From 4d411354ad8ddf7c9a445a48844ac7a22dd96839 Mon Sep 17 00:00:00 2001
From: Philip MacMenamin <macmenaminpe@nih.gov>
Date: Fri, 9 Aug 2024 11:30:26 -0600
Subject: [PATCH] tag brt runs, update imod version

---
 em_workflows/config.py          | 11 ++++++-----
 em_workflows/sem_tomo/config.py |  7 ++++---
 em_workflows/utils/utils.py     |  2 ++
 setup.py                        |  2 +-
 4 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/em_workflows/config.py b/em_workflows/config.py
index cca6bbd7..73d0814b 100644
--- 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
index 0bb44e9b..8319f442 100644
--- 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
index 4df1cb6b..cf98bff8 100644
--- 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
index 154eb16e..ea891913 100644
--- 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="bioinformatics@niaid.nih.gov",
     description="Workflows for Microscopy related file processing.",