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BIRCH currently has the following dependencies:
- Java Runtime
Environment, version 8 or newer
- Python 2.7 AND
Python 3
- Csh/Tcsh installed
- MacOS - also requires
Xcode, which is available at the App Store.
You can check if you have
these by running this script,
or by typing these commands at a terminal:
Java:
java -version |
should output 1.8 or greater
Important: If the word "headless" appears, you
must install the full Java JDK. |
Python:
python
--version
python3
--version |
should output 2.7 or greater
should output
3.6 or greater
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Tcsh/csh
tcsh
--version
|
if it outputs anything it
should be good enough... |
Optional
dependencies - BIRCH will function without these,
but specific programs require them.
- numpy - Python numerical
libraries, required by WebLogo.
If numpy is installed you should be able to run python
and try to import numpy. (User input shown in bold
below). If you get an error, you need to install
numpy.
{venus:/home/psgendb}python
Python 2.6.6 (r266:84292, Nov 21 2013,
10:50:32)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on
linux2
Type "help", "copyright", "credits" or
"license" for more information.
>>> import numpy
>>>
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A more comprehensive list of
dependencies can be found at Dependencies.
If you are missing one of them, follow the steps below:
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- Update to the newest version of
java using the update manager
- Download and
install Python
Shortcut: If you type 'python3
--version', you will be prompted to install python,
which in turn will install Xcode as a dependency.
Thus, both python3 and Xcode are installed in a single
step.
- Download
and install numpy
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Ubuntu/Debian
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- Open a terminal
- Check whether java is headless:
dpkg -l |grep
openjdk
If you have the headless version of Java, uninstall
it:
sudo apt-get
remove openjdk-8-jre-headless
- Execute:
sudo apt
install default-jdk
sudo apt-get install python numpy python3
sudo
apt-get install tcsh
For Ubuntu 22:
sudo apt-get install python-is-python3
With Ubuntu 22, there is no 'python' command. This
package creates an alias so that 'python' will run
'python3'. Since many of the Python calls in BIRCH are
just to 'python', many of the scripts won't work unless
you install this package.
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Fedora/RedHat
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- Open a terminal
- Execute:
su
#become administrator
yum
install java python tcsh
yum
install numpy
Fedora31 (and possibly other
RedHat-derived linux distros) have ONLY the headless Java
installed by default. Before running getbirch.jar, you
need to install the full JKD using the following command:
sudo dnf
install java-latest-openjdk.x86_64
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(Other Linux distros)
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- Download and install Java
- Download and
install Python
- Download
and
install tcsh
- Download
and install numpy
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