Merge pull request #4 from pdimens/dev

Merge dev into main, pending release v0.2

misc/buildlocal.sh

@@ -1,7 +1,13 @@
 #! /usr/bin/env bash
 
+if [ -z "$CONDA_PREFIX" ]; then
+    echo "Error: active conda environment not detected."
+    echo "To use this installation script, you need to already be in an active conda environment."
+    exit 1
+fi
+
 mkdir -p ${CONDA_PREFIX}/bin
-cp misc/ema-h ${CONDA_PREFIX}/bin
+cp -n misc/ema-h ${CONDA_PREFIX}/bin
 
 # Harpy executable
 cp harpy ${CONDA_PREFIX}/bin/
@@ -14,25 +20,3 @@ cp utilities/*.{py,R,pl} ${CONDA_PREFIX}/bin/
 
 # reports
 cp reports/*.Rmd ${CONDA_PREFIX}/bin/
-
-
-### deprecated? ###
-#export C_INCLUDE_PATH=${PREFIX}/include
-#export CPLUS_INCLUDE_PATH=${PREFIX}/include
-#export CPP_INCLUDE_PATH=${PREFIX}/include
-#export CXX_INCLUDE_PATH=${PREFIX}/include
-#export LIBRARY_PATH=${PREFIX}/lib
-
-# create conda PATH, if not already existing
-
-# build and install ema
-#rm -rf ema || true
-#git clone --recursive https://github.com/EdHarry/ema.git
-#cd ema && git checkout haplotag
-#git submodule update --remote
-#git apply ../harpy/misc/makefile.patch
-#git apply ../harpy/misc/remove_native.patch
-#make CC="$CC -fcommon" CXX="$CXX -fcommon" LDFLAGS="$LDFLAGS"
-#chmod +x ema
-#cp ema $CONDA_PREFIX/bin/ema-h
-#cd ..