feat: add Sauron conda environment file

angelettilab · Nov 11, 2020 · 8739d62 · 8739d62
1 parent 9ecd13c
commit 8739d62
Showing 1 changed file with 47 additions and 0 deletions.
diff --git a/envs/sauron/sauron_environment.yml b/envs/sauron/sauron_environment.yml
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+name: Sauron.v1
+channels:
+ - conda-forge
+ - bioconda
+ - defaults
+ - anaconda
+dependencies:
+ - r-base=3.5
+ - rstudio=1.1.456
+ - bioconductor-biomart=2.38
+ - bioconductor-flowpeaks=1.28
+ - bioconductor-genomeinfodbdata=1.2.0
+ - bioconductor-scater=1.10
+ - bioconductor-scran=1.10
+ - bioconductor-singlecellexperiment=1.4
+ - bioconductor-sva=3.30
+# - bioconductor-slingshot=1.2.0
+# - bioconductor-destiny=2.12.0
+ - bioconductor-monocle=2.10.0
+ - r-devtools=2.1.0
+ - r-biocmanager=1.30
+ - r-data.table=1.11
+ - r-dbscan=1.1
+ - r-dplyr=0.8
+ - r-fields=9.6
+ - r-igraph=1.2
+ - r-ineq=0.2
+ - r-optparse=1.6
+ - r-pheatmap=1.0
+ - r-rafalib=1.0
+ - r-rcolorbrewer=1.1
+ - r-scales=1.0
+ - r-seurat=3.0.1
+ - r-vegan=2.5
+ - r-venn=1.7
+ - r-hdf5r=1.2.0
+ - r-umap=0.2
+ - leidenalg=0.7.0
+ - umap-learn=0.3.7
+ - r-grr=0.9.5
+ - r-pbmcapply=1.4.1
+ - r-plot3d=1.1.1
+ - r-circlize
+ - r-wgcna
+# - snakemake=5.5.4
+# - r-raceid=0.1.3
+ - wget=1.19.4  # For compatibility with genomeinfodbdata (currently broken)