meta-strains
To install modified Clomial package
In R:
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install.packages("matrixStats", lib="~/R/libs")
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install.packages("permute", lib="~/R/libs", repos='http://cran.rstudio.com/')
In console:
- R CMD INSTALL -l ~/R/libs/ Clomial_meta
To run Clomial pipeline
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Create an empty directory in "experiments".
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Copy your reference file to directory "refs" and run "bwa index" on it.
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Copy "Snakefile_Clomial" to your directory and rename it to "Snakefile".
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Change settings in first lines of your Snakefile.
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Run "snakemake --cores (number_of_threads)".
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Do not forget to clear GitHub repository from gigabytes of data.
To run PhyloWGS pipeline
Same as Clomial pipeline, but for "Snakefile_PhyloWGS"