NCI-CGR / annotate_rsids_from_linker

Use linker file to map chr:pos to rsID labels, for plco-analysis

annotate_rsids_from_linker

Brief Summary

Use linker file to map chr:pos to rsID labels, for plco-analysis

Overview

This README is an automated stub generated from a cookiecutter template. Documentation below reflects the state of the templated project immediately after creation and may not reflect the current state of the project after development updates.

Requirements

• g++ >= 8.2.0
• automake/autoconf
• make >= 4.2
• git >= 2.28.0
• nodejs (for commitizen)
• pre-commit
• associated linting tools for C++: cppcheck, clang-format
• zlib headers and library
• bzip2 headers and library

Build

By default, a build process involving a conda environment is supported.

• if you wish to use conda and it's not currently available, you can install it with the instructions here

• navigate into your project directory (annotate_rsids_from_linker)

• create the conda environment for installation as follows:

  conda env create -f environment.yaml

• activate the conda environment:

  conda activate annotate_rsids_from_linker-env

• (one time only per environment) install commitizen:

  npm install -g commitizen cz-conventional-changelog

• (one time only per environment) install pre-commit linters:

  pre-commit install

• update (create) the necessary configure scripts with autoreconf:

  autoreconf --force --install

  • note that this can also be run with ./generate.bash inside the repo

• run configure:

  ./configure --with-boost=/path/to/miniconda3/envs/annotate_rsids_from_linker-env --with-boost-libdir=/path/to/miniconda3/envs/annotate_rsids_from_linker-env/lib

  • if you are planning on installing software to a local directory, run instead ./configure --prefix=/install/dir [...]
  • periodically there are some incompatibility issues between configure and conda. if so, you may need to override some default locations detected by configure. for example, you might override the detected compiler with: CC=gcc CXX=g++ ./configure [...]

• run make CPPFLAGS=""

  • this is a non-standard make invocation. the reason this is included is because the project is configured to specifically use a boost installation in the accompanying conda environment. if you'd rather remove boost from the conda environment, or ignore it in favor of a system-wide boost installation, you can adjust the appropriate configure parameters accordingly and instead invoke make without any further variable overrides

• if desired, run make install. if permissions issues are reported, see above for reconfiguring with ./configure --prefix.

  • as above, if you run installation without compiling first, you will again need to override CPPFLAGS as follows: make CPPFLAGS="" check

Usage

By default, the final compiled program can be run with

./annotate_rsids_from_linker.out

Version History

24 01 2021: project generated from cookiecutter template