sbatch in conda

Author: antgonza

.github/workflows/qiita-plugin-ci.yml

@@ -48,12 +48,6 @@ jobs:
         run: |
           echo "Testing: " $COVER_PACKAGE
 
-          # creating sbatch executable
-          ls ./; pwd
-          ls -laht /home/runner/.local/bin
-          echo '/usr/bin/bash "$@"' > /home/runner/.local/bin/sbatch
-          chmod +x /home/runner/.local/bin/sbatch
-
           # we need to download qiita directly so we have "easy" access to
           # all config files
           wget https://github.com/biocore/qiita/archive/dev.zip
@@ -72,6 +66,10 @@ jobs:
           conda activate qiita
           pip install sphinx sphinx-bootstrap-theme nose-timer Click
 
+          # creating sbatch executable
+          echo '/usr/bin/bash "$@"' > ${CONDA_PREFIX}/bin/sbatch
+          chmod +x ${CONDA_PREFIX}/bin/sbatch
+
       - name: Qiita install
         shell: bash -l {0}
         run: |
@@ -93,6 +91,10 @@ jobs:
 
           conda activate klp
 
+          # creating sbatch executable
+          echo '/usr/bin/bash "$@"' > ${CONDA_PREFIX}/bin/sbatch
+          chmod +x ${CONDA_PREFIX}/bin/sbatch
+
           export QIITA_ROOTCA_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt
           export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg
           pip --quiet install -U pip