feat: set default singularity sif dir

resolves #53

CHANGELOG.md

@@ -13,6 +13,7 @@
 - Fix RSeQC environments:
   - Set RSeQC envmodule version to 4.0.0, which synchronizes it with the version in the docker container used by singularity. (#122, @kelly-sovacool)
   - Update docker with RSeQC's tools properly added to the path. (#123, @kelly-sovacool)
+- Set default shared singularity SIF directory for biowulf and frce. (#94, @kelly-sovacool)
 
 ## RENEE 2.5.11
 

src/renee/__main__.py

@@ -24,6 +24,7 @@
 import argparse
 
 # local imports
+from .cache import get_sif_cache_dir
 from .run import run
 from .dryrun import dryrun
 from .gui import launch_gui
@@ -907,6 +908,7 @@ def parsed_arguments(name, description):
         type=lambda option: os.path.abspath(os.path.expanduser(option)),
         required=False,
         help=argparse.SUPPRESS,
+        default=get_sif_cache_dir(),
     )
 
     # Create NIDAP output folder

src/renee/cache.py

@@ -2,6 +2,17 @@
 import os
 import sys
 
+from .util import get_hpcname
+
+
+def get_sif_cache_dir(hpc=get_hpcname()):
+    sif_dir = None
+    if hpc == "biowulf":
+        sif_dir = "/data/CCBR_Pipeliner/SIFS"
+    elif hpc == "frce":
+        sif_dir = "/mnt/projects/CCBR-Pipelines/SIFs"
+    return sif_dir
+
 
 def image_cache(sub_args, config):
     """Adds Docker Image URIs, or SIF paths to config if singularity cache option is provided.

tests/test_cache.py

@@ -3,6 +3,8 @@
 import os.path
 import subprocess
 
+from src.renee.cache import get_sif_cache_dir
+
 renee_run = (
     "./bin/renee run "
     "--mode local --runmode init --dry-run "
@@ -42,7 +44,15 @@ def test_cache_sif():
 def test_cache_nosif():
     output, config = run_in_temp(f"{renee_run}")
     assertions = [
-        config["images"]["arriba"] == "docker://nciccbr/ccbr_arriba_2.0.0:v0.0.1",
-        "The singularity command has to be available" in output.stderr,
+        config["images"]["arriba"] == "docker://nciccbr/ccbr_arriba_2.0.0:v0.0.1"
     ]
     assert all(assertions)
+
+
+def test_get_sif_cache_dir():
+    assertions = [
+        "'CCBR_Pipeliner/SIFS' in get_sif_cache_dir('biowulf')",
+        "'CCBR-Pipelines/SIFs' in get_sif_cache_dir('frce')",
+    ]
+    errors = [assertion for assertion in assertions if not eval(assertion)]
+    assert not errors, "errors occurred:\n{}".format("\n".join(errors))