bash: biom: command not found...Error while running CSS normalisation
normalize_table.py -i otu_table.biom -a CSS -o otu_table_CSSnorm.biomLibrary biom not found.
To install, open R and run the command: install.packages("biom") If you already have the biom package installed in a local directory, please store the path to that directory in an environment variable called "R_LIBRARY_PATH". This may be necessary if you are running QIIME on a cluster, and the cluster instances of R don't know about your local R libraries. If you don't know your R library paths, you can list them by opening R and running with the command, ".libPaths()". The current R instance knows about these paths: [/usr/lib64/R/library, /usr/share/R/library] Warning message: In library(lib.name, character.only = TRUE, logical.return = TRUE, : there is no package called ‘biom’ Problem: biom package is not installed in R
"Package ‘biom’ was removed from the CRAN repository."
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("biomformat") install development version of the R biom package 1) install libssl libcurl libxml on linux
sudo apt-get install libssl-dev curl libcurl4-openssl-dev libxml2-dev # Debian/Ubuntu sudo yum install -y openssl-devel curl libcurl libcurl-devel libxml2 libxml2-devel # CentOS 2) In R: install development tools
to be able to download and install biom from git
R install.packages("devtools") library("devtools") install_github("joey711/biom")# Error in R
Warning messages:
1: In install.packages("devtools") : installation of package ‘curl’ had non-zero exit status 2: In install.packages("devtools") : installation of package ‘openssl’ had non-zero exit status 3: In install.packages("devtools") : installation of package ‘git2r’ had non-zero exit status 4: In install.packages("devtools") : installation of package ‘httr’ had non-zero exit status 5: In install.packages("devtools") : installation of package ‘devtools’ had non-zero exit status # requires Linux/Ubuntu installation of libssl libcurl and libxml, see (1) above.
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