From db74a4f6e5c96cc9cf64be1a3a669109cc9056ec Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Tue, 6 Aug 2024 11:52:05 -0400 Subject: [PATCH] fix: do not change fqscreen path with shared resources they are no longer in shared resources dir --- src/renee/gui.py | 2 +- src/renee/setup.py | 5 ----- src/renee/util.py | 2 +- tests/test_run.py | 4 ++-- 4 files changed, 4 insertions(+), 9 deletions(-) diff --git a/src/renee/gui.py b/src/renee/gui.py index d122dc0..12aad81 100755 --- a/src/renee/gui.py +++ b/src/renee/gui.py @@ -183,7 +183,7 @@ def launch_gui(sub_args, debug=True): output_dir, os.environ.get("SINGULARITY_CACHEDIR", None) ), tmp_dir=get_tmp_dir(None, output_dir), - shared_resources=get_shared_resources_dir(None, output_dir), + shared_resources=get_shared_resources_dir(None), star_2_pass_basic=False, small_rna=False, create_nidap_folder=False, diff --git a/src/renee/setup.py b/src/renee/setup.py index 9130ae8..ed2bb51 100644 --- a/src/renee/setup.py +++ b/src/renee/setup.py @@ -110,11 +110,6 @@ def setup(sub_args, ifiles, repo_path, output_path): ] = os.path.join( sub_args.shared_resources, "fastq_screen_db", "fastq_screen.conf" ) - config["bin"]["rnaseq"]["tool_parameters"][ - "FASTQ_SCREEN_CONFIG2" - ] = os.path.join( - sub_args.shared_resources, "fastq_screen_db", "fastq_screen_2.conf" - ) config["bin"]["rnaseq"]["tool_parameters"]["KRAKENBACDB"] = os.path.join( sub_args.shared_resources, "20180907_standard_kraken2" ) diff --git a/src/renee/util.py b/src/renee/util.py index fb50948..0ffad74 100644 --- a/src/renee/util.py +++ b/src/renee/util.py @@ -66,7 +66,7 @@ def get_tmp_dir(tmp_dir, outdir, hpc=get_hpcname()): return tmp_dir -def get_shared_resources_dir(shared_dir, outdir, hpc=get_hpcname()): +def get_shared_resources_dir(shared_dir, hpc=get_hpcname()): """Get default shared resources directory for biowulf and frce. Allow user override.""" if not shared_dir: if hpc == "biowulf": diff --git a/tests/test_run.py b/tests/test_run.py index 11a0ffc..229d40a 100644 --- a/tests/test_run.py +++ b/tests/test_run.py @@ -9,7 +9,7 @@ renee_base, ) from renee.src.renee.cache import get_sif_cache_dir -from renee.src.renee.run import run_in_context +from renee.src.renee.run import run, run_in_context from renee.src.renee.util import get_hpcname @@ -28,7 +28,7 @@ def test_dryrun(): sif_cache=get_sif_cache_dir(), singularity_cache=os.environ["SINGULARITY_CACHEDIR"], tmp_dir=tmp_dir, - shared_resources=None, + shared_resources=get_shared_resources_dir(None), star_2_pass_basic=False, small_rna=False, create_nidap_folder=False,