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Functions for writing commands and post processing the MiXCR pipeline.
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DESCRIPTION
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NAMESPACE
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README.md

Functions for writing commands and post processing the MiXCR pipeline.

Given a sample data matrix that indicates the sample name, sample folder name and input paths this script can write out pipeline commands to run MiXCR on the cluster and post process the data.

Example commands

In R:

diversity_dir = file.path(POST_PROCESSING_DIR, "mixcr")
dir.create(mixcr_dir, showWarnings = F)
output_path = file.path(diversity_dir, "diversity_data.tsv" )


input_file_paths = system(paste0("ls ", RAW_DATA_DIR, "/mixcr/sample_output/*/*_clones.txt"), 
                          intern = TRUE)

my_chains = c( "IGH", "IGK", "IGL", "TRA", "TRB", "TRD", "TRG")

if(!("PrePostMiXCR" %in% rownames(installed.packages())))
  devtools::install_github("Benjamin-Vincent-Lab/PrePostMiXCR")
  
PrePostMiXCR::post_process_mixcr(
  input_file_paths = input_file_paths,
  my_chains = my_chains,
  output_path = output_path,
  sample_data_table = fread(sample_data_path),
  thread_num = 1, # works pretty slow with mutliple cores.  probably memory limited.
  sample_folder_column = "run_accession"
)

Assembling this package

In R:

housekeeping::assemble_package(package_name = "PrePostMiXCR", my_version = "0.0-27",
  my_dir = "/datastore/alldata/shiny-server/rstudio-common/dbortone/packages/PrePostMiXCR")

Push changes

In bash:

cd /datastore/alldata/shiny-server/rstudio-common/dbortone/packages/PrePostMiXCR
my_comment="Updated readme."
git commit -am "$my_comment"; git push origin master
git tag -a 0.0-27 -m "$my_comment"; git push -u origin --tags

Install

Restart R In R (local library, packrat library):

devtools::install_github("Benjamin-Vincent-Lab/PrePostMiXCR")

Or for a specific version:

devtools::install_github("Benjamin-Vincent-Lab/PrePostMiXCR", ref = "0.0-27")

Previous location

https://bitbucket.org/unc_lineberger/prepostmixcr/src/master/

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