From 1acbd66afd3c1abb39d813cf604332ba62a43adf Mon Sep 17 00:00:00 2001 From: UCDNJJ Date: Fri, 13 Sep 2024 10:04:29 -0700 Subject: [PATCH] update to new schema --- Dockerfile | 101 ------------------------------------------------ README.md | 6 +-- docker_building | 9 ----- 3 files changed, 3 insertions(+), 113 deletions(-) delete mode 100644 Dockerfile delete mode 100644 docker_building diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index 3c25bfa..0000000 --- a/Dockerfile +++ /dev/null @@ -1,101 +0,0 @@ -FROM rocker/tidyverse:4.2 - -MAINTAINER Nelson Johansen nelson.johansen@alleninstitute.org - -RUN export GITHUB_PAT=1000 - -## Would have liked to do these next 2 RUN under FROM:python3.8 but artifact passing wasn't immediatly clear. build-essential libxml2-dev python-is-python3 -RUN apt-get update -RUN apt-get install -y wget python3-dev python3-venv python3-pip -RUN pip3 install anndata==0.8.0 numpy - -RUN R -e 'install.packages("reticulate")' -RUN R -e 'install.packages("anndata", update=TRUE)' - -RUN R -e 'install.packages("BiocManager", update=FALSE)' -RUN R -e 'BiocManager::install(c( "AnnotationDbi", "data.table", "GO.db", \ - "impute", "limma", "preprocessCore", "xml2", "rols"), dependenceis=NA, update=TRUE)' -RUN R -e 'BiocManager::install(c( "munsell", "rhdf5", "dplyr", \ - "optparse", "foreach", "doParallel", "futile.logger", \ - "ggplot2", "WGCNA"), dependenceis=NA, update=TRUE)' -RUN R -e 'BiocManager::install(c( "randomForest", "LaplacesDemon", "reshape2", \ - "feather", "future", "tibble", "dendextend", \ - "Matrix", "MatrixExtra"), dependenceis=NA, update=TRUE)' -RUN R -e 'BiocManager::install(c( "mgcv", "edgeR", "caret", \ - "ggbeeswarm", "pvclust", \ - "cowplot" ), dependenceis=NA, update=TRUE)' -RUN R -e 'BiocManager::install(c("bigstatsr", "umap"), dependenceis=NA, update=TRUE)' -RUN R -e 'BiocManager::install(c("beachmat", "BiocNeighbors"), dependenceis=NA, update=TRUE)' - -RUN R -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/Rcpp/Rcpp_1.0.5.tar.gz", repos=NULL, type="source")' -RUN R -e 'install.packages("https://cloud.r-project.org/src/contrib/profmem_0.6.0.tar.gz", repos=NULL, type="source")' -RUN R -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/Hmisc/Hmisc_4.8-0.tar.gz", repos=NULL, type="source")' -RUN R -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz", repos=NULL, type="source")' - -RUN R -e 'install.packages("reticulate")' -RUN R -e 'install.packages("arrow")' -RUN R -e 'install.packages("anndata", update=TRUE)' -RUN R -e 'install.packages("jsonlite", update=TRUE)' - - -## Seurat setup -RUN apt-get update && \ - apt-get install -y libgeos-dev libglpk-dev -RUN R -e 'install.packages("sp")' -RUN R -e 'install.packages("spam")' -RUN R -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.6-4.tar.gz", repos=NULL, type="source",)' -RUN R -e 'install.packages("SeuratObject")' -RUN R -e 'install.packages("Seurat")' - -## Remote installs -RUN R -e 'install.packages("remotes", update=TRUE)' -RUN R -e 'remotes::install_github("krlmlr/bindrcpp")' -RUN R -e 'remotes::install_github("igraph/rigraph")' -RUN R -e 'remotes::install_github("i-cyto/Rphenograph")' -RUN R -e 'remotes::install_github("PavlidisLab/patchSeqQC")' -RUN R -e 'remotes::install_github("cysouw/qlcMatrix")' - -## Allen Institute R installs -RUN R -e 'remotes::install_github("AllenInstitute/CCN")' -RUN R -e 'remotes::install_github("AllenInstitute/patchseqtools")' -RUN R -e 'remotes::install_github("AllenInstitute/tasic2016data")' -RUN R -e 'remotes::install_github("AllenInstitute/hodge2019data")' -RUN R -e 'remotes::install_github("AllenInstitute/scrattch.io", ref="dev")' -RUN R -e 'remotes::install_github("AllenInstitute/scrattch.vis")' -RUN R -e 'remotes::install_github("AllenInstitute/scrattch.hicat")' -RUN R -e 'remotes::install_github("AllenInstitute/scrattch.bigcat")' -RUN R -e 'remotes::install_github("AllenInstitute/mfishtools")' - -## set python virtual environment -ENV VIRTUAL_ENV=/pyenv -RUN python3 -m venv $VIRTUAL_ENV -ENV PATH="$VIRTUAL_ENV/bin:$PATH" - -# cell_type_mapper install from GitHub -RUN git clone -b update/uns/to/precomp/stats/params --single-branch https://github.com/AllenInstitute/cell_type_mapper.git -RUN pip install -r ./cell_type_mapper/requirements.txt -RUN pip install -e ./cell_type_mapper -RUN pip install anndata==0.8.0 numpy==1.26.4 - -## scrattch-taxonomy install from local source -COPY scrattch.taxonomy_0.5.12.tar.gz ./scrattch.taxonomy_0.5.12.tar.gz -RUN R -e 'install.packages("scrattch.taxonomy_0.5.12.tar.gz", repos=NULL, type="source")' - -## scrattch-mapping install from local source -COPY scrattch.mapping_0.55.5.tar.gz ./scrattch.mapping_0.55.5.tar.gz -RUN R -e 'install.packages("scrattch.mapping_0.55.5.tar.gz", repos=NULL, type="source")' - -## -#COPY matrixStats_1.1.0.tar.gz ./matrixStats_1.1.0.tar.gz -#RUN R -e 'install.packages("matrixStats_1.1.0.tar.gz", repos=NULL, type="source")' -RUN R -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz", repos=NULL, type="source")' - -## Clean up -RUN rm -rf /var/lib/apt/lists/* -RUN rm -rf /tmp/downloaded_packages - -## Strip binary installed libraries from RSPM -## https://github.com/rocker-org/rocker-versioned2/issues/340 -RUN strip /usr/local/lib/R/site-library/*/libs/*.so - -## \ No newline at end of file diff --git a/README.md b/README.md index 8384cea..31d4a46 100644 --- a/README.md +++ b/README.md @@ -10,15 +10,15 @@ Update notes are here: ![Versions](https://github.com/AllenInstitute/scrattch-ma ## Docker -We have setup a docker environemnt for scrattch.taxonomy and scrattch.mapping that contains all the required dependencies and the current version of both scrattch.taxonomy and scrattch.mapping. This docker is accessible through docker hub via: `njjai/scrattch_mapping:0.6.3`. +We have setup a docker environemnt for scrattch.taxonomy and scrattch.mapping that contains all the required dependencies and the current version of all scrattch packages. This docker is accessible through docker hub via: `njjai/scrattch_mapping:0.6.6`. #### HPC usage: ##### Non-interactive -`singularity exec --cleanenv docker://njjai/scrattch_mapping:0.6.3 Rscript YOUR_CODE.R` +`singularity exec --cleanenv docker://njjai/scrattch_mapping:0.6.6 Rscript YOUR_CODE.R` ##### Interactive -`singularity shell --cleanenv docker://njjai/scrattch_mapping:0.6.3` +`singularity shell --cleanenv docker://njjai/scrattch_mapping:0.6.6` ## Installation diff --git a/docker_building b/docker_building deleted file mode 100644 index 33e7cbf..0000000 --- a/docker_building +++ /dev/null @@ -1,9 +0,0 @@ -cp /home/nelson.johansen/scripts/R/github/scrattch.mapping_0.55.5.tar.gz /allen/programs/celltypes/workgroups/hct/NelsonJ/docker/scrattch-mapping_dev -cp /home/nelson.johansen/scripts/R/github/scrattch.taxonomy_0.5.12.tar.gz /allen/programs/celltypes/workgroups/hct/NelsonJ/docker/scrattch-mapping_dev -cp /home/nelson.johansen/scripts/R/github/scrattch.mapping/Dockerfile /allen/programs/celltypes/workgroups/hct/NelsonJ/docker/scrattch-mapping_dev -cd /allen/programs/celltypes/workgroups/hct/NelsonJ/docker/scrattch-mapping_dev -sudo docker build . -t njjai/scrattch_mapping:0.6.2 --progress=plain 2>&1 | tee build.log -sudo docker push njjai/scrattch_mapping:0.6.2 -singularity build scrattch_mapping_0_6_2.sif docker://njjai/scrattch_mapping:0.6.2 - -## singularity shell --cleanenv docker://njjai/scrattch_mapping:0.6.2 \ No newline at end of file