Installation and updating¶
Requirements¶
READemption was started to be developed using Python 3.2 and the user
is advised to run READemption with this or a higher version. In any
case setuptools and pip should be available on the system in
order to make the installation easy. READemption uses the short read
mapper segemehl for the
mapping and this software needs to be installed. The subcommands
viz_align
, viz_gene_quanti
, viz_deseq
require the Python
library Matplotlib. R and the bioconductor package DESeq2 are
necessary for the subcommand deseq
which performs differential
gene expression analysis. Don’t worry - in the following the
installation of all these requirements will be covered.
Installing on a fresh Ubuntu system¶
The following installation procedure was tested on a Amazon AWS t1.micro instance with Ubuntu Server 14.04 LTS image.
1. Installing all required Debian/Ubuntu packages¶
Before starting it is a good idea to update the package list:
sudo apt-get update
Now you can install the packages:
sudo apt-get install python3 python3-setuptools python3-pip python3-matplotlib cython3 zlib1g-dev make libncurses5-dev r-base libxml2-dev
Some comments:
- Ubuntu 16.04 should have Python 3.5 already installed.
cython
is required forpysam
make
,libncurses5-dev
andzlib1g-dev
are needed forsegemehl
libxml2
is required for the installation of some of the R-packages
2. Install segemehl¶
curl www.bioinf.uni-leipzig.de/Software/segemehl/old/segemehl_0_2_0.tar.gz > segemehl_0_2_0.tar.gz
tar xzf segemehl_0_2_0.tar.gz
cd segemehl_*/segemehl/ && make && cd ../../
In the future segemehl version 0.3.0 will be integrated into Reademption. For the time being we recommend using version 0.2.0.
Copying the executable to a location that is part of the PATH
e.g
/usr/bin/
…
sudo cp segemehl_0_2_0/segemehl/segemehl.x /usr/bin/segemehl.x
sudo cp segemehl_0_2_0/segemehl/lack.x /usr/bin/lack.x
… or the bin folder of your home directory:
mkdir ~/bin
cp segemehl_0_2_0/segemehl/segemehl.x ~/bin
3. Install DESeq2¶
Start R
:
R
and install the DESeq2 package inside of the interactive command line interface. You might be asked to confirm the installation path:
source("http://bioconductor.org/biocLite.R")
biocLite("DESeq2")
Leave R
:
quit(save = "no")
Install READemption and it’s dependcies¶
Now you can use pip
to install READemption
and further python
packages:
sudo pip3 install READemption
Voilà! You should now be able to call READemption:
reademption -h
Installing on a Apple OS X¶
(Many thanks to Lei Li for contribution this part!)
1. Installing all required software/packages¶
To download and install Python 3 follow the instruction at this download page.
Download and install xcode (page) and R (download links are on the frontpage).
To install pip
open a terminal and run
curl -O https://bitbucket.org/pypa/setuptools/raw/bootstrap/ez_setup.py python3 ez_setup.py # download and install pip
curl -O https://raw.github.com/pypa/pip/master/contrib/get-pip.py
python3 get-pip.py
Install matplotlib
:
pip3 install matplotlib
2. Installing segemehl, DESeq, pysam and READemption¶
The remaining installation steps are the same as descibed above. Just open a terminal and run the commands.
Updating READemption¶
Once you have installed READemption as described above you can easily upgrade it to the newest version by running
pip3 install --upgrade READemption