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Merge pull request maximilianh#52 from pcm32/patch-3
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Add bioconda installation alternative.
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maximilianh committed Dec 4, 2018
2 parents 10d1447 + 59e4e6a commit 3cb13bc
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26 changes: 21 additions & 5 deletions README.rst
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Expand Up @@ -30,7 +30,8 @@ The following documentation explains how to create a cellbrowser from a:
This is early research software. You are likely to find bugs. Please open a Github
ticket or email us at cells@ucsc.edu, we can usually fix them quickly.

# Installation
Installation: pip-based
-----------------------

You need Python2.5+ or Python3+ and pip. On a Mac or any Linux, simply run:

Expand All @@ -44,18 +45,32 @@ On Linux, if you you're not allowed to run the sudo command, you can install int

pip install --user cellbrowser
export PATH=$PATH:~/.local/bin

Installation: conda-based
-------------------------

Alternatively, if you prefer to install through bioconda, since 0.4.23 you can do:

As an alternative to these pip commands, you can also git clone the repo and
conda install -c bioconda ucsc-cell-browser

Installation: git clone
-----------------------

As an alternative to pip or conda, you can also git clone the repo and
run the command line scripts under cellbrowser/src:

git clone https://github.com/maximilianh/cellBrowser.git --depth=10
cd cellBrowser/src

Create site with data
---------------------

Now you should be able to run the cbBuild command and see the help messages:
After installing through one of the methods above, you should be able to run the cbBuild command and see the help messages:

cbBuild

# Create a browser for a sample dataset
Create a browser for a sample dataset
-------------------------------------

Here is a small example dataset (Nowakowski et al 2018, fetal brains). The
expression matrix includes only the first 100 genes, otherwise quite a few
Expand Down Expand Up @@ -95,7 +110,8 @@ your ~/.bashrc to point to your html directory:

export CBOUT=/var/www

# Using a real webserver
Using a real webserver
----------------------

The -p 8888 is optional. A more permanent alternative to the -p option is to
run a webserver on your machine and build directly into its web directory.
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