lab-framework

A framework and command line interface (CLI) for computational lab work.

Installation

cd ~/
mkdir -p bin
cd bin
git clone --recurse-submodules https://github.com/lasseignelab/lab-framework.git
. lab-framework/install.sh
. ~/.bash_profile

Update

cd ~/bin/lab-framework
git pull
git submodule update --init --recursive

Usage

The lab CLI provides commands to help with reproducible research.

lab <command> params...

help

Shows help for the lab command line tool.

Definition:

lab help [COMMAND]

Example:

$ lab help

  Commands:

  help  Shows help for the lab command line tool.
  md5   Calculates a combined MD5 checksum for one or more files.

$ lab help md5

  Calculates a combined MD5 checksum for one or more files.

  The "md5" command produces a combined MD5 checksum for all the files
  specified.  It will show a list of all files included to ensure that the
  result is as expected.

  Usage:
    lab md5 FILE...

    FILE... can be one or more file and/or directory specifications.

  Example:
    $ lab md5 *

    Files included:
    43bd364a97a38fb1da7c57e6381886c1  lab-framework/LICENSE
    b794df25f796ac80680c0e4d27308bce  lab-framework/commands/md5.sh
    0d9281c3586c420130bcb5d25c8a151a  lab-framework/lab
    5e79c988140af1b7bd5735b0bf96306b  lab-framework/README.md
    783a44ffae97afbce3f1649c5ff517a5  lab-framework/install.sh

    Combined MD5 checksum:
    a225199964b84bdeef33bafe3df7c10b

md5

The lab md5 command will produce an md5sum for the file or files specified. This makes it easy to determine whether files are identical.

Definition:

lab md5 FILE...

Example:

$ lab md5 *

Files included:
43bd364a97a38fb1da7c57e6381886c1  lab-framework/LICENSE
b794df25f796ac80680c0e4d27308bce  lab-framework/commands/md5.sh
0d9281c3586c420130bcb5d25c8a151a  lab-framework/lab
5e79c988140af1b7bd5735b0bf96306b  lab-framework/README.md
783a44ffae97afbce3f1649c5ff517a5  lab-framework/install.sh

Combined MD5 checksum:
a225199964b84bdeef33bafe3df7c10b

new

The lab new command will create a new research project based on the project-template submodule in the lab-framework repository. The project repository will be created with the origin remote pointed to a Github repository owner specified by the Github account and project name parameters.

Definition:

lab new GITHUB_OWNER PROJECT_NAME

GITHUB_OWNER Github owner the project repo will be created under.  This may
             be a personal or organization account.
PROJECT_NAME Name of the project which will match the Github repo name.

Example:

$ lab new lasseignelab PKD_Research

Create an empty repository for 'PKD_Research' on GitHub by using the
following link and settings:

  https://github.com/organizations/lasseignelab/repositories/new

  * No template
  * Owner: lasseignelab
  * Repository name: PKD_Research
  * Private
  * No README file
  * No .gitignore
  * No license

Where you able to create a repository (y/N)? y


Cloning into 'PKD_Research'...
done.

...

Happy researching!!!