase
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OS X wheels should ship with working copy of bwa as an alternative aligner
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make pysamtools functions return running processes that can be waited for
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convert and split vcf/bcf files
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extend covstats tool
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sample dropdown select menus
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teach tool wrappers about GALAXY_MEMORY_MB
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MiModD on public Galaxy servers
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make annotate tool robust against very verbose snpEff output
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prepare for ssl certificate expiration
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MiModD released /MiModD-0.1.9/README.txt
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