From d28a5fcd39e97dfbbfecf0824ea3b0f7b7bb63e9 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Wed, 3 Jul 2024 09:01:57 -0700
Subject: [PATCH] Add --break-system-packages to pip commands

---
 SequenceAnalysis/pipeline_code/sequence_tools_install.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/SequenceAnalysis/pipeline_code/sequence_tools_install.sh b/SequenceAnalysis/pipeline_code/sequence_tools_install.sh
index feef079c7..2e0b5e79f 100755
--- a/SequenceAnalysis/pipeline_code/sequence_tools_install.sh
+++ b/SequenceAnalysis/pipeline_code/sequence_tools_install.sh
@@ -866,9 +866,9 @@ then
       install ./cutadapt-1.8.1/bin/_preamble.py ${LKTOOLS_DIR}/_preamble.py
       cp -R ./cutadapt-1.8.1/cutadapt ${LKTOOLS_DIR}/cutadapt
     else
-      $PIP_EXE install --user cutadapt==4.2
+      $PIP_EXE install --user --break-system-packages cutadapt==4.2
       $PIP_EXE show cutadapt
-      $PIP_EXE install --user pyinstaller
+      $PIP_EXE install --user --break-system-packages pyinstaller
       $PIP_EXE show pyinstaller
       ~/.local/bin/pyinstaller --onefile --clean ~/.local/bin/cutadapt
       cp ./dist/cutadapt ${LKTOOLS_DIR}/cutadapt