From 7eed49bb4cd8b290ef9cfe1e543707f64907774e Mon Sep 17 00:00:00 2001
From: YoshitakaMo <virgospica93@gmail.com>
Date: Sat, 11 Dec 2021 10:58:25 +0900
Subject: [PATCH] preferentially use commands in colabfold-conda/bin

---
 install_colabbatch_M1mac.sh    | 3 ++-
 install_colabbatch_intelmac.sh | 3 ++-
 install_colabbatch_linux.sh    | 3 ++-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/install_colabbatch_M1mac.sh b/install_colabbatch_M1mac.sh
index 651ce4a..4592f03 100755
--- a/install_colabbatch_M1mac.sh
+++ b/install_colabbatch_M1mac.sh
@@ -46,6 +46,7 @@ wget -qnc https://raw.githubusercontent.com/deepmind/alphafold/main/docker/openm
 rm openmm.patch
 # Download the updater
 wget -qnc https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/update_M1mac.sh --no-check-certificate
+chmod +x update_M1mac.sh
 # install ColabFold and Jaxlib
 colabfold-conda/bin/python3.8 -m pip install tensorflow-macos
 colabfold-conda/bin/python3.8 -m pip install git+git://github.com/deepmind/tree.git
@@ -64,7 +65,7 @@ cd $COLABFOLDDIR/bin
 cat << EOF > colabfold_batch
 #!/bin/sh
 export COLABFOLDDIR=$COLABFOLDDIR
-export PATH="\$PATH:\${COLABFOLDDIR}/colabfold-conda/bin"
+export PATH="\${COLABFOLDDIR}/colabfold-conda/bin:\$PATH"
 \$COLABFOLDDIR/colabfold-conda/bin/colabfold_batch --cpu \$@
 EOF
 chmod +x colabfold_batch
diff --git a/install_colabbatch_intelmac.sh b/install_colabbatch_intelmac.sh
index 339e516..72c1e4d 100755
--- a/install_colabbatch_intelmac.sh
+++ b/install_colabbatch_intelmac.sh
@@ -45,6 +45,7 @@ wget -qnc https://raw.githubusercontent.com/deepmind/alphafold/main/docker/openm
 rm openmm.patch
 # Download the updater
 wget -qnc https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/update_intelmac.sh --no-check-certificate
+chmod +x update_intelmac.sh
 # install ColabFold and Jaxlib
 colabfold-conda/bin/python3.7 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold"
 colabfold-conda/bin/python3.7 -m pip install https://storage.googleapis.com/jax-releases/mac/jaxlib-0.1.74-cp37-none-macosx_10_9_x86_64.whl
@@ -56,7 +57,7 @@ cd $COLABFOLDDIR/bin
 cat << EOF > colabfold_batch
 #!/bin/sh
 export COLABFOLDDIR=$COLABFOLDDIR
-export PATH="\$PATH:\${COLABFOLDDIR}/colabfold-conda/bin"
+export PATH="\${COLABFOLDDIR}/colabfold-conda/bin:\$PATH"
 \$COLABFOLDDIR/colabfold-conda/bin/colabfold_batch --cpu \$@
 EOF
 chmod +x colabfold_batch
diff --git a/install_colabbatch_linux.sh b/install_colabbatch_linux.sh
index b9498cb..cc18def 100755
--- a/install_colabbatch_linux.sh
+++ b/install_colabbatch_linux.sh
@@ -24,6 +24,7 @@ wget -qnc https://raw.githubusercontent.com/deepmind/alphafold/main/docker/openm
 rm openmm.patch
 # Download the updater
 wget -qnc https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/update_linux.sh --no-check-certificate
+chmod +x update_linux.sh
 # install alignment tools
 conda install -c conda-forge -c bioconda kalign3=3.2.2 hhsuite=3.3.0 -y
 # install ColabFold and Jaxlib
@@ -40,7 +41,7 @@ export TF_FORCE_UNIFIED_MEMORY="1"
 export XLA_PYTHON_CLIENT_MEM_FRACTION="4.0"
 export COLABFOLDDIR=$COLABFOLDDIR
 export XDG_CACHE_HOME="\${COLABFOLDDIR}"
-export PATH="\$PATH:\${COLABFOLDDIR}/colabfold-conda/bin"
+export PATH="\${COLABFOLDDIR}/colabfold-conda/bin:\$PATH"
 \$COLABFOLDDIR/colabfold-conda/bin/colabfold_batch \$@
 EOF
 chmod +x colabfold_batch