Merge pull request #67 from seiboldlab/dev

Dev

Author: epruesse

rules/rnaseq.rules

@@ -158,7 +158,7 @@ with Stage("report_vp") as S:
             "exec >{log} 2>&1;"
             "SRCS=({input});"
             "DSTS=({output});"
-            "MSG=\"New RNA-Seq (v{params.version}) results for \`{params.project}\`:\n\n\";"
+            "MSG=\"New RNA-Seq (v{params.version}) results for \\`{params.project}\\`:\n\n\";"
             "LABEL={params.label};"
             "for i in \"${{!SRCS[@]}}\"; do"
             "  echo Copying ${{SRCS[i]}} to ${{DSTS[i]}};"
@@ -175,7 +175,7 @@ with Stage("report_vp") as S:
             "  REPORT=$(date +{params.reporttpl});"
             "  echo Copying ${{SRCS[i]}} to $REPORT;"
             "  cp -a ${{SRCS[i]}} $REPORT;"
-            "  MSG=\"$MSG\n- \`$REPORT\`\";"
+            "  MSG=\"$MSG\n- \\`$REPORT\\`\";"
             "done;"
             "if [ -n \"{params.slack_hook}\" ]; then"
             "  curl"

rules/virprof.rules

@@ -615,7 +615,7 @@ with Stage("report_pathogen_vp") as S:
             "exec >{log} 2>&1;"
             "SRCS=({input});"
             "DSTS=({output});"
-            "MSG=\"New Pathogen (v{params.version}) results for \`{params.project}\`:\n\n\";"
+            "MSG=\"New Pathogen (v{params.version}) results for \\`{params.project}\\`:\n\n\";"
             "LABEL={params.label};"
             "for i in \"${{!SRCS[@]}}\"; do"
             "  echo Copying ${{SRCS[i]}} to ${{DSTS[i]}};"
@@ -632,7 +632,7 @@ with Stage("report_pathogen_vp") as S:
             "  REPORT=$(date +{params.reporttpl});"
             "  echo Copying ${{SRCS[i]}} to $REPORT;"
             "  cp -a ${{SRCS[i]}} $REPORT;"
-            "  MSG=\"$MSG\n- \`$REPORT\`\";"
+            "  MSG=\"$MSG\n- \\`$REPORT\\`\";"
             "done;"
             "if [ -n \"{params.slack_hook}\" ]; then"
             "  curl"

setup.py

@@ -15,6 +15,7 @@
         "rules/*",
         "test_data/*",
         "*.yml",
+        "respiratory_virus_whitelist.txt",
         "README.md",
     ]
 }
@@ -37,7 +38,7 @@
             shutil.copy(src, dst)
         with open(os.path.join(submodule, "__init__.py"), "w"):
             pass
-    setup(package_data=package_data)
+    setup(package_data=package_data, zip_safe=False)
 finally:
     for submodule in extra_package_data:
         shutil.rmtree(submodule)

virprof/__init__.py

@@ -1,7 +1,14 @@
 """Virprof pipeline custom functions for pathogen recovery"""
 
+from pathlib import Path
 
-import os
+def get_resource(path):
+    roots = [Path(__file__).parent.parent, Path(__file__).parent / "pipeline"]
+    for root in roots:
+        loc = root / path
+        if loc.exists():
+            return loc
+    raise Exception(f"Unable to find {path}. Please check your installation")
 
 def get_ymp_yml():
-    return os.path.realpath(__file__)
+    return str(get_resource("virprof.yml"))

virprof/cli/__init__.py

@@ -141,6 +141,7 @@ def get_command(self, ctx, cmd_name):
 
 
 @click.command(cls=AutoLoadCommand)
+@click.version_option()
 @click.option(
     "--profile",
     is_flag=True,

virprof/cli/init_test.py

@@ -0,0 +1,21 @@
+import click
+import pathlib
+from .. import get_resource
+from subprocess import run
+
+@click.command()
+@click.argument("path", type=click.Path(path_type=pathlib.Path))
+def cli(path) -> bool:
+    """Set up a demo/test directory"""
+    testdata = get_resource("test_data")
+
+    if not path.exists():
+        path.mkdir(parents=True)
+    elif not path.is_dir():
+        raise click.ClickException("Not a directory: {path}")
+    elif any(path.iterdir()):
+        raise click.ClickException("Directory not empty: {path}")
+
+    run(testdata / "install_testdata.sh", cwd = path, check = True)
+    
+    return True