From 5ccf144b92ce46e80964c3820856e80e955630a2 Mon Sep 17 00:00:00 2001
From: davidebolo1993 <davidebolognini7@gmail.com>
Date: Mon, 7 Aug 2023 16:53:29 +0200
Subject: [PATCH] fix Dockerfile

---
 .gitignore                                           |  1 +
 Dockerfile                                           | 10 +---------
 cosigt_smk/workflow/rules/pgrtk.smk                  |  2 +-
 cosigt_smk/workflow/scripts/{pgrtk.py => pypgrtk.py} |  4 +++-
 4 files changed, 6 insertions(+), 11 deletions(-)
 rename cosigt_smk/workflow/scripts/{pgrtk.py => pypgrtk.py} (96%)

diff --git a/.gitignore b/.gitignore
index 1464e2c..419978c 100644
--- 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
index 4ad2ed0..f59a425 100644
--- 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
\ No newline at end of file
diff --git a/cosigt_smk/workflow/rules/pgrtk.smk b/cosigt_smk/workflow/rules/pgrtk.smk
index 86dac29..d9f6fcf 100644
--- 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}
 		'''
\ No newline at end of file
diff --git a/cosigt_smk/workflow/scripts/pgrtk.py b/cosigt_smk/workflow/scripts/pypgrtk.py
similarity index 96%
rename from cosigt_smk/workflow/scripts/pgrtk.py
rename to cosigt_smk/workflow/scripts/pypgrtk.py
index 19255f5..d52d29d 100644
--- a/cosigt_smk/workflow/scripts/pgrtk.py
+++ b/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)
 
 
 
+