diff --git a/src/datasets/loaders/bruker_cosmx/config.vsh.yaml b/src/datasets/loaders/bruker_cosmx/config.vsh.yaml index 0c33c89d2..5fd748dfb 100644 --- a/src/datasets/loaders/bruker_cosmx/config.vsh.yaml +++ b/src/datasets/loaders/bruker_cosmx/config.vsh.yaml @@ -76,4 +76,4 @@ runners: - type: executable - type: nextflow directives: - label: [veryhighmem, midcpu, hightime] + label: [midmem, midcpu, hightime] diff --git a/src/methods_expression_correction/split/config.vsh.yaml b/src/methods_expression_correction/split/config.vsh.yaml index 9cb227219..d6fe7e14c 100644 --- a/src/methods_expression_correction/split/config.vsh.yaml +++ b/src/methods_expression_correction/split/config.vsh.yaml @@ -28,12 +28,12 @@ engines: setup: - type: docker run: | - apt-get update + apt-get update && apt-get install -y libcurl4-openssl-dev libssl-dev libgit2-dev libxml2-dev # - type: r # packages: [fs, rlang, lifecycle] - type: r - bioc: [SingleCellExperiment, anndataR, rhdf5, devtools, scater] - # bioc: [SpatialExperiment, anndataR, rhdf5, devtools, scater] + bioc: [SingleCellExperiment, anndataR, rhdf5, scater] + # bioc: [SpatialExperiment, anndataR, rhdf5, scater] # SingleCellExperiment part can probably be left out again in the future. It currently fixes a bug described in these issues: # https://github.com/drighelli/SpatialExperiment/issues/171 @@ -41,8 +41,9 @@ engines: # The reinstall of SingleCellExperiment triggers the correct re-install of SpatialExperiment. - type: r github: dmcable/spacexr - - type: r - github: bdsc-tds/SPLIT + - type: docker + run: | + Rscript -e 'remotes::install_github("bdsc-tds/SPLIT")' - type: native