fix Dockerfile

davidebolo1993 · Aug 7, 2023 · 5ccf144 · 5ccf144
1 parent b662bc8
commit 5ccf144
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Showing 4 changed files with 6 additions and 11 deletions.
diff --git a/.gitignore b/.gitignore
@@ -12,3 +12,4 @@ cosigt_smk/singularity_bind_paths.csv
 cosigt_smk/config/config.yaml
 cosigt_smk/config/samples.tsv
 cosigt_smk/*.pdf
+cosigt_smk/workflow/scripts/__pycache__
diff --git a/Dockerfile b/Dockerfile
@@ -133,12 +133,4 @@ RUN git clone https://github.com/davidebolo1993/cosigt.git \
 	&& go mod tidy \
 	&& go build cosigt
 
-ENV PATH /opt/cosigt:$PATH
-
-RUN mkdir -p pyscripts \
-	&& cd pyscripts \
-	&& wget https://raw.githubusercontent.com/davidebolo1993/cosigt/master/cosigt_smk/workflow/scripts/pgrtk.py \
-	&& chmod +x pgrtk.py
-
-ENV PATH /opt/pyscripts:$PATH
-
+ENV PATH /opt/cosigt:$PATH
diff --git a/cosigt_smk/workflow/rules/pgrtk.smk b/cosigt_smk/workflow/rules/pgrtk.smk
@@ -12,5 +12,5 @@ rule pgrtk_get_seq:
 		padding=config['pgrtk']['padding']
 	shell:
 		'''
-		pgrtk.py {input.agc} {input.region} {params.padding} {output}
+		python workflow/scripts/pypgrtk.py {input.agc} {input.region} {params.padding} {output}
 		'''
diff --git a/cosigt_smk/workflow/scripts/pgrtk.py → cosigt_smk/workflow/scripts/pypgrtk.py b/cosigt_smk/workflow/scripts/pgrtk.py → cosigt_smk/workflow/scripts/pypgrtk.py
@@ -6,7 +6,7 @@
 
 def main(agc_file,bed_file,padding,out_file):
 
-    #load acg_file
+    #load agc_file
     ref_db=pgrtk.AGCFile(agc_file)
 
     #load region
@@ -73,7 +73,9 @@ def main(agc_file,bed_file,padding,out_file):
     bed_file=os.path.abspath(sys.argv[2])
     padding=int(sys.argv[3])
     out_file=os.path.abspath(sys.argv[4])
+    print(agc_file,bed_file,padding,out_file)
     main(agc_file,bed_file,padding,out_file)
 
 
 
+