From afdb2615c5a44cfe3b573c013d2818084a10e8eb Mon Sep 17 00:00:00 2001
From: pratas <6882743+pratas@users.noreply.github.com>
Date: Wed, 25 Jan 2023 14:37:50 +0000
Subject: [PATCH] ivar to development version

---
 input_data/index.txt  | 2 +-
 src/TRACES_install.sh | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/input_data/index.txt b/input_data/index.txt
index 5e1c612..4e5901e 100644
--- a/input_data/index.txt
+++ b/input_data/index.txt
@@ -1 +1 @@
-#place your input fastq files in this folder in gzip format
+#place your input fastq files in this folder in gzip format [symlinks can be used, for example: ls ../../*.fastq.gz | xargs ln -s -t . ]
diff --git a/src/TRACES_install.sh b/src/TRACES_install.sh
index 5df83af..d53af43 100755
--- a/src/TRACES_install.sh
+++ b/src/TRACES_install.sh
@@ -60,7 +60,7 @@ if [[ "$INSTALL_PIPELINE" -eq "1" ]];
   conda install -c bioconda art --yes
   conda install -c bioconda blast --yes
   conda install -c bioconda mummer4 --yes
-  conda install -c bioconda ivar --yes
+#  conda install -c bioconda ivar --yes
   #
   Program_installed "trimmomatic";
   Program_installed "cryfa";
@@ -83,7 +83,7 @@ if [[ "$INSTALL_PIPELINE" -eq "1" ]];
   Program_installed "art_illumina";
   Program_installed "blastn";
   Program_installed "dnadiff";
-  Program_installed "ivar";
+#  Program_installed "ivar";
   fi
 #
 # ==============================================================================