weishwu/squeezemeta repository overview

FROM quay.io/broadinstitute/viral-baseimage:0.2.0

RUN mamba create -n SqueezeMeta -c conda-forge -c bioconda -c fpusan squeezemeta=1.6 --no-channel-priority

# docker run -v /nfs/mm-isilon/bioinfcore/ActiveProjects/BFXcore_projects/metagenomics/ref_data/:/usr/share/ -it weishwu/squeezemeta:04052023

source /opt/miniconda/bin/activate SqueezeMeta
mkdir /usr/share/squeezemeta_dbs
download_databases.pl /usr/share/squeezemeta_dbs
test_install.pl

# docker container commit e8a391e74662 weishwu/squeezemeta:04052023

docker run -v /nfs/mm-isilon/bioinfcore/ActiveProjects/BFXcore_projects/metagenomics/ref_data/squeezemeta_dbs/:/nfs/mm-isilon/bioinfcore/ActiveProjects/BFXcore_projects/metagenomics/ref_data/squeezemeta_dbs/ -it weishwu/squeezemeta:1.6.5
source /opt/miniconda/bin/activate SqueezeMeta
configure_nodb.pl /nfs/mm-isilon/bioinfcore/ActiveProjects/BFXcore_projects/metagenomics/ref_data/squeezemeta_dbs/db
docker container commit cb45c19c1ea2 weishwu/squeezemeta:1.6.5
docker tag weishwu/squeezemeta:1.6.5 weishwu/squeezemeta:1.6.5db
docker push weishwu/squeezemeta:1.6.5db

# install sqm:
FROM continuumio/miniconda3
RUN conda update -n base conda
RUN conda install -n base conda-libmamba-solver
RUN conda config --set solver libmamba
RUN CONDA_OVERRIDE_CUDA=12.4 conda create -n SqueezeMeta -c conda-forge -c bioconda -c fpusan squeezemeta-dev --no-channel-priority --override-channels

# then follow steps above to download db and install other R packages (added vegan). 
# new db is under: /nfs/mm-isilon/bioinfcore/ActiveProjects/BFXcore_projects/metagenomics/ref_data/squeezemeta_dev_dbs/squeezemeta_dbs/

# FROM continuumio/miniconda3

RUN conda update -n base conda 
RUN conda install -n base conda-libmamba-solver
RUN conda config --set solver libmamba

RUN CONDA_OVERRIDE_CUDA=12.4 conda create -n SqueezeMeta -c conda-forge -c bioconda -c fpusan squeezemeta=1.7 --no-channel-priority --override-channels
RUN conda run -n SqueezeMeta conda install -y bioconda::gtdbtk

# downloaded databases as described above. Also downloaded gtdb (https://data.ace.uq.edu.au/public/gtdb/data/releases/release226/226.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r226_data.tar.gz) following https://ecogenomics.github.io/GTDBTk/installing/index.html (manual download to squeezemeta db path and untar)
# installed R libraries: 
# conda install conda-forge::r-tidyverse
# install.packages(c('gridExtra','ggplot2','cowplot','pheatmap'))
# install.packages("remotes")
# remotes::install_github("vegandevs/vegan")

## on top of 1.7.0, added ggpubr and indicspecies:
conda install -y conda-forge::r-ggpubr
install.packages('indicspecies')