From 93a03528bd0bed4643833114de19a776e49177cd Mon Sep 17 00:00:00 2001
From: Reid Wagner <wagnerr@umn.edu>
Date: Fri, 5 Jul 2024 15:36:04 -0500
Subject: [PATCH] Copy all FragPipe files from conda install locally.

---
 tools/fragpipe/macros.xml | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/tools/fragpipe/macros.xml b/tools/fragpipe/macros.xml
index 708e6b597..907ed5f58 100644
--- a/tools/fragpipe/macros.xml
+++ b/tools/fragpipe/macros.xml
@@ -31,14 +31,7 @@
       Prepares enviroment variables for FragPipe.
     -->
     <token name="@PREPARE_ENVIRONMENT@"><![CDATA[
-        mkdir -p fragpipe_local/lib &&
-        for dir in bin philosopher tools workflows; do
-            ln -s \${CONDA_PREFIX}/share/fragpipe*/\${dir} fragpipe_local/\${dir};
-        done &&
-        for file in \${CONDA_PREFIX}/share/fragpipe*/lib/*; do
-            ln -s \${file} fragpipe_local/lib/\$(basename \${file});
-        done &&
-        cp \${CONDA_PREFIX}/share/fragpipe*/lib/fragpipe-*.jar fragpipe_local/lib/ &&
+        cp -r \${CONDA_PREFIX}/share/fragpipe*/ fragpipe_local/ &&
         mkdir .cache .config tmp &&
         export XDG_CONFIG_HOME=\$(pwd)/.config &&
         export XDG_CACHE_HOME=\$(pwd)/.cache &&