dcgc-bfx/dcgc-single-cell:latest
$ singularity pull shub://dcgc-bfx/dcgc-single-cell:latest
Singularity Recipe
Bootstrap: shub
From: dcgc-bfx/dcgc-jupyter-rstudio:0.2.0
%help
Container for single cell analysis.
Start jupyter lab:
singularity run --writable-tmpfs --app jupyter library://fabianrost84/dcgc/single-cell.sif
Start rstudio server listening on port 8787:
singularity run --writable-tmpfs --app rserver library://fabianrost84/dcgc/single-cell.sif 8787
%environment
export DEBIAN_FRONTEND=noninteractive
export PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
%post
export DEBIAN_FRONTEND=noninteractive
export PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
apt-get update -q
apt-get install -y -q libatlas-base-dev
apt-get clean -q
rm -rf /var/lib/apt/lists/*
# install python packages with mamba
mamba install --quiet --yes \
anndata \
anndata2ri \
bbknn \
bioservices \
cellrank \
cython \
gsl \
h5py \
joblib \
leidenalg \
libtiff=4.1 `# version 4.2 breaks plotting` \
loompy \
louvain \
pybedtools \
pybiomart \
pypairs \
pytables \
python-igraph \
scanpy \
scikit-learn \
scrublet \
scvi \
statsmodels \
xlrd \
xlwt \
`# R packages` \
bioconductor-annotationhub \
bioconductor-biomart \
bioconductor-clusterexperiment \
bioconductor-complexheatmap \
bioconductor-deseq2 \
bioconductor-dropletutils \
bioconductor-genomeinfodb \
bioconductor-genomeinfodbdata \
bioconductor-hsmmsinglecell \
bioconductor-loomexperiment \
bioconductor-mast \
bioconductor-monocle \
bioconductor-scater \
bioconductor-scran \
bioconductor-singlecellexperiment \
bioconductor-slingshot \
r-argparse \
r-biocmanager \
r-enrichr \
r-factoextra \
r-fastmatch \
r-furrr \
r-future \
r-gam \
r-ggthemes \
r-kableextra \
r-loomr \
r-monocle3 \
r-openxlsx \
r-parallelly \
r-pheatmap \
r-readr \
r-refmanager \
r-remotes \
r-rgl \
r-sctransform \
r-seurat=4 \
r-spam \
r-spatstat=1.64_1 \
r-spatstat.core \
r-upsetr \
r-utf8 \
r-venndiagram \
`# cerebro app deps` \
bioconductor-biocparallel \
bioconductor-delayedarray \
bioconductor-gseabase \
bioconductor-gsva \
bioconductor-iranges \
bioconductor-matrixgenerics \
bioconductor-qvalue \
bioconductor-s4vectors \
bioconductor-glmgampoi \
r-colourpicker \
r-formatr \
r-msigdbr \
r-shinycssloaders \
r-shinydashboard \
r-shinyfiles \
r-shinyjs \
r-shinywidgets
# clean conda cache
mamba clean -ai --quiet --yes
# pip
pip -q --no-cache-dir install -U \
fa2 \
gprofiler-official \
magic-impute
pip install -q --no-cache-dir git+https://github.com/theislab/diffxpy
pip install -q --no-cache-dir git+https://github.com/theislab/scachepy
pip install -q --no-cache-dir git+https://github.com/calico/solo.git
# install R dependencies not available from conda
R --quiet -e "devtools::install_github(repo = 'yanlinlin82/ggvenn', dependencies = FALSE, quiet = TRUE)"
R --quiet -e 'devtools::install_github("cellgeni/sceasy", dependencies = FALSE, quiet = TRUE)'
R --quiet -e 'remotes::install_github("chris-mcginnis-ucsf/DoubletFinder")'
R --quiet -e 'BiocManager::install(c(
"GenomeInfoDbData",
"romanhaa/cerebroApp"
), ask = FALSE, update = FALSE, dependencies = FALSE, quiet = TRUE)'
R --quiet -e "devtools::install_github(repo = 'cboettig/knitcitations', quiet = TRUE)"
R --quiet -e 'install.packages(c(
"PoiClaClu",
"hutils",
"singleCellHaystack"), repos="http://cran.r-project.org", quiet = TRUE)'
chmod -R a+w /opt
%test
# scanpy
bash <<-EOF
source ~/.bashrc
conda activate /opt/conda
NUMBA_CACHE_DIR=/tmp python -c "import scanpy; scanpy.logging.print_versions()"
EOF
# Seurat
bash <<-EOF
source ~/.bashrc
conda activate /opt/conda
R --quiet -e "library(Seurat); sessionInfo()"
EOF
Collection
- Name: dcgc-bfx/dcgc-single-cell
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/dcgc-bfx-dcgc-single-cell-latest |
collection name | dcgc-bfx/dcgc-single-cell |
branch | main |
tag | latest |
commit | 108d2bdadbba7e1db69941743ceb6382143bd515 |
version (container hash) | dc1a4c6d7fef4d6ed157c44bd22babab36b635bdd70b31adee18020e21294fd8 |
build date | 2021-04-12T08:42:46.400Z |
size (MB) | 2685.14453125 |
size (bytes) | 2815578112 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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