Merge pull request #481 from niaid/fix/update_brt_version

tag brt runs, update imod version
niaid · Aug 9, 2024 · abbc3f6 · abbc3f6
2 parents a1d8e7a + 4d41135
commit abbc3f6
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Showing 4 changed files with 13 additions and 9 deletions.
diff --git a/em_workflows/config.py b/em_workflows/config.py
@@ -63,7 +63,7 @@ def SLURM_exec(asynchronous: bool = False, **cluster_kwargs):
         asynchronous=asynchronous,
         **cluster_kwargs,
     )
-    cluster.scale(1)
+    cluster.scale(5)
     # cluster.adapt(minimum=1, maximum=6)
     # to get logger, we must be within an active flow/task run
     print("Dask cluster started")
@@ -73,14 +73,15 @@ def SLURM_exec(asynchronous: bool = False, **cluster_kwargs):
 
 class Config:
     # location in RML HPC
+    imod_root = "/gs1/apps/user/spack-0.16.0/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.1/imod-4.12.47-2fcggru32s3f4jl3ar5m2rztuqz5h2or"
     bioformats2raw = os.environ.get(
         "BIOFORMATS2RAW_LOC",
         "/gs1/apps/user/spack-0.16.0/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.1/bioformats2raw-0.7.0-7kt7dff7f7fxmdjdk57u6xjuzmsxqodn/bin/bioformats2raw",
     )
-    brt_binary = os.environ.get("BRT_LOC", "/opt/rml/imod/bin/batchruntomo")
-    header_loc = os.environ.get("HEADER_LOC", "/opt/rml/imod/bin/header")
-    mrc2tif_loc = os.environ.get("MRC2TIF_LOC", "/opt/rml/imod/bin/mrc2tif")
-    newstack_loc = os.environ.get("NEWSTACK_LOC", "/opt/rml/imod/bin/newstack")
+    brt_binary = os.environ.get("BRT_LOC", f"{imod_root}/bin/batchruntomo")
+    header_loc = os.environ.get("HEADER_LOC", f"{imod_root}/bin/header")
+    mrc2tif_loc = os.environ.get("MRC2TIF_LOC", f"{imod_root}/bin/mrc2tif")
+    newstack_loc = os.environ.get("NEWSTACK_LOC", f"{imod_root}/bin/newstack")
 
     HIGH_SLURM_EXECUTOR = DaskTaskRunner(
         cluster_class=SLURM_exec,

diff --git a/em_workflows/sem_tomo/config.py b/em_workflows/sem_tomo/config.py
@@ -7,6 +7,7 @@ class SEMConfig(Config):
     convert_loc = os.environ.get(
         "CONVERT_LOC", "/usr/bin/convert"
     )  # requires imagemagick
-    tif2mrc_loc = os.environ.get("TIF2MRC_LOC", "/opt/rml/imod/bin/tif2mrc")
-    xfalign_loc = os.environ.get("XFALIGN_LOC", "/opt/rml/imod/bin/xfalign")
-    xftoxg_loc = os.environ.get("XFTOXG_LOC", "/opt/rml/imod/bin/xftoxg")
+    imod_root = "/gs1/apps/user/spack-0.16.0/spack/opt/spack/linux-centos7-sandybridge/gcc-8.3.1/imod-4.12.47-2fcggru32s3f4jl3ar5m2rztuqz5h2or"
+    tif2mrc_loc = os.environ.get("TIF2MRC_LOC", f"{imod_root}/bin/tif2mrc")
+    xfalign_loc = os.environ.get("XFALIGN_LOC", f"{imod_root}/bin/xfalign")
+    xftoxg_loc = os.environ.get("XFTOXG_LOC", f"{imod_root}/bin/xftoxg")
diff --git a/em_workflows/utils/utils.py b/em_workflows/utils/utils.py
@@ -322,6 +322,8 @@ def copy_template(working_dir: Path, template_name: str) -> Path:
 
 @task(
     name="Batchruntomo conversion",
+    tags=["brt"],
+    # timeout_seconds=600,
     on_failure=[collect_exception_task_hook],
 )
 def run_brt(

diff --git a/setup.py b/setup.py
@@ -7,7 +7,7 @@
 
 setup(
     name="em_workflows",
-    version="2.1.1",
+    version="2.1.2",
     author="Philip MacMenamin, Bradley Lowekamp, Anish Shrestha",
     author_email="[email protected]",
     description="Workflows for Microscopy related file processing.",