handling pgrtk script in Dockerfile

davidebolo1993 · Aug 7, 2023 · 1217555 · 1217555
1 parent d49ae2e
commit 1217555
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diff --git a/Dockerfile b/Dockerfile
@@ -134,3 +134,11 @@ RUN git clone https://github.com/davidebolo1993/cosigt.git \
 	&& 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
+
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:
 		'''
-		python workflow/scripts/pgrtk.py {input.agc} {input.region} {params.padding} {output}
+		pgrtk.py {input.agc} {input.region} {params.padding} {output}
 		'''
diff --git a/cosigt_smk/workflow/scripts/__pycache__/pgrtk.cpython-310.pyc b/cosigt_smk/workflow/scripts/__pycache__/pgrtk.cpython-310.pyc