Question: Install DESeq2 and edgeR with Anaconda
gravatar for salamandra
2.8 years ago by
salamandra280 wrote:

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?


You can search for this package on 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.

edger anaconda deseq2 • 5.0k views
ADD COMMENTlink modified 2.4 years ago by Linkrw1230 • written 2.8 years ago by salamandra280

if you don't have sudo create an environment first

conda create -n myawesomeenvironment python=3.6
source activate myawesomeenvironment
ADD REPLYlink written 2.4 years ago by Jeremy Leipzig19k
gravatar for Michael Dondrup
2.8 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

At least samtools is in the bioconda repo. Google the instructions for activation of bioconda. See the instructions here: 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.

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Michael Dondrup47k
gravatar for Sean Davis
2.8 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

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:

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Sean Davis26k

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.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by steve2.5k
gravatar for Linkrw12
2.4 years ago by
Philadelphia, PA
Linkrw1230 wrote:

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 = within R to install dependencies that were already on CRAN.

ADD COMMENTlink written 2.4 years ago by Linkrw1230
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1619 users visited in the last hour