Merge pull request #68 from maxplanck-ie/docs

Docs
deeptools · Mar 12, 2017 · c00a131 · c00a131
2 parents f705ae2 + 312a270
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diff --git a/README.rst b/README.rst
@@ -1,9 +1,11 @@
 .. image:: https://zenodo.org/badge/21196/maxplanck-ie/HiCExplorer.svg
    :target: https://zenodo.org/badge/latestdoi/21196/maxplanck-ie/HiCExplorer
-
+.. image:: https://travis-ci.org/maxplanck-ie/HiCExplorer.svg?branch=master
+   :target: https://travis-ci.org/maxplanck-ie/HiCExplorer
+.. image:: https://readthedocs.org/projects/hicexplorer/badge/?version=docs
+   :target: http://hicexplorer.readthedocs.io/?badge=docs
 .. image:: https://anaconda.org/bioconda/hicexplorer/badges/installer/conda.svg
    :target: https://anaconda.org/bioconda/hicexplorer
-
 .. image:: https://quay.io/repository/biocontainers/hicexplorer/status
    :target: https://quay.io/repository/biocontainers/hicexplorer
 
@@ -21,8 +23,43 @@ long-range contacts. Moreover, it allows the visualization of multiple contact m
 data like genes, compartments, ChIP-seq coverage tracks (and in general any type of genomic scores) and long range contacts.
 
 
+Citation:
+^^^^^^^^^
+
+Fidel Ramirez, Vivek Bhardwaj, Jose Villaveces, Laura Arrigoni, Bjoern A Gruening, Kin Chung Lam, Bianca Habermann, Asifa Akhtar, Thomas Manke
+**"High-resolution TADs reveal DNA sequences underlying genome organization in flies"**. bioRxiv 115063; doi: https://doi.org/10.1101/115063
 
 .. image:: ./docs/images/hicex2.png
 
+Installation
+^^^^^^^^^^^^
+
+HiCExplorer is available for:
+
+-  Command line usage (via pip/anaconda/github)
+-  Integration into Galaxy servers (via toolshed/API/web-browser)
+
+There are many easy ways to install HiCExplorer. Details can be found
+`here <https://http://hicexplorer.readthedocs.io/content/installation.html>`__
+
+**Install by cloning this repository:**
+
+You can install any one of the HiCExplorer branches on command line
+(linux/mac) by cloning this git repository:
+
+::
+
+    $ git clone https://github.com/maxplanck-ie/HiCExplorer.git
+    $ cd HiCExplorer
+    $ python setup.py install
+
+If you don't have root permission, you can set a specific folder using the ``--prefix`` option
+
+::
+
+	$ python setup.py install --prefix /User/Tools/hicexplorer
+
 
-For more the complete documentation visit `<http://hicexplorer.readthedocs.org/>`_
+Documentation:
+^^^^^^^^^^^^^^
+Please visit our complete documentation `Here <http://hicexplorer.readthedocs.org/>`_
diff --git a/docs/conf.py b/docs/conf.py
@@ -77,7 +77,7 @@
 def get_version():
     import re
     try:
-        f = open("../deeptools/_version.py")
+        f = open("../hicexplorer/_version.py")
     except EnvironmentError:
         return None
     for line in f.readlines():

diff --git a/docs/content/News.rst b/docs/content/News.rst
@@ -0,0 +1,43 @@
+News and Developments
+=====================
+
+
+Preprint introducing HiCExplorer is now online
+----------------------------------------------
+
+**March 8, 2017**
+
+Our #biorXiv preprint on DNA sequences behind Fly genome architecture is online!
+
+Read the article here : `<http://biorxiv.org/content/early/2017/03/08/115063>`_
+
+In this article, we introduce HiCExplorer : Our easy to use tool for HiC data analysis, also available in `Galaxy <https://galaxyproject.org/>`_.
+
+We also introduce `HiCBrowser <https://github.com/maxplanck-ie/HiCBrowser>`_ : A standalone software to visualize HiC along with other genomic datasets.
+
+Based on HiCExplorer and HiCBrowser, we built a useful resource for anyone to browse and download the chromosome
+conformation datasets in Human, Mouse and Flies. It's called `the chorogenome navigator <http://chorogenome.ie-freiburg.mpg.de/>`_
+
+Along with these resources, we present an analysis of DNA sequences behind 3D genome of Flies. Using high-resolution
+HiC analysis, we find a set of DNA motifs that characterize TAD boundaries in Flies and show the importance of these motifs in genome organization.
+
+We hope that these resources and analysis would be useful for the community and welcome any feedback.
+
+
+HiCExplorer wins best poster prize at VizBi2016
+-----------------------------------------------
+
+**March 20, 2016**
+
+We are excited to announce that HiCExplorer has won
+the `NVIDIA Award for Best Scientific Poster <https://vizbi.org/blog/2016/02/11/nvidia-award-for-best-scientific-poster/>`_
+in VizBi2016, the international conference on visualization of biological data.
+
+`Read more here <https://vizbi.org/blog/2016/03/20/winner-of-nvidia-best-scientific-poster-award-2/>`_
+
+This was our poster :
+
+.. image:: https://vizbi.org/Posters/Images/2016/B12.png
+   :scale: 50 %
+   :alt: HiCExplorer
+   :align: left
diff --git a/docs/content/installation.rst b/docs/content/installation.rst
@@ -8,12 +8,14 @@ Requirements
 -------------
 
 * Python 2.7
-* numpy >= 1.8.1
-* scipy >= 0.14.0
+* numpy >= 1.10.4
+* scipy >= 0.17.1
+* matplotlib >= 1.5.3
 * pysam >= 0.8.3
-* matplotlib >= 1.3.1
-* bx-python >= 0.7.1
+* intervaltree >= 2.1.0
 * biopython >= 1.65
+* tables >= 3.2.2
+* pyBigWig >=0.2.8
 
 The fastet way to obtain **Python 2.7 together with numpy and scipy** is
 via the `Anaconda Scientific Python
@@ -23,7 +25,7 @@ follow the directions for its installation. All of the requirements for HiCExplo
 
 .. code:: bash
 
-    $ conda install -c bioconda hicexplorer=0.1
+    $ conda install hicexplorer=1.6 -c bioconda -c conda-forge
 
 Command line installation using ``pip``
 -----------------------------------------
@@ -54,8 +56,34 @@ You are highly recommended to use `pip` rather than these more complicated steps
 
 	$ git clone https://github.com/maxplanck-ie/HiCExplorer.git
 
-3. install the source code (if you don't have root permission, you can set
+or if you want a particular release, choose one from https://github.com/maxplanck-ie/HiCExplorer/releases:
+::
+
+	$ wget https://github.com/maxplanck-ie/HiCExplorer/archive/1.5.12.tar.gz
+	$ tar -xzvf
+
+3. To install the source code (if you don't have root permission, you can set
 a specific folder using the ``--prefix`` option)
 ::
 
 	$ python setup.py install --prefix /User/Tools/hicexplorer
+
+
+Galaxy installation
+--------------------
+
+HiCExplorer can be easily integrated into a local `Galaxy <http://galaxyproject.org>`_.
+
+Installation with Docker
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+The HiCExplorer Galaxy instance is also available as a docker container, for those wishing to use the Galaxy
+framework but who also prefer a virtualized solution. This container is quite simple to install:
+
+::
+
+    $ sudo docker pull quay.io/bgruening/galaxy-hicexplorer
+
+To start and otherwise modify this container, please see the instructions on `the docker-galaxy-stable github repository <https://github.com/bgruening/docker-galaxy-stable>`__. Note that you must use `bgruening/galaxy-deeptools` in place of `bgruening/galaxy-stable` in the examples, as the deepTools Galaxy container is built on top of the galaxy-stable container.
+
+.. tip:: For support, or feature requests contact: [email protected]
diff --git a/docs/index.rst b/docs/index.rst
@@ -32,16 +32,12 @@ tool                            description
 =============================== ===========================================================================================
 
 
-Mailing list
+Getting Help
 ------------
 
-If you have questions, requests, or bugs to report, please email the
-`deepTools mailing list <https://groups.google.com/forum/#!forum/deeptools>`_
-
-
-
-This tool suite is developed by the `Bioinformatics Unit <http://www.ie-freiburg.mpg.de/bioinformaticsfac>`_
-at the `Max Planck Institute for Immunobiology and Epigenetics <http://www.ie-freiburg.mpg.de/>`_, Freiburg.
+* For general questions, please use Biostars with Tag `hicexplorer` : `Biostars <https://www.biostars.org/t/hicexplorer/>`_
+* For specific questions and feature requests, use the `deepTools mailing list <https://groups.google.com/forum/#!forum/deeptools>`_
+* For suggesting changes/enhancements and to report bugs, please create an issue on `our GitHub repository <https://github.com/maxplanck-ie/HiCExplorer>`_
 
 
 Contents:
@@ -53,11 +49,17 @@ Contents:
    content/installation
    content/list-of-tools
    content/example_usage
+   content/News
 
+Citation
+---------
+
+Please cite HiCExplorer as follows:
+
+Fidel Ramirez, Vivek Bhardwaj, Jose Villaveces, Laura Arrigoni, Bjoern A Gruening,Kin Chung Lam, Bianca Habermann, Asifa Akhtar, Thomas Manke.
+**"High-resolution TADs reveal DNA sequences underlying genome organization in flies". bioRxiv 115063** doi: https://doi.org/10.1101/115063
 
-Indices and tables
-==================
+.. image:: images/logo_mpi-ie.jpg
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+This tool suite is developed by the `Bioinformatics Unit <http://www.ie-freiburg.mpg.de/bioinformaticsfac>`_
+at the `Max Planck Institute for Immunobiology and Epigenetics <http://www.ie-freiburg.mpg.de/>`_, Freiburg.
diff --git a/setup.py b/setup.py
@@ -92,8 +92,8 @@ def checkProgramIsInstalled(self, program, args, where_to_download,
 setup(
     name='HiCExplorer',
     version=get_version(),
-    author='Fidel Ramirez',
-    author_email='[email protected]',
+    author='Fidel Ramirez, Vivek Bhardwaj, Björn Grüning',
+    author_email='[email protected]',
     packages=['hicexplorer'],
     scripts=['bin/findRestSite', 'bin/hicBuildMatrix', 'bin/hicCorrectMatrix',
              'bin/hicCorrelate', 'bin/hicFindEnrichedContacts', 'bin/hicFindTADs',