Dev-newSNP #12
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Dev-newSNP #12
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Added a script to download and format GTDB and GTDBtk databases, as well as to try to automatically udpate environment MGTKgtdbtk for different versions.
When concatenating parts of the GTDBtk database, the correct directory is now used. Created stub data (`helpers/install/get_gtdb`) for testing extraction logic. Use flag `--test` to use this stub data. Additionally fixed an error in arguments passed to `_processing_metadata` when downloading.
* scripts to autogenerate a QC report * changes to existing files to create the QC report * remove hardcoded path in QC_html_report.Rmd * Remove hardcoded path in QC_html_report.Rmd * The actual call was commented out in MG-TK.pl * bugs anthony noticed - coerce char type to num, some report looks weird
* GTDBtk v2.5 * remove mash, don't install tk default * fix(get_gtdb.py): remove mash for new versions, fix DBDir iterpolation, remove default GTDB-Tk install Newer versions of GTDB-Tk (>=2.5) do not use mash, so when configuring for this, comments out the GTDBtk_mash line in config_DBs.txt [DBDir] is now appropriately used in config, was previously not detected due to a newline character. No longer install GTDB-Tk by default, allow MG-TK to install based on environment yamls. Added --install-tk flag to install a version of GTDB-Tk which is compataible with the GTDB released being configured. --------- Co-authored-by: Falk Hildebrand <falk.hildebrand@gmail.com>
* scripts to autogenerate a QC report * changes to existing files to create the QC report * remove hardcoded path in QC_html_report.Rmd * Remove hardcoded path in QC_html_report.Rmd * The actual call was commented out in MG-TK.pl * bugs anthony noticed - coerce char type to num, some report looks weird
Co-authored-by: Falk Hildebrand <falk.hildebrand@gmail.com>
GTDBtk v2.5
Added new FAQ entries regarding MAG extraction and installation errors.
…the fly in parrallel, storage space reduced by gz_ing more files. rtk2 v2.14: clearer reports. vcf2fna v0.22: now also integrates INDELs. Installer will install newer versions of samtools, bcftools, strobealign, mmseqs2.
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