Install DESeq2 and edgeR with Anaconda

Question

[salamandra]

I tried to install DESeq2, edgeR and others wilth Anaconda in ubuntu machine with the code:

conda install wget samtools r-essentials bioconductor-deseq2 bioconductor-edger

as suggested here. It gave the error

Error:  Packages missing in current linux-64 channels: 
  - samtools
  - r-essentials
  - bioconductor-deseq2
  - bioconductor-edger

Did you mean one of these?

    apptools

You can search for this package on anaconda.org with

    anaconda search -t conda bioconductor-edger

 (and similarly for the other packages)

I used the version 4.4.0 of Anaconda and then downgraded to 4.0.0 to solve the issue as suggested somewhere else.

Also tried the command

conda install wget samtools r-essentials bioconductor-deseq2 bioconductor-edger --unknown

It didn't work. What is missing here?

Note: I don't have sudo privileges.

[Jeremy Leipzig]

if you don't have sudo create an environment first

conda create -n myawesomeenvironment python=3.6
source activate myawesomeenvironment

Answer 1

[Michael]

At least samtools is in the bioconda repo. Google the instructions for activation of bioconda. See the instructions here: https://bioconda.github.io/ or just run the cited commands, should be sufficient.

conda config --add channels conda-forge
conda config --add channels defaults
conda config --add channels r
conda config --add channels bioconda

or if it is just for one tool, you can simply do conda install -c bioconda samtools

You don't need superuser privileges, that is the idea behind conda.

Answer 2

[Sean Davis]

The Bioconductor project does not support bioconda directly, so your mileage may vary when using bioconda. The recommended way to install Bioconductor packages is from within R using:

source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
biocLite("edgeR")

[steve]

I recently tried this, and ended up with a huge mess. My conda R was on version 3.3.2, while my global R was on version 3.3.0. Despite having activated my conda R, R still installed the packages to my global R's library directory, overwriting my 3.3.0 packages with 3.3.2 packages. I did not realize the problem until I later ran some pipelines which utilized the global R 3.3.0, and all my Bioconductor packages were broken. Still trying to find a solution, I think it might require running export R_LIBS_USER="/path/to/miniconda2/envs/r.3.3/lib/R/library" in the terminal after activating conda & the conda environment, and before loading R to start the Bioconductor installation. Using biocLite(..., loc = "/path/to/miniconda2/envs/r.3.3/lib/R/library") did not work.

Answer 3

[Robert W Link]

Adding this for completeness sake:

Sometimes Bioconductor packages will not be in the bioconda repo and when I tried Sean's solution, my computer yelled at me (I also don't have sudo privaleges). I ended up downloading the source code into the anaconda R library directory and installing it from the command line. My general scheme is shown below:

~$ cd anaconda2/lib/R/library/ # This line will change if you are using a specific env in Conda
~/anaconda2/lib/R/library$ wget *URL to "source package" from package's web page*
~/anaconda2/lib/R/library$ R CMD INSTALL source_package.tar.gz

If it required dependencies, I went down the rabbit hole and either repeated the above method to download the Bioconductor packages or I just used install.packages(package, repos = https://cran.r-project.org/) within R to install dependencies that were already on CRAN.