README.md

In DanteBortone/MiXCR: Functions for writing commands and post processing the MiXCR pipeline.

This repo is antiquated and has largely been absorbed by binfotron here: https://github.com/Benjamin-Vincent-Lab/binfotron

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.

Assembling this package

In R:

housekeeping::assemble_package(package_name = "MiXCR", my_version = "0.0-03",
  my_dir = "/datastore/alldata/shiny-server/rstudio-common/dbortone/packages/MiXCR")

Push changes

In bash:

cd /datastore/alldata/shiny-server/rstudio-common/dbortone/packages/MiXCR
my_comment="Added convergence."
git commit -am "$my_comment"; git push origin master
git tag -a 0.0-03 -m "$my_comment"; git push -u origin --tags

Install

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

devtools::install_github("DanteBortone/MiXCR")

Or for a specific version:

devtools::install_github("DanteBortone/MiXCR", ref = "0.0-03")

DanteBortone/MiXCR documentation built on Aug. 14, 2022, 2:41 p.m.