From 2c00a556b06984dd5087de38ac3d87adb0d41387 Mon Sep 17 00:00:00 2001
From: egluckthaler <emilegluckthaler@gmail.com>
Date: Sun, 17 Dec 2023 22:17:06 -0600
Subject: [PATCH] updates to gcc_linux-64 invocation

---
 .github/workflows/conda_build.yml | 4 +++-
 build.sh                          | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml
index 1e05b737..968cd111 100644
--- a/.github/workflows/conda_build.yml
+++ b/.github/workflows/conda_build.yml
@@ -28,7 +28,9 @@ jobs:
       run: |
         conda config --add channels bioconda
         conda config --add channels conda-forge
-        conda install -c conda-forge conda-build conda-verify gcc_linux-64
+        conda activate starfish_build_env
+        conda install -c conda-forge gcc_linux-64
+        conda install conda-build conda-verify
         conda build .
       # This step installs conda-build and then uses it to build your Conda package.
     
diff --git a/build.sh b/build.sh
index 251379c5..c9e44cc3 100644
--- a/build.sh
+++ b/build.sh
@@ -1,7 +1,9 @@
+#!/bin/bash
+
 # compile CNEFinder
 cd $SRC_DIR/CNEFinder/
 ./pre-install.sh
-make -f Makefile CC=/usr/share/miniconda/bin/x86_64-conda-linux-gnu-gcc CXX=/usr/share/miniconda/bin/x86_64-conda-linux-gnu-g++
+make -f Makefile CC=$CONDA_PREFIX/bin/x86_64-conda-linux-gnu-gcc CXX=$CONDA_PREFIX/bin/x86_64-conda-linux-gnu-g++
 mv cnef ../bin/
 
 # copy git directory structure to conda package location