Setting up bioconductor on a Linux server using conda
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Entering edit mode
Daniel • 0
@daniel-25120
Last seen 6 months ago

Hi everyone

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 cat /etc/os-release

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

dada2 conda phyloseq • 345 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

This is most likely a question for the conda people. This isn't really related to Bioconductor per se, and we have nothing to do with them, so they would almost surely be better positioned to help you.

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