Merge pull request #9 from openproblems-bio/cistarget-db

Bug fixes in scenicplus + change python version + generate cistopic databases from scratch

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
@@ -15,10 +22,3 @@ WORKDIR ..
 RUN apt update
 RUN apt install -y openjdk-17-jdk
 ENV JAVA_HOME /usr/lib/jvm/java-17-openjdk-amd64/
-
-# Re-install scenicplus
-RUN git clone https://github.com/aertslab/scenicplus
-WORKDIR scenicplus/
-RUN git checkout fa55dae55203951c0c42e359b65a28010cd544f6
-RUN pip install .
-WORKDIR ..

src/methods/multi_omics/scenicplus/config.vsh.yaml

@@ -27,22 +27,16 @@ functionality:
       required: true
       direction: output
       description: "Cell-topics prob scores"
-    - name: --rankings_db
-      type: file
-      direction: input
-    - name: --scores_db
-      type: file
-      direction: input
-
-
-
   resources:
     - type: python_script
       path: script.py
 
 platforms:
   - type: docker
-    image: apassemi/scenicplus:latest
+    image: apassemi/scenicplus:1.0.0
+    setup:
+      - type: python
+        packages: [ flatbuffers ]
   - type: native
   - type: nextflow
     directives: