Commit 857d585e authored by aknecht2's avatar aknecht2
Browse files

Updated installation documentation.

parent 6fc166b6
Installation
==============
Installation is made much easier by using the pre-built
`anaconda <https://anaconda.org/>`_ packages. There are two different packages
located under the `hcc channel <https://anaconda.org/hcc>`_.
The chipathlon package contains all software necessary to run & generate
workflows. The chipathlon-client packages contains all software necessary to
generate workflows with the expectation that the execute host has the
necessary software installed. idr uses python3 however, so it must be
created in a separate environment. Once you have conda installed:
.. code-block:: bash
# Add the required channels for all software
conda config --add channels conda-forge
conda config --add channels r
conda config --add channels HCC
conda config --add channels bioconda
# Create the chip env with all software except idr
conda create -n chip python=2.7 chipathlon
# Create the idr environment
conda create -n idr python=3.5 idr
This will create the two environments necessary to run workflows. The chip
environment can also be used to generate and submit workflows:
.. code-block:: bash
# Activate chip env
source activate chip
# Generate the workflow
chip-gen...
Below is the full list of dependencies if you don't want to use conda.
Dependencies
^^^^^^^^^^^^
**Dependencies for chipathlon**
Dependencies for chipathlon
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* `Pegasus <http://pegasus.isi.edu/>`_
* `pymongo <https://api.mongodb.com/python/current/>`_
* `yaml <http://pyyaml.org/>`_
Dependencies for running workflows
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Dependencies for running workflows**
* `Gem <http://groups.csail.mit.edu/cgs/gem/>`_
* `Zerone <https://omictools.com/zerone-tool>`_
* `MACS2 <https://github.com/taoliu/MACS>`_
......@@ -22,9 +57,23 @@ Dependencies for running workflows
* `picard <https://github.com/pezmaster31/bamtools>`_
* `bwa <http://bio-bwa.sourceforge.net>`_
* `bowtie2 <http://bowtie-bio.sourceforge.net/bowtie2/index.shtml>`_
* `idr <https://github.com/nboley/idr>`_
**Dependencies for building docs**
Dependencies for building docs
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* `Sphinx <http://www.sphinx-doc.org/en/stable/>`_
* `Sphinx Argparse <https://github.com/ribozz/sphinx-argparse>`_
* `Read the Docs Theme <https://github.com/rtfd/sphinx_rtd_theme>`_
Setting up bosco
^^^^^^^^^^^^^^^^^
To use bosco with the chipathlon-client package a small amount of setup must
be done first. Namely, adding the target cluster that you wish to use.
This can be done with the following command:
.. code-block:: bash
bosco_cluster -a USERNAME@HOST.org slurm
This will generate and copy ssh keys that will be used to transfer files
between your submit host and your execute host.
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