From f9008f8e701a9c37594f02cdb103f7fd343820b6 Mon Sep 17 00:00:00 2001
From: CSTE7007 <mikparadox@outlook.com>
Date: Wed, 19 Jul 2023 16:21:45 +0600
Subject: [PATCH 1/2] added bash executable code

---
 condor.sh | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 condor.sh

diff --git a/condor.sh b/condor.sh
new file mode 100644
index 0000000..4009081
--- /dev/null
+++ b/condor.sh
@@ -0,0 +1,39 @@
+
+#inspired from SCARLET[https://github.com/raphael-group/scarlet]
+
+if [ "$#" -le 3 ]; then
+    echo """
+    
+    usage: condor.py [-h] [-i I] [-r R] [-v V] [-s S] [-a A] [-b B] [--ado ADO] [-k K] -o O [-t T]
+
+optional arguments:
+  -h, --help  show this help message and exit
+  -i I        csv file with mutation matrix and cluster id
+  -r R        csv file with total read count matrix
+  -v V        csv file with variant read count matrix
+  -s S        file containing list of SNPs
+  -a A        false positive error rate [0.001]
+  -b B        false negative error rate [0.001]
+  --ado ADO   precision parameter for ADO
+  -k K        maximum number of losses for an SNV
+  -o O        output prefix
+  -t T        time limit in seconds [1800]
+    
+    """
+    exit 1
+fi
+
+
+character_matrix=$1
+read_count=$2
+variant_count=$3
+output_prefix=$4
+
+
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+
+python $DIR/src/condor.py -i  $character_matrix -a 0.0018 -b 0.001 -k 1 -r $read_count -v $variant_count -o $output_prefix
+
+
+dot -Tpdf ${output_prefix}_tree.dot -o ${output_prefix}_tree.pdf -v
+dot -Tpdf ${output_prefix}_tree_without_cells.dot -o ${output_prefix}_tree_without_cells.pdf -v

From d74a1ffb6a9b6d136b28b4b38081ebfbc925801d Mon Sep 17 00:00:00 2001
From: CSTE7007 <mikparadox@outlook.com>
Date: Wed, 19 Jul 2023 16:22:58 +0600
Subject: [PATCH 2/2] updated README.md with bash executable code

---
 README.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/README.md b/README.md
index 4f4b343..8aaf3c2 100644
--- a/README.md
+++ b/README.md
@@ -57,3 +57,8 @@ python src/simulation_reads.py -n 25 -m 25 -p 5 -k 1 -s 0 -d 0.1 -a 0.001 -b 0.0
 An example of usage is as follows.
 
     $ python src/condor.py -i  data/sample/overview_character_matrix.csv -a 0.0018 -b 0.001 -k 1 -r data/sample/overview_read_count.csv -v data/sample/overview_variant_count.csv -o data/sample/overview 
+
+**An example of usage with only bash command**
+```
+bash condor.sh data/sample/overview_character_matrix.csv data/sample/overview_read_count.csv data/sample/overview_variant_count.csv data/sample/overview 
+```
\ No newline at end of file