Merge pull request #3 from openproblems-bio/scenicplus

Add pycistopic

dockerfiles/pycistopic/Dockerfile

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+# Use the base image
+FROM janursa/scenicplus:19-08-2024
+
+# Install HTSlib and tabix
+RUN git clone https://github.com/samtools/htslib.git
+WORKDIR htslib/
+RUN autoreconf -i
+RUN git submodule update --init --recursive
+RUN ./configure
+RUN make
+RUN make install
+WORKDIR ..
+
+# Install Java
+RUN apt update
+RUN apt install -y openjdk-17-jdk
+ENV JAVA_HOME /usr/lib/jvm/java-17-openjdk-amd64/

src/methods/pycistopic/config.vsh.yaml

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+# __merge__: ../../api/comp_method.yaml
+
+functionality:
+  name: pycistopic
+  info:
+    label: pycistopic
+    summary: "Cis-regulatory topic modeling using pycisTopic"
+    description: |
+      Cis-regulatory topic modeling using pycisTopic.
+    documentation_url: https://pycistopic.readthedocs.io/en/latest/
+  arguments:
+    - name: --multiomics_atac
+      type: file
+      must_exist: true
+      example: resources/grn-benchmark/multiomics_atac.h5ad
+      info:
+        label: multiomics_atac
+        summary: "ATAC data"
+        file_type: h5ad
+        columns: 
+          - name: dummpy
+            type: string
+            required: false
+      required: true
+    - name: --out_dir
+      type: file
+      direction: output
+      create_parent: true
+      default: 'output/pycistopic'
+    - name: --cell_topic
+      type: file
+      example: resources/grn-benchmark/supp/cell_topic.csv
+      info:
+        label: Cell topic probability database
+        summary: "annotation file"
+        file_type: csv
+        columns: 
+          - name: topic
+            type: string
+            required: false
+      required: true
+    - name: --qc
+      type: boolean_true
+      description: Whether to perform quality control
+  resources:
+    - type: python_script
+      path: script.py
+
+platforms:
+  - type: docker
+    image: apassemi/scenicplus:latest
+    setup:
+      - type: docker
+        run: |
+          export JAVA_HOME=/usr/lib/jvm/java-17-openjdk-amd64/
+  - type: native
+  - type: nextflow
+    directives:
+      label: [midtime,himem,hicpu]

src/methods/pycistopic/run.sh

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+viash build src/methods/pycistopic/config.vsh.yaml --platform docker -o bin/pycistopic && bin/pycistopic/pycistopic --multiomics_atac resources/resources_test/grn-benchmark/multiomics_atac.h5ad --prediction bin/pycistopic/prediction.csv --cell_topic resources/resources_test/grn-benchmark/supp/cell_topic.csv --out_dir output/pycistopic