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Installation

Remember -- deepTools are available for command line usage as well as for integration into Galaxy servers!

Requirements

  • Python 2.7
  • numpy, scipy, bx-python, and pyBigWig
  • pysam >= 0.8

The fastet way to obtain Python 2.7 together with numpy and scipy is via the Anaconda Scientific Python Distribution. Just download the version that's suitable for your operating system and follow the directions for its installation. All of the requirements for deepTools can be installed in Anaconda with:

$ conda install -c https://conda.anaconda.org/bioconda pysam pyBigWig bx-python

Command line installation using pip

Install deepTools using the following command:

$ pip install git+https://github.com/fidelram/deepTools.git

All python requirements are automatically installed.

Command line installation without pip

1. Download source code

$ git clone https://github.com/fidelram/deepTools.git

or if you want a particular release, choose one from https://github.com/fidelram/deepTools/releases:

$ wget https://github.com/fidelram/deepTools/archive/1.5.12.tar.gz
$ tar -xzvf

2. The config file will tell you what deepTools expects to be installed properly:

$ cat deepTools/deeptools/config/deeptools.cfg

[external_tools]
sort: sort

[general]
# if set to max/2 (no quotes around)
# half the available processors will
# be used
default_proc_number: max/2
test_root: ../deeptools/test/

# temporary dir:
# deepTools bamCoverage, bamCompare and correctGCbias
# write files to a temporary dir before merging them
# and creating a final file. This can be speed up
# by writting to /dev/shm but for this a large
# physical memory of the server is required. If
# this is the case in your system, uncomment
# the following line. Otherwise, setting the
# variable to 'default', deepTools will use the
# temporary file configured in the system.
# Any other path that wants to be used for temporary
# files can by given as well (ie, /tmp)
#tmp_dir: /dev/shm
tmp_dir: default

3. 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 /Users/frd2007/Tools/deepTools

Galaxy installation

deepTools can be easily integrated into a local Galaxy. All wrappers and dependencies are available in the Galaxy Tool Shed.

Installation via Galaxy API (recommended)

First generate an API Key for your admin user and run the the installation script:

$ python ./scripts/api/install_tool_shed_repositories.py \
        --api YOUR_API_KEY -l http://localhost:8080 \
        --url http://toolshed.g2.bx.psu.edu/ \
        -o bgruening -r <revision> --name deeptools \
        --tool-deps --repository-deps --panel-section-name deepTools

The -r argument specifies the version of deepTools. You can get the latest revsion number from the test tool shed or with the following command:

$ hg identify http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools

You can watch the installation status under: Top Panel --> Admin --> Manage installed tool shed repositories

Installation via web browser

  • go to the admin page
  • select Search and browse tool sheds
  • Galaxy tool shed --> Sequence Analysis --> deeptools
  • install deeptools

remember: for support, questions, or feature requests contact: deeptools@googlegroups.com