Install caRpools on Linux using Conda

conda-caRpools.md

Create a conda environment to be used with caRpools

$ conda create -n carpools -y pip

Activate the new env

$ source activate carpools

You have to install Pandoc as sudo (sorry :( ), if you don't have already installed it.

# Ubuntu
$ sudo apt-get install pandoc
# CentOS
$ sudo yum install pandoc

Download and compile new packages

Install Mageck

$ mkdir $HOME/caRpools
$ cd ~/caRpools
$ wget https://sourceforge.net/projects/mageck/files/0.5/mageck-0.5.4.tar.gz/download -O mageck-0.5.4.tar.gz
$ tar zxvf mageck-0.5.4.tar.gz
$ cd mageck-0.5.4
$ python setup.py install --prefix=$HOME/caRpools

Modif your .bashrc with this new entries. To save the path configuration (so you don't have to type it every time), place the above command in your ~/.bashrc (for Linux)

$ export PATH="$HOME/caRpools/bin:$PATH"
$ export PYTHONPATH="$HOME/caRpools/lib/python3.5/site-packages:$PYTHONPATH"
$ source ~/.bashrc

Install TexLive

$ mkdir $HOME/caRpools/texlive
$ cd ~/caRpools/texlive
$ wget http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz
$ tar xzvf install-tl-unx.tar.gz
$ cd install-tl{data}
$ ./install-tl
D
1
$HOME/caRpools/texlive {Note: You have to put the full path here. Do not use $HOME}
R
I {Note: This will take a while. You can go to have a coffee :P}

Modif your .bashrc with this new entries.

$ export PATH="$HOME/caRpools/texlive/bin/x86_64-linux:$PATH" 
$ source ~/.bashrc

Install packages to conda

$ conda install -y -c bioconda bowtie2
$ conda install -y -c cyclus java-jdk=8.45.14
$ conda install -y -c cyclus java-jre=8.45.14
$ conda install -y -c anaconda gcc=4.8.5
$ conda install -y -c r r-base=3.3

Configure Java to be used by R

$ export PATH="$HOME/miniconda3/envs/carpools/bin:$PATH"
$ export JAVA_HOME="$HOME/miniconda3/envs/carpools/bin"
$ export JAVA_LD_LIBRARY_PATH="$HOME/miniconda3/envs/carpools/jre/lib/amd64/server"
$ source ~/.bashrc

It is better if you logoff and login again with your user. Set Java to be available to R.

# Dry-run to check if all the variables is ok .
R CMD javareconf -n
R CMD javareconf -e
R
install.packages('rJava') {Note: You will need to select a mirror to download the package. Select the better one for you. If you are in Brazil, you can use the mirror from SP (6) }
source("http://bioconductor.org/biocLite.R")
biocLite(c("BiocGenerics"))
biocLite(c("biomaRt"))
biocLite(c("DESeq2"))
install.packages('seqinr')
install.packages('xlsx')
install.packages('xlsxjars')
install.packages('stringi')
install.packages('scatterplot3d')
install.packages('rmarkdown')
install.packages('knitr')
install.packages('VennDiagram')
install.packages('sm')
install.packages("caRpools")

Still using R, check if the installation were ok.

library('caRpools')
check.caRpools()
q()

Deactivate the enviroment

$ source deactivate carpools

Test of caRpools

Download the example data and test if all the components of the software are working good.