I am trying to port my 16S workflow that uses dada2, phyloseq and DECIPHER onto a Linux server. I have split the jobs up and am using snakemake to run through them. Seems fine.
When I go onto the server, I use conda to create a new environment and then install snakemake and R v4.0.3 into it.
# first install mamba as its faster for installing than conda conda install -c conda-forge mamba # create an environment mamba create -n dada2_pipeline # open the environment conda activate dada2_pipeline # install needed dependencies for the pipeline mamba install -c bioconda -c conda-forge snakemake=6.0.5 mamba install -c bioconda fasttree mamba install -c conda-forge r-base=4.0.3
I then planned on going into R to install the necessary dependencies, but
Rsamtools fails, see here, but what more curious is when I try and install bioconductor packages using conda, they regularly ask me to downgrade my R to install them, which of course I do not want to do.
mamba install -c bioconda bioconductor-rsamtools=2.6.0
Wants me to downgrade my R (which is 4.0.3) to 3.3.1. And also gives me the issue
Problem: nothing provides icu 54.* needed by r-base-3.3.1-1.
Just wondering how best to set up an environment with a standalone version of R and to install all the necessary packages from Bioconductor.
Linux system as output from
NAME="Ubuntu" VERSION="18.04.3 LTS (Bionic Beaver)" ID=ubuntu ID_LIKE=debian PRETTY_NAME="Ubuntu 18.04.3 LTS" VERSION_ID="18.04" HOME_URL="https://www.ubuntu.com/" SUPPORT_URL="https://help.ubuntu.com/" BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/" PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy" VERSION_CODENAME=bionic UBUNTU_CODENAME=bionic
Many thanks Dan