From 79b5fa14348762b75f79d6d93683d5a96b368234 Mon Sep 17 00:00:00 2001
From: "Dr. K.D. Murray" <foss@kdmurray.id.au>
Date: Tue, 16 Jan 2024 12:47:37 +0100
Subject: [PATCH] GHA: use bash login shells

---
 .github/workflows/run-snakemake.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/run-snakemake.yml b/.github/workflows/run-snakemake.yml
index 1b64fe6..7b0cf7e 100644
--- a/.github/workflows/run-snakemake.yml
+++ b/.github/workflows/run-snakemake.yml
@@ -33,18 +33,16 @@ jobs:
       - name: setup data
         shell: bash -el {0}
         run: |
-          export BASH_ENV=~/.bashrc
           mamba info
           pushd tests
-          bash setup.sh
+          bash -el setup.sh
           popd
 
       - name: run workflow
         shell: bash -el {0}
         run: |
-          export BASH_ENV=~/.bashrc
           pushd tests
-          bash test.sh
+          bash -el test.sh
           popd
 
       - name: cat all log files on failure