Merge remote-tracking branch 'origin/main' into marco/documentation

.gitignore

@@ -2,6 +2,7 @@
 .DS_Store
 
 # related to files
+params*
 resources*
 output/
 out/

README.md

@@ -104,8 +104,8 @@ approaches to assess both accuracy and comprehensiveness.
 | name               | roles  |
 |:-------------------|:-------|
 | Jalil Nourisa      | author |
-| Robrecht Cannoodt  | author |
 | Antoine Passemiers | author |
+| Robrecht Cannoodt  | author |
 
 ## API
 

_viash.yaml

@@ -11,5 +11,5 @@ config_mods: |
   .platforms[.type == 'docker'].target_image_source := 'https://github.com/openproblems-bio/task_grn_inference'
   .platforms[.type == "nextflow"].directives.tag := "$id"
   .platforms[.type == "nextflow"].auto.simplifyOutput := false
-  .platforms[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" }
+  .platforms[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", onedaytime : "time = 24.h", threedaystime : "time = 72.h", oneweektime : "time = 168.h" }
   .platforms[.type == "nextflow"].config.script := "process.errorStrategy = 'ignore'"

dockerfiles/figr/Dockerfile

@@ -0,0 +1,39 @@
+# Use the base image
+FROM ghcr.io/openproblems-bio/base_r:1.0.2
+
+# Install required dependencies for the R packages
+RUN apt-get update && apt-get install -y \
+    libcurl4-openssl-dev \
+    libxml2-dev \
+    libssl-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install R packages
+RUN R -e "install.packages(c('dplyr', 'FNN', 'chromVAR', 'doParallel', 'BuenColors', 'FigR', 'BSgenome.Hsapiens.UCSC.hg38'), 
+repos='http://cran.rstudio.com/')"
+
+# Set the working directory
+WORKDIR /workspace
+
+# Default command
+CMD ["R"]
+# Use the base image
+FROM ghcr.io/openproblems-bio/base_r:1.0.2
+
+# Install required dependencies for the R packages
+RUN apt-get update && apt-get install -y \
+    libcurl4-openssl-dev \
+    libxml2-dev \
+    libssl-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install R packages
+RUN R -e "install.packages(c('dplyr', 'FNN', 'chromVAR', 'doParallel', 'BuenColors', 'FigR', 'BSgenome.Hsapiens.UCSC.hg38'), 
+repos='http://cran.rstudio.com/')"
+
+# Set the working directory
+WORKDIR /workspace
+
+# Default command
+CMD ["R"]
+

dockerfiles/granie/Dockerfile

@@ -0,0 +1,24 @@
+# Use the base image
+FROM  bioconductor/bioconductor_docker:devel-R-4.4.1
+
+
+#Install R packages
+RUN R -e "install.packages(c('devtools'))"
+
+# Set the working directory
+WORKDIR /workspace
+
+# Default command
+CMD ["R"]
+
+#Version 1.9.4 of GRaNIE.
+RUN R -e "devtools::install_gitlab('grp-zaugg/[email protected]', host = 'git.embl.de', subdir = 'src/GRaNIE', dependencies = TRUE, upgrade = 'never')"
+
+#Version 0.3.1 of GRaNIEverse
+RUN R -e "devtools::install_gitlab('grp-zaugg/[email protected]', host = 'git.embl.de', upgrade = 'never', dependencies = TRUE)"
+
+#There is an incompatibility with the Matrix and irlba package, see https://github.com/satijalab/seurat/issues/8000
+RUN R -e "install.packages('irlba',type='source', rebuild = TRUE)"
+
+# biovizbase is only needed to create the ATAC assay along with annotation
+RUN R -e "BiocManager::install(c('BSgenome.Hsapiens.UCSC.hg38', 'EnsDb.Hsapiens.v86', 'EnsDb.Mmusculus.v79', 'BSgenome.Mmusculus.UCSC.mm39', 'biovizBase', 'Signac', 'glmGamPoi'))"

dockerfiles/pidc/Dockerfile

@@ -0,0 +1,14 @@
+# Use the base image
+FROM continuumio/anaconda3:2024.02-1
+
+# Install Python packages
+RUN pip install anndata
+
+# Install Julia
+RUN wget https://julialang-s3.julialang.org/bin/linux/x64/1.9/julia-1.9.3-linux-x86_64.tar.gz
+RUN tar -xvzf julia-1.9.3-linux-x86_64.tar.gz
+RUN mv julia-1.9.3 /opt/
+RUN ln -s /opt/julia-1.9.3/bin/julia /usr/local/bin/julia
+
+# Install Julia packages
+RUN julia -e 'using Pkg; Pkg.resolve(); Pkg.add(PackageSpec(name="InformationMeasures", version="0.3.0")); Pkg.add(PackageSpec(name="PyPlot", version="2.8.0")); Pkg.add(PackageSpec(name="LightGraphs", version="1.2.0")); Pkg.add(PackageSpec(name="GraphPlot", version="0.3.1")); Pkg.add(PackageSpec(name="NetworkInference", version="0.1.0"))'

dockerfiles/pycistopic/Dockerfile → dockerfiles/scenicplus/Dockerfile

@@ -1,5 +1,12 @@
 # Use the base image
-FROM janursa/scenicplus:19-08-2024
+FROM python:3.11.8
+
+# Install scenicplus
+RUN git clone https://github.com/aertslab/scenicplus
+WORKDIR scenicplus/
+RUN git checkout fa55dae55203951c0c42e359b65a28010cd544f6
+RUN pip install .
+WORKDIR ..
 
 # Install HTSlib and tabix
 RUN git clone https://github.com/samtools/htslib.git

dockerfiles/scglue/Dockerfile

@@ -0,0 +1,29 @@
+
+FROM nvidia/cuda:11.7.1-base-ubuntu20.04
+# Install required dependencies for the R packages
+RUN apt-get update && apt-get install -y \
+    bedtools \
+    build-essential \
+    curl \
+    bash \
+    python3 \
+    python3-pip \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install Python packages
+RUN pip install \
+    scglue==0.3.2 \
+    pyscenic==0.12.1 \
+    numpy==1.23.4 \
+    scanpy \
+    networkx \
+    pyarrow \
+    cytoolz \
+    scikit-misc \
+    cuda-python
+
+# Set the working directory
+WORKDIR /workspace
+
+# Default command
+CMD ["python"]