- This package was originally hosted at https://github.com/Benjamin-Vincent-Lab/PrePostMiXCR and was moved here on 2/13/2024
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.
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"
)In R:
housekeeping::assemble_package(package_name = "PrePostMiXCR", my_version = "0.0-29",
my_dir = "/datastore/alldata/shiny-server/rstudio-common/dbortone/packages/PrePostMiXCR")In bash:
cd /datastore/alldata/shiny-server/rstudio-common/dbortone/packages/PrePostMiXCR
my_comment="git issues."
git commit -am "$my_comment"; git push origin master
git tag -a 0.0-29 -m "$my_comment"; git push -u origin --tagsRestart 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")https://bitbucket.org/unc_lineberger/prepostmixcr/src/master/