fix decontam script path

Author: pirovc

grimer/func.py

@@ -639,7 +639,7 @@ def update_tax_nodes(nodes, tax):
     return updated_nodes
 
 
-def run_decontam(run_decontam, cfg, table, metadata, control_samples):
+def run_decontam(run_decontam, cfg, table, metadata, control_samples, script_dir):
 
     if not run_decontam:
         print_log("Not activated, skipping")
@@ -732,7 +732,7 @@ def run_decontam(run_decontam, cfg, table, metadata, control_samples):
             else:
                 table.data[rank].to_csv(out_table, sep="\t", header=True, index=True)
 
-            cmd = " ".join(["scripts/run_decontam.R",
+            cmd = " ".join([os.path.join(script_dir, "scripts", "run_decontam.R"),
                             "--resout " + tmp_output_prefix + "decontam_out.tsv",
                             "--modout " + tmp_output_prefix + "decontam_mod.tsv",
                             "--counts " + out_table,

grimer/grimer.py

@@ -36,6 +36,8 @@ def main(argv=sys.argv[1:]):
     # Setup global _debug variable to be used by other files with #from grimer.grimer import _debug
     global _debug
     _debug = args.debug
+    # Define path of running script to get static files
+    script_dir, _ = os.path.split(__file__)
 
     # 1) Load data/analysis
     # If not parsed, skipped or error, var is None
@@ -76,7 +78,7 @@ def main(argv=sys.argv[1:]):
     mgnify = parse_mgnify(args.mgnify, cfg, tax, table.ranks())
 
     print_log("- Running DECONTAM")
-    decontam = run_decontam(args.decontam, cfg, table, metadata, control_samples)
+    decontam = run_decontam(args.decontam, cfg, table, metadata, control_samples, script_dir)
 
     print_log("- Running hierarchical clustering")
     hcluster, dendro = run_hclustering(table, args.linkage_methods, args.linkage_metrics, args.transformation, args.skip_dendrogram, args.optimal_ordering)
@@ -296,8 +298,6 @@ def main(argv=sys.argv[1:]):
 
     # 5) Draw layout
     print_log("- Drawing layout")
-    # Define path of running script to get static files
-    script_dir, _ = os.path.split(__file__)
     logo_path = os.path.join(script_dir, "img", "logo.png")
 
     final_layout = make_layout(ele, sizes, Config.version, logo_path, args.title, args.output_plots)

grimer/scripts/__init__.py

@@ -22,7 +22,7 @@ def read(filename):
     long_description=read("README.md"),
     packages=['grimer'],
     package_data={
-        'grimer': ['js/*', 'css/*', 'img/*']
+        'grimer': ['css/*', 'img/*', 'js/*', 'scripts/*']
     },
     entry_points={'console_scripts': ['grimer=grimer.grimer:main']},
     classifiers=[