installation docs

docs/getting_started/installation.rst

@@ -285,6 +285,194 @@ This example bewlow is for the `Stored Sequence Read Data <https://iliad-readthe
 Academic HPC cluster - Linux
 ====================================================================
 
+Step 1: Install Snakemake and Snakedeploy
+*****************************************
+
+Snakemake and Snakedeploy are best installed via the `Mamba package manager <https://github.com/mamba-org/mamba>`_ (a newer package manager for Conda replacement). 
+From our testing, Conda is perfectly fine as an alternative, and you can use them interchangeably below.
+If you have neither Conda nor Mamba, it can be installed via `Mambaforge <https://github.com/conda-forge/miniforge#mambaforge>`_. 
+For other options see `here <https://github.com/mamba-org/mamba>`_.
+
+You will need to add Mamba to PATH so follow their instructions_ for such.
+
+Here is my suggested install guidance for Conda on an academic HPC:
+
+.. code-block:: console
+
+    $ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
+    $ CONDA_DIR=/opt/conda
+    $ /bin/bash ~/miniconda.sh -b -p /opt/conda
+    $ PATH=$CONDA_DIR/bin:$PATH
+    $ conda init bash
+    $ source ~/.bashrc
+
+Given that Mamba (or Conda) is installed, run the following in your command line interface tool 
+(i.e. `Putty <https://www.putty.org/>`_, 
+`MacOS Terminal <https://support.apple.com/guide/terminal/open-or-quit-terminal-apd5265185d-f365-44cb-8b09-71a064a42125/mac>`_,
+or `VS Code <https://code.visualstudio.com/>`_).
+If you need guidance for a specific platform you are using, see the specific `platform`_ preparation guides and they will help lead you to this point.
+
+.. code-block:: console
+
+    $ conda create -c conda-forge -c bioconda --name iliadEnv snakemake=7.19.0 snakedeploy openpyxl pandas
+
+to install Snakemake, Snakedeploy, and a necessary python library for parsing user input tables in an isolated environment.
+For all following commands ensure that this environment is activated via
+
+
+.. code-block:: console
+
+    $ conda activate iliadEnv
+
+**Estimated time: 15-20 minutes**
+
+Step 2: Install Singularity
+***************************
+
+Typically users will not have root access on a shared HPC cluster in an academic setting. It is likely that Singularity is already installed on your school's system. 
+In the case of Indiana University, a user can run the following command to load Singularity:
+
+.. code-block:: console
+
+    $ module load singularity/3.6.4
+
+Your school will likely have a different version and you can check by either spamming the TAB button to autofill or with:
+
+.. code-block:: console
+
+    $ module avail
+
+If your school does not have Singularity, you may have to ask your HPC IT team to install it or use an alternative Iliad installation method.
+
+Step 3: Clone the Iliad repository and workflows
+************************************************
+
+.. Given that Snakemake and Snakedeploy are installed and available (see Step 1), the workflow can be deployed as follows.
+
+First, create an appropriate project working directory (/path/to/project) on your system and enter it:
+
+.. code-block:: console
+
+    $ mkdir -p project
+    $ cd project
+
+In the next step, you will clone the Iliad repo. This will create an Iliad directory that you will cd into.
+If you are not an active github user, you may have to create an account and a personal access token that is entered 
+for password when prompted to do so on the command line in the following step. 
+Here is a link for token_ information and creation_.
+
+.. **OPTION 1: snakedeploy**
+
+.. .. code-block:: console
+
+..     $ snakedeploy https://github.com/ncherric/Iliad . --tag v1.0.0
+..     $ cd Iliad
+
+**Clone the repository using git:**
+
+.. Git clone the `GitHub repository <https://github.com/ncherric/Iliad>`_.
+
+.. code-block:: console
+
+    $ git clone https://github.com/ncherric/Iliad.git
+    $ cd Iliad
+
+Now, there should be an ``./Iliad`` directory cloned into your ``/path/to/project/`` like such ``/path/to/project/Iliad/``.
+And your current working directory should be ``/path/to/project/Iliad/``.
+
+Two important folders found in the Iliad directory are **workflow** and **config**.
+The ``workflow`` contains rules and scripts that a designated Snakefile in Iliad call on to run a specific module.
+The ``config`` contains one configuration file ``Iliad/config/config.yaml`` which will be modified in the next step in order to configure the workflow to your needs.
+It also contains ``Excel`` files and ``TSV`` files where you will input your sample information.
+
+.. **side note**
+.. ( Once this pipeline is publicly available, and added to the Snakemake Workflow Catalog, run below. For now, just **clone ABOVE** )
+
+
+Step 4: Configure Workflow
+**************************
+
+There are 2 methods: Automatic and Manual 
+
+**Automatic**
+
+.. code-block:: console
+
+    $ conda install questionary -c conda-forge -b
+    $ cd config
+    $ python auto_config.py
+
+There will be interactive questions on the command line that will ask you to enter your 1) working directory and 2) sample table file with download URLs. 
+Answer the interactive prompts accordingly and then press RETURN/ENTER.
+
+
+
+**Manual**
+
+To configure this workflow, modify ``Iliad/config/config.yaml`` according to your needs. 
+The file is clearly denoted into sections that you can change according to your needs. 
+There are many defaults set that you do not have to change. The one most important change you will have to make is the following:
+
+.. code-block:: console
+
+    $ nano config/config.yaml
+
+And INSERT your working directory path where NEED PATH HERE is. should look like this: **/path/to/project/Iliad/**
+
+.. code-block:: console
+
+    #####################################
+    #####################################
+    #####################################
+
+    #  #  # USER INPUT VARIABLES  #  #  #
+
+    #####################################
+    #####################################
+    #####################################
+
+    # You must insert your /PATH/TO/Iliad/
+    # use 'pwd' command to find your current working directory when you are inside of Iliad directory
+    # e.g. /path/to/Iliad/ <---- must include forward slash at the end of working directory path
+
+    # must include forward slash, '/', at the end of working directory path
+    workdirPath: NEED PATH HERE
+
+
+Step 5: Run workflow
+********************
+
+Given that the workflow has been properly deployed and configured, and your conda environment is activated, it can be executed as follows.
+
+For running the workflow while deploying any necessary software via singularity and conda (using the Mamba package manager by default), run Snakemake with
+
+.. code-block:: console
+
+    $ snakemake -p --use-singularity --use-conda --cores 1 --jobs 1 --default-resource=mem_mb=10000 --latency-wait 120
+
+Other workflows
+********************
+
+When executing the workflow, Snakemake will automatically find the main Snakefile in the workflow subfolder which is the **Raw Sequence Read Data** module.
+However, there are other Snakefiles that are specific to the other Modules that you will have to call using ``--snakefile [desired module snakefile]``
+
+* ``--snakefile workflow/Snakefile`` -> Raw Sequence Read Data
+* ``--snakefile workflow/cram_Snakefile`` -> Stored Sequence Read Data
+* ``--snakefile workflow/snpArray_Snakefile`` -> SNP Array Data
+* ``--snakefile workflow/LiftoverTo38_Snakefile`` -> Submodule to liftover GRCh37 assembly VCF data to GRCh38 assembly
+* ``--snakefile workflow/LiftoverTo37_Snakefile`` -> Submodule to liftover GRCh38 assembly VCF data to GRCh37 assembly
+* ``--snakefile workflow/merger_Snakefile`` -> Submodule to merging list of VCFs
+* ``--snakefile workflow/mergeRefTarget_Snakefile`` -> Submodule that will merge your processed Reference and Target data if you have previously completed both modules 
+
+Visit the How-To Guides pages for further info about each of the Modules and Submodules in the bulleted list above.
+
+This example bewlow is for the `Stored Sequence Read Data <https://iliad-readthedocs.readthedocs.io/en/latest/tutorial/stored_sequence.html>`_
+
+.. code-block:: console
+
+    $ snakemake -p --use-singularity --use-conda --cores 1 --jobs 1 --snakefile workflow/cram_Snakefile --default-resource=mem_mb=10000 --latency-wait 120
+
+
 
 
 Local machine - Docker