From 8c8f8e715150fb28cc3642303b54ca1587186f35 Mon Sep 17 00:00:00 2001
From: "Overduin, Sam" <sam.overduin@wur.nl>
Date: Thu, 12 Mar 2020 12:25:47 +0100
Subject: [PATCH] Update reset_spades_for_taxa.sh
---
scripts/reset_spades_for_taxa.sh | 11 ++---------
1 file changed, 2 insertions(+), 9 deletions(-)
diff --git a/scripts/reset_spades_for_taxa.sh b/scripts/reset_spades_for_taxa.sh
index 077d4565..cbfc5cc6 100644
--- a/scripts/reset_spades_for_taxa.sh
+++ b/scripts/reset_spades_for_taxa.sh
@@ -1,7 +1,8 @@
#!/bin/bash
# Author: Sam Overduin
-spades_folder="$1"
+spades_py_executable="/mnt/LTR_userdata/overd008/tools/bin/spades.py"
+spades_folder="$1"
#cd "$spades_folder"
if [ "$2" == "barcode" ]; then
@@ -14,8 +15,6 @@ else
echo "$2 not found. Usage: reset_spades_for_taxa.sh spades-folder [barcode|repeat] ."
fi
-spades_py_executable="$HOME/mnt/ltr/tools/taxa_spades_install_final/bin/spades.py"
-
rm "$spades_folder"/pipeline_state/stage_3_k55
rm "$spades_folder"/pipeline_state/stage_4_copy_files
rm "$spades_folder"/pipeline_state/stage_5_as_finish
@@ -26,12 +25,6 @@ rm "$spades_folder"/pipeline_state/stage_8_copy_files
rm "$spades_folder"/pipeline_state/stage_9_as_finish
-#overd008/both_norm/corrected/both_normalized
-#overd008/both_norm_corrected_reads/both_normalized
-
-
-#rm -r "$spades_folder"/K55/saves/barcode_map_construction
-
echo "Do you wish to continue the spades pipeline?
with: $spades_py_executable --continue -o $1 (y/n)"
read continue_pipeline
--
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