GAMtools is intended to run in a command line environment on UNIX, LINUX and Apple OS X operating systems. GAMtools can also be installed on Windows using cygwin.
The recommended way to install GAMtools is to use python’s package manager,
pip. This method should ensure that all of GAMtools required dependencies
are installed automatically.
Alternatively, GAMtools can be installed by downloading the source code and compiling it manually.
Installing stable releases using pip¶
To install the latest stable release using pip, you need to run the following command:
$ pip install gamtools
pip should automatically find and install any mandatory dependencies that are not currently installed. Additional optional dependencies are required for full GAMtools functionality, but these must be installed manually.
Installing from source (GitHub)¶
If you want to install the latest development version of GAMtools, you will need to install from source code. First, clone the GAMtools repository from GitHub:
$ git clone https://github.com/pombo-lab/gamtools.git
Then install the downloaded package using pip:
$ pip install gamtools/
Or if pip is not installed:
$ cd gamtools $ python setup.py install
Installation using pip is the preferred method, as this will handle installing
the mandatory dependencies automatically. If GAMtools is installed using
python setup.py install you may need to manually install
mandatory dependencies yourself.
GAMtools requires numpy and cython to be installed before it can compile
properly. If you are installing using
pip, numpy and cython should be installed
automatically, but there is a chance this might not work. If you are having issues
installing GAMtools, the first step is to ensure both numpy and cython are
$ pip install cython numpy
If you are still having problems, please post a ticket on our GitHub issues page.
GAMtools depends on a number of additional python libraries, which must be installed for it to function correctly. These libraries are normally installed automatically during the GAMtools installation process.
Some features in GAMtools depend on additional libraries and/or programs which are not installed automatically.
gamtools plot_np command requires some python plotting libraries to be
installed. These may also be required for the
gamtools call_windows command
--fitting-folder flag is specified.
Working with raw sequencing data¶
gamtools process_nps command is used to map and process raw sequencing
data from NPs. This can require a number of additional command line programs
to be installed and configured:
Mapping and processing programs¶
|Bowtie2||Mapping raw sequencing data.|
|samtools||Mapping raw sequencing data.|
|bedtools||Calling positive windows for an NP.|
|bedGraphToBigWig||Creating bigwigs (
|bedToBigBed||Creating bigbeds (
|fastqc||Performing dataset quality control (
|fastq_screen||Performing dataset quality control (
Testing your installation¶
To test that you have installed gamtools and all its dependencies correctly you
can run the command
gamtools test. If you have skipped installing any
optional dependencies, you may get a warning message saying something like “x
could not be found, and is required for y”. You can safely ignore these
messages unless you need the particular gamtools functionality in the message.