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Install DESeq2 and edgeR with Anaconda

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.

anaconda deseq2 edger
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updated by Robert W Link • Robert W Link • written by salamandra salamandra

if you don't have sudo create an environment first

conda create -n myawesomeenvironment python=3.6
source activate myawesomeenvironment
• 0 views • link
written by Jeremy Leipzig Jeremy Leipzig

3 answers

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.

• 0 views • link
written by Michael Dondrup Michael Dondrup

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")
• 0 views • link
written by Sean Davis Sean Davis

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.

• 0 views • link
written by steve steve

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.

• 0 views • link
written by Robert W Link • Robert W Link

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