Commit cd089d65 authored by Christian Arnold's avatar Christian Arnold

Integrated first version of Sphinx documentation

parent effb517b
![logo|small](/doc/logo.png "diffTF logo")
![logo|small](/docs/logo.png "diffTF logo")
Genome-wide quantification of differential transcription factor activity: diffTF
=====================================================
Thank you for the interest in diffTF! If you have questions or comments, feel free to contact us. We will be happy to answer any questions related to this project as well as questions related to the software implementation.
Thank you for the interest in diffTF! If you have questions or comments, feel free to contact us. We will be happy to answer any questions related to this project as well as questions related to the software implementation.
Summary
-------
......@@ -13,36 +13,36 @@ Transcription factor (TF) activity constitutes an important readout of cellular
Documentation
-------
[A detailed Documentation is available here](https://git.embl.de/grp-zaugg/diffTF/blob/master/doc/Documentation.pdf)
[A detailed Documentation is available here](https://git.embl.de/grp-zaugg/diffTF/blob/master/docs/Documentation.pdf)
Installation and Quick Start
-------
The following quick start briefly summarizes the necessary steps to use our pipeline:
1. Install the necessary tools (Snakemake, samtools, bedtools, and Subread). We recommend installing them via conda, in which case the installation is as easy as
1. Install the necessary tools (Snakemake, samtools, bedtools, and Subread). We recommend installing them via conda, in which case the installation is as easy as
``conda install -c bioconda snakemake bedtools samtools subread``
If conda is not yet installed, follow the [installation instructions](https://conda.io/docs/user-guide/install/index.html). If you want to install the tools manually and outside of the conda framework, see the following instructions for each of the tools: [snakemake](http://snakemake.readthedocs.io/en/stable/getting_started/installation.html), [samtools](http://www.htslib.org/download/), [bedtools](http://bedtools.readthedocs.io/en/latest/content/installation.html), [Subread](http://subread.sourceforge.net/).
2. Clone the Git repository:
2. Clone the Git repository:
``git clone https://git.embl.de/grp-zaugg/diffTF``
3. To run the example analysis for 50 TF, simply perform the following steps:
* Change into the *example/input* directory within the Git repository
``cd diffTF/example/input``
* Download the data via the download script
``sh downloadAllData.sh``
* To test if the setup is correct, start a dryrun via the first helper script
``sh startAnalysisDryRun.sh``
* Once the dryrun is successful, start the analysis via the second helper script
``sh startAnalysis.sh``
4. To run your own analysis, modify the files config.json and sampleData.tsv. See the instructions in Section 3 in the [Documentation](https://git.embl.de/grp-zaugg/diffTF/blob/master/doc/Documentation.pdf) for more details.
5. If your analysis finished successfully, take a look into the *FINAL_OUTPUT* folder within your specified output directory, which contains the summary tables and visualization of your analysis. If you received an error, take a look into Section 4 in the [Documentation](https://git.embl.de/grp-zaugg/diffTF/blob/master/doc/Documentation.pdf) to troubleshoot.
4. To run your own analysis, modify the files config.json and sampleData.tsv. See the instructions in Section 3 in the [Documentation](https://git.embl.de/grp-zaugg/diffTF/blob/master/docs/Documentation.pdf) for more details.
5. If your analysis finished successfully, take a look into the *FINAL_OUTPUT* folder within your specified output directory, which contains the summary tables and visualization of your analysis. If you received an error, take a look into Section 4 in the [Documentation](https://git.embl.de/grp-zaugg/diffTF/blob/master/docs/Documentation.pdf) to troubleshoot.
Citation
......
# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = python -msphinx
SPHINXPROJ = diffTF
SOURCEDIR = .
BUILDDIR = _build
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help:
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.PHONY: help Makefile
# Catch-all target: route all unknown targets to Sphinx using the new
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: a54403ec71e99900e401d4e99958ed29
tags: 645f666f9bcd5a90fca523b33c5a78b7
.. diffTF documentation master file, created by
sphinx-quickstart on Thu Nov 30 12:48:48 2017.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to diffTF's documentation!
==================================
.. toctree::
:maxdepth: 2
:caption: Contents:
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
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