<commit_before>VM Workflow Tools Installation Cheat Sheet
##########################################

When working with a new Virtual Machine (VM), more often than not installing software, packages and dependencies is required, and the process can be cumbersome. This cheat sheet was created with running workflows on Google Cloud VM in mind. It contains quick shortcuts to install common software, dependencies, and quick fixes.

********
NEXTFLOW
********

Install:
========
::

    $ export NXF_VER=20.01.0
    $ export NXF_MODE=google
    $ curl https://get.nextflow.io | bash



*******************
SNAKEMAKE
*******************
Step 1 install Miniconda:
=========================
`Installer  <https://docs.conda.io/en/latest/miniconda.html#linux-installers>`_
| `Instruction <https://conda.io/projects/conda/en/latest/user-guide/install/index.html>`_

.. note::  After “conda init fish” step **restarting your VM command line** is needed.
 In addition, if the conda command is not found, try: $export PATH=./miniconda3/bin/:$PATH



Step 2 install Snakemake:
=========================

`Instruction <https://snakemake.readthedocs.io/en/stable/getting_started/installation.html#conda-install>`_


Snakemake environment:
----------------------
Create and activate Environment for Snakemake from a file (yml/yaml):
::

  $ conda env create --name <yourEnvironmentName> --file environment.yaml
  $ source activate <yourEnvironmentName>

Updating current environment

::

    $ conda env update -f environment.yml

.. note:: for more conda commands, visit: `Conda Cheat sheet <https://docs.conda.io/projects/conda/en/4.6.0/_downloads/52a95608c49671267e40c689e0bc00ca/conda-cheatsheet.pdf>`_



***
WDL
***

`Installers <https://github.com/broadinstitute/cromwell/releases>`_ for Cromwell and Womtool

***
CWL
***
::

  $ sudo apt-get install python-pip
  $ pip install --upgrade pip
  $ pip install cwltool



*******************
Common dependencies
*******************

Java
====

::

  $ sudo apt install default-jre<commit_msg>Update Cheatsheet.rst<commit_after>VM Workflow Tools Installation Cheat Sheet
##########################################

When working with a new Virtual Machine (VM), more often than not installing software, packages and dependencies is required, and the process can be cumbersome. This cheat sheet was created with running workflows on Google Cloud VM in mind. It contains quick shortcuts to install common software, dependencies, and quick fixes.

********
NEXTFLOW
********

Install:
========
::

    $ export NXF_VER=20.01.0
    $ export NXF_MODE=google
    $ curl https://get.nextflow.io | bash



*******************
SNAKEMAKE
*******************
Step 1 install Miniconda:
=========================
`Installer  <https://docs.conda.io/en/latest/miniconda.html#linux-installers>`_
| `Instruction <https://conda.io/projects/conda/en/latest/user-guide/install/index.html>`_

.. note::  After “conda init fish” step **restarting your VM command line** is needed.
 In addition, if the conda command is not found, try: $export PATH=./miniconda3/bin/:$PATH



Step 2 install Snakemake:
=========================

`Instruction <https://snakemake.readthedocs.io/en/stable/getting_started/installation.html#conda-install>`_
Installer:
::

  $ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
  
Snakemake environment:
----------------------
Create and activate Environment for Snakemake from a file (yml/yaml):
::

  $ conda env create --name <yourEnvironmentName> --file environment.yaml
  $ source activate <yourEnvironmentName>

Updating current environment

::

    $ conda env update -f environment.yml

.. note:: for more conda commands, visit: `Conda Cheat sheet <https://docs.conda.io/projects/conda/en/4.6.0/_downloads/52a95608c49671267e40c689e0bc00ca/conda-cheatsheet.pdf>`_



***
WDL
***

`Installers <https://github.com/broadinstitute/cromwell/releases>`_ for Cromwell and Womtool

::

   $ wget https://github.com/broadinstitute/cromwell/releases/download/52/cromwell-52.jar
   $ wget https://github.com/broadinstitute/cromwell/releases/download/52/womtool-52.jar
   
   
***
CWL
***
::

  $ sudo apt-get install python-pip
  $ pip install --upgrade pip
  $ pip install cwltool



*******************
Common dependencies
*******************

Java
====

::

  $ sudo apt install default-jre
{'fraction_non_alphanumeric': 0.1960514233241506, 'fraction_numerical': 0.01859504132231405, 'mean_word_length': 4.365763546798029, 'pattern_counts': {'":': 0, '<': 17, '<?xml version=': 0, '>': 17, 'https://': 15, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1046', 'n_tokens_mistral': 1436, 'n_tokens_neox': 1300, 'n_words': 351}