Merge pull request #14 from openproblems-bio/scenicplus-fix

New scenicplus Docker image
openproblems-bio · Sep 30, 2024 · 24aab52 · 24aab52
2 parents 8258d0a + 141edd3
commit 24aab52
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diff --git a/dockerfiles/scenicplus/Dockerfile b/dockerfiles/scenicplus/Dockerfile
@@ -8,15 +8,11 @@ RUN git checkout fa55dae55203951c0c42e359b65a28010cd544f6
 RUN pip install .
 WORKDIR ..
 
-# 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 missing Python dependencies
+RUN pip install flatbuffers
+
+# Install Tabix (from htslib)
+RUN apt update && apt install -y tabix bedtools
 
 # Install Java
 RUN apt update

diff --git a/src/methods/multi_omics/scenicplus/config.vsh.yaml b/src/methods/multi_omics/scenicplus/config.vsh.yaml
@@ -39,12 +39,9 @@ functionality:
 
 platforms:
   - type: docker
-    # image: apassemi/scenicplus:1.0.1
+    image: apassemi/scenicplus:1.0.4
     # image: vanallenlab/scenicplus_x86_64:initial
-    image: aertslab/pyscenic:0.12.1
-    # setup:
-    #   - type: python
-    #     packages: [ flatbuffers ]
+    #image: aertslab/pyscenic:0.12.1
   - type: native
   - type: nextflow
     directives: