From 494ee56f92339f409172c9b9e1581e01f8537490 Mon Sep 17 00:00:00 2001
From: "Josh L. Espinoza" <jol.espinoz@gmail.com>
Date: Fri, 30 Aug 2024 13:52:49 -0700
Subject: [PATCH] Update N_JOBS

---
 install/download_databases-annotate.sh      | 2 +-
 install/download_databases-classify.sh      | 2 +-
 install/download_databases-contamination.sh | 2 +-
 install/download_databases-markers.sh       | 2 +-
 install/download_databases.sh               | 8 ++++++--
 5 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/install/download_databases-annotate.sh b/install/download_databases-annotate.sh
index 7ea4346..7e8d5cc 100644
--- a/install/download_databases-annotate.sh
+++ b/install/download_databases-annotate.sh
@@ -10,7 +10,7 @@ REALPATH_DATABASE_DIRECTORY=$(realpath $DATABASE_DIRECTORY)
 SCRIPT_DIRECTORY=$(dirname "$0")
 
 MAXIMUM_NUMBER_OF_CPU=$(python -c "from multiprocessing import cpu_count; print(cpu_count())")
-N_JOBS=$(2:-${MAXIMUM_NUMBER_OF_CPU})
+N_JOBS=${3:-${MAXIMUM_NUMBER_OF_CPU}}
 
 # Database structure
 echo ". .. ... ..... ........ ............."
diff --git a/install/download_databases-classify.sh b/install/download_databases-classify.sh
index 7140413..744e048 100644
--- a/install/download_databases-classify.sh
+++ b/install/download_databases-classify.sh
@@ -10,7 +10,7 @@ REALPATH_DATABASE_DIRECTORY=$(realpath $DATABASE_DIRECTORY)
 SCRIPT_DIRECTORY=$(dirname "$0")
 
 MAXIMUM_NUMBER_OF_CPU=$(python -c "from multiprocessing import cpu_count; print(cpu_count())")
-N_JOBS=$(2:-${MAXIMUM_NUMBER_OF_CPU})
+N_JOBS=${3:-${MAXIMUM_NUMBER_OF_CPU}}
 
 # Database structure
 echo ". .. ... ..... ........ ............."
diff --git a/install/download_databases-contamination.sh b/install/download_databases-contamination.sh
index fac6c26..2cc5a1e 100644
--- a/install/download_databases-contamination.sh
+++ b/install/download_databases-contamination.sh
@@ -10,7 +10,7 @@ REALPATH_DATABASE_DIRECTORY=$(realpath $DATABASE_DIRECTORY)
 SCRIPT_DIRECTORY=$(dirname "$0")
 
 MAXIMUM_NUMBER_OF_CPU=$(python -c "from multiprocessing import cpu_count; print(cpu_count())")
-N_JOBS=$(2:-${MAXIMUM_NUMBER_OF_CPU})
+N_JOBS=${3:-${MAXIMUM_NUMBER_OF_CPU}}
 
 # Database structure
 echo ". .. ... ..... ........ ............."
diff --git a/install/download_databases-markers.sh b/install/download_databases-markers.sh
index ceb2c67..1d715d4 100644
--- a/install/download_databases-markers.sh
+++ b/install/download_databases-markers.sh
@@ -10,7 +10,7 @@ REALPATH_DATABASE_DIRECTORY=$(realpath $DATABASE_DIRECTORY)
 SCRIPT_DIRECTORY=$(dirname "$0")
 
 MAXIMUM_NUMBER_OF_CPU=$(python -c "from multiprocessing import cpu_count; print(cpu_count())")
-N_JOBS=$(2:-${MAXIMUM_NUMBER_OF_CPU})
+N_JOBS=${3:-${MAXIMUM_NUMBER_OF_CPU}}
 
 # Database structure
 echo ". .. ... ..... ........ ............."
diff --git a/install/download_databases.sh b/install/download_databases.sh
index 4be5df2..1de8f0d 100644
--- a/install/download_databases.sh
+++ b/install/download_databases.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 # __version__ = "2024.8.30"
 # MICROEUKAYROTIC_DATABASE_VERSION = "MicroEuk_v3"
-# usage: bash veba/download_databases.sh /path/to/veba_database_destination/ [optional positional argument: /path/to/conda_environments/]
+# usage: bash veba/download_databases.sh /path/to/veba_database_destination/ [optional positional argument: /path/to/conda_environments/ number_of_threads]
 # Version
 VEBA_DATABASE_VERSION="VDB_v7"
 
@@ -13,7 +13,11 @@ SCRIPT_DIRECTORY=$(dirname "$0")
 CONDA_ENVS_PATH=${2:-"$(conda info --base)/envs/"}
 
 MAXIMUM_NUMBER_OF_CPU=$(python -c "from multiprocessing import cpu_count; print(cpu_count())")
-N_JOBS=$(3:-${MAXIMUM_NUMBER_OF_CPU})
+N_JOBS=${3:-${MAXIMUM_NUMBER_OF_CPU}}
+echo ". .. ... ..... ........ ............."
+echo "Detected ${MAXIMUM_NUMBER_OF_CPU} available threads"
+echo "Using ${N_JOBS} threads"
+echo ". .. ... ..... ........ ............."
 
 # Database structure
 echo ". .. ... ..... ........ ............."