make graphviz with an import exception, otherwise the ascii file is w…

…ritten to file.

.github/condaBuildCI.yml

@@ -2,8 +2,9 @@ name: condaBuild_CI
 channels:
   - uibcdf
   - conda-forge
-  - defaults
   - bioconda
 dependencies:
+  - python=3.11
   - anaconda-client
-  - conda-build
+  - conda-build
+  - conda-verify

.github/snakePipesEnvCI.yml

@@ -1,4 +1,3 @@
 name: snakePipes_CI
 dependencies:
-  - python >= 3.11
-  - graphviz
+  - python >= 3.11

.github/workflows/conda-build.yml

@@ -9,7 +9,6 @@ jobs:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: 3.11
           environment-file: .github/condaBuildCI.yml
           auto-update-conda: false
           auto-activate-base: false

conda-recipe/meta.yaml

@@ -10,18 +10,18 @@ source:
 build:
   number: 0
   noarch: python
-  script: python -m pip install --no-deps --ignore-installed .
+  script: pip install .
 
 requirements:
   host:
     - python >=3
     - pip
+    - seaborn
   run:
     - python >=3.11
     - snakemake >=8
     - snakemake-executor-plugin-cluster-generic >=1.0.9
     - pandas
-    - graphviz
     - thefuzz
     - pyyaml >=5.1
 

snakePipes/common_functions.py

@@ -14,7 +14,6 @@
 import smtplib
 from email.message import EmailMessage
 from importlib.metadata import version
-import graphviz
 
 def set_env_yamls():
     """
@@ -687,10 +686,17 @@ def plot_DAG(args, snakemake_cmd, calling_script, defaults):
     # Read DOT data from stdout
     dot = DAGproc.stdout.read()
 
-    # Use graphviz to render DAG
-    graph = graphviz.Source(dot)
+    # Use graphviz to render DAG, if it is available
+    # conda graphviz doesn't provide the python bindings, the pip graphviz does, but has no executable.
+    # If graphviz is not available, write out the ASCII as file.
     output_file = os.path.join(args.outdir, f"{workflow_name}_pipeline")
-    graph.render(output_file, format='png')
+    try:
+        import graphviz
+        graph = graphviz.Source(dot)
+        graph.render(output_file, format='png')
+    except ModuleNotFoundError:
+        with open(output_file + 'DAG.txt', 'w') as f:
+            f.write(dot)
 
 
 def print_DAG(args, snakemake_cmd, callingScript, defaults):

snakePipes/workflows/ATACseq/ATACseq.py

@@ -121,7 +121,7 @@ def main():
     cf.runAndCleanup(args, snakemake_cmd, logfile_name)
 
     #CreateDAG
-    cf.print_DAG(args,snakemake_cmd, __file__,defaults)
+    cf.plot_DAG(args,snakemake_cmd, __file__,defaults)
 
 
 if __name__ == "__main__":

snakePipes/workflows/ChIPseq/ChIPseq.py

@@ -189,7 +189,7 @@ def main():
     cf.runAndCleanup(args, snakemake_cmd, logfile_name)
 
     #CreateDAG
-    cf.print_DAG(args,snakemake_cmd, __file__,defaults)
+    cf.plot_DAG(args,snakemake_cmd, __file__,defaults)
 
 
 if __name__ == "__main__":

snakePipes/workflows/DNAmapping/DNAmapping.py

@@ -156,7 +156,7 @@ def main():
     cf.runAndCleanup(args, snakemake_cmd, logfile_name)
 
     #CreateDAG
-    cf.print_DAG(args,snakemake_cmd, __file__,defaults)
+    cf.plot_DAG(args,snakemake_cmd, __file__,defaults)
 
 
 if __name__ == "__main__":

snakePipes/workflows/HiC/HiC.py

@@ -187,7 +187,7 @@ def main():
     cf.runAndCleanup(args, snakemake_cmd, logfile_name)
 
     # CreateDAG
-    cf.print_DAG(args, snakemake_cmd, __file__, defaults)
+    cf.plot_DAG(args, snakemake_cmd, __file__, defaults)
 
 
 if __name__ == "__main__":

snakePipes/workflows/WGBS/WGBS.py

@@ -180,7 +180,7 @@ def main():
     cf.runAndCleanup(args, snakemake_cmd, logfile_name)
 
     #CreateDAG
-    cf.print_DAG(args,snakemake_cmd, __file__,defaults)
+    cf.plot_DAG(args,snakemake_cmd, __file__,defaults)
 
 
 if __name__ == "__main__":

snakePipes/workflows/createIndices/createIndices.py

@@ -125,7 +125,7 @@ def main():
     cf.runAndCleanup(args, snakemake_cmd, logfile_name)
 
     #CreateDAG
-    cf.print_DAG(args,snakemake_cmd, __file__,defaults)
+    cf.plot_DAG(args,snakemake_cmd, __file__,defaults)
 
 
 if __name__ == "__main__":

snakePipes/workflows/mRNAseq/mRNAseq.py

@@ -196,4 +196,4 @@ def main():
     cf.runAndCleanup(args, snakemake_cmd, logfile_name)
 
     #CreateDAG
-    cf.print_DAG(args,snakemake_cmd, __file__,defaults)
+    cf.plot_DAG(args,snakemake_cmd, __file__,defaults)

snakePipes/workflows/ncRNAseq/ncRNAseq.py

@@ -121,7 +121,7 @@ def main():
     cf.runAndCleanup(args, snakemake_cmd, logfile_name)
 
     #CreateDAG
-    cf.print_DAG(args,snakemake_cmd, __file__,defaults)
+    cf.plot_DAG(args,snakemake_cmd, __file__,defaults)
 
 
 if __name__ == "__main__":

snakePipes/workflows/preprocessing/preprocessing.py

@@ -137,7 +137,7 @@ def main():
     cf.runAndCleanup(args, snakemake_cmd, logfile_name)
 
     #CreateDAG
-    cf.print_DAG(args,snakemake_cmd, __file__,defaults)
+    cf.plot_DAG(args,snakemake_cmd, __file__,defaults)
 
 
 if __name__ == "__main__":

snakePipes/workflows/scRNAseq/scRNAseq.py

@@ -150,7 +150,7 @@ def main():
     cf.runAndCleanup(args, snakemake_cmd, logfile_name)
 
     #CreateDAG
-    cf.print_DAG(args,snakemake_cmd, __file__,defaults)
+    cf.plot_DAG(args,snakemake_cmd, __file__,defaults)
 
 
 if __name__ == "__main__":