Update bash scripts for training in the cluster (#234)

* Use source activate rather than conda activate in hpc * Remove sourcing bashrc
SainsburyWellcomeCentre · Nov 5, 2024 · c992a79 · c992a79
1 parent 39add90
commit c992a79
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/bash_scripts/run_training_array.sh b/bash_scripts/run_training_array.sh
@@ -21,7 +21,7 @@
 # Source bashrc
 # ----------------------
 # Otherwise `which python` points to the miniconda module's Python
-source ~/.bashrc
+# source ~/.bashrc
 
 
 # memory
@@ -82,7 +82,7 @@ conda create \
     python=3.10
 
 # activate environment
-conda activate $ENV_PREFIX
+source activate $ENV_PREFIX
 
 # install crabs package in virtual env
 python -m pip install git+https://github.com/SainsburyWellcomeCentre/crabs-exploration.git@$GIT_BRANCH

diff --git a/bash_scripts/run_training_single.sh b/bash_scripts/run_training_single.sh
@@ -16,7 +16,7 @@
 # Source bashrc
 # ----------------------
 # Otherwise `which python` points to the miniconda module's Python
-source ~/.bashrc
+# source ~/.bashrc
 
 
 # memory
@@ -67,7 +67,8 @@ conda create \
     python=3.10
 
 # activate environment
-conda activate $ENV_PREFIX
+source activate $ENV_PREFIX
+
 
 # install crabs package in virtual env
 python -m pip install git+https://github.com/SainsburyWellcomeCentre/crabs-exploration.git@$GIT_BRANCH