--- a
+++ b/gui.py
@@ -0,0 +1,176 @@
+# -*- coding: utf-8 -*-
+"""
+@Time ： 2024/1/15 11:45
+@Auth ： Juexiao Zhou
+@File ：app.py
+@IDE ：PyCharm
+@Page: www.joshuachou.ink
+"""
+
+import argparse
+import os
+from src.agent import Agent
+import gradio as gr
+import time
+import yaml
+import subprocess
+import sys
+
+def parse_args():
+    parser = argparse.ArgumentParser(description="AutoBA-GUI v0.1")
+    parser.add_argument('--port', type=int, default=5904)
+    args = parser.parse_args()
+    return args
+
+def gradio_reset():
+    return None, None, None
+
+def get_an_example():
+    _input_file_path_description = "./experiments/case1.1/data/SRR1234567_R1.fastq.gz: Paired-end Illumina WGS reads, forward\n" \
+                                   "./experiments/case1.1/data/SRR1234567_R2.fastq.gz: Paired-end Illumina WGS reads, reverse\n" \
+                                   "./experiments/case1.1/data/TruSeq3-PE.fa: Adapter sequences for trimming\n" \
+                                   "./experiments/case1.1/data/Reference.fasta: Reference genome for the organism under study in FASTA format"
+    _input_outoput_path = "./experiments/case1.1/output"
+    _input_goal = "To perform genome assembly using paired-end WGS data"
+    return _input_file_path_description, _input_outoput_path, _input_goal
+
+def print_to_textbox(*args, **kwargs):
+    global HISTORY
+    text = " ".join(map(str, args)) + "\n"
+    if len(HISTORY) > 100:
+        HISTORY = HISTORY[1:]
+        HISTORY.append(text)
+    else:
+        HISTORY.append(text)
+
+def run(input_file_path_description, input_outoput_path, input_goal, model_engine, openai_api, execute):
+    AIAgent = Agent(initial_data_list=input_file_path_description.split('\n'),
+                    output_dir=input_outoput_path,
+                    initial_goal_description=input_goal,
+                    model_engine=model_engine,
+                    openai_api=openai_api,
+                    execute=execute,
+                    blacklist='STAR,java,perl,annovar',
+                    gui_mode=False)
+    AIAgent.run()
+    return 'Job Finished!'
+
+
+if __name__ == '__main__':
+    args = parse_args()
+    # model_folder = args.model_root
+    # model_files = [os.path.join(model_folder, f) for f in os.listdir(model_folder) if os.path.isfile(os.path.join(model_folder, f))]
+    FORCE_STOP = False
+    HISTORY = []
+
+    with gr.Blocks() as demo:
+        gr.Markdown("""<h1 align="center">AutoBA-GUI v0.1</h1>""")
+
+        gr.Markdown("""<h3>An AI Agent for Fully Automated Multi-omic Analyses</h3>""")
+
+        with gr.Row():
+            with gr.Column():
+                input_file_path_description = gr.TextArea(
+                    label="File path and description",
+                    placeholder="Enter the absolute file path and file description in the following format, e.g.: \n"
+                                "/data/SRR1234567_R1.fastq.gz: Paired-end Illumina WGS reads, forward\n"
+                                "/data/SRR1234567_R2.fastq.gz: Paired-end Illumina WGS reads, reverse\n"
+                                "/data/TruSeq3-PE.fa: Adapter sequences for trimming\n"
+                                "/data/Reference.fasta: Reference genome for the organism under study in FASTA format",
+                    max_lines=999999,
+                    container=True,
+                )
+
+                input_outoput_path = gr.TextArea(
+                    label="Output path",
+                    placeholder="Enter absolute output path, e.g.: \n"
+                                "/output",
+                    max_lines=999999,
+                    container=True,
+                )
+
+                input_goal = gr.TextArea(
+                    label="Goal",
+                    placeholder="Describe your goal for analysis, e.g.: \n"
+                                "To perform genome assembly using paired-end WGS data",
+                    max_lines=999999,
+                    container=True,
+                )
+
+                local_model_engines = ['codellama-7bi',
+                                       'codellama-13bi',
+                                       'codellama-34bi',
+                                       'llama2-7bc',
+                                       'llama2-13bc',
+                                       'llama2-70bc']
+
+                gpt_model_engines = ['gpt-3.5-turbo',
+                                     'gpt-4',
+                                     'gpt-3.5-turbo-1106',
+                                     'gpt-4-0613',
+                                     'gpt-4-32k-0613',
+                                     'gpt-4-1106-preview']
+
+                model_engines = local_model_engines + gpt_model_engines
+
+                with gr.Row():
+                    model_engine = gr.Dropdown(
+                        label="Select model engine",
+                        choices=model_engines,
+                        value='gpt-4-1106-preview',
+                        max_choices=1,
+                        container=True,
+                        interactive=True
+                    )
+
+                    openai_api = gr.Textbox(
+                        label="OpenAI API",
+                        placeholder="sk-xxxxx. Leave it empty for local version ",
+                        max_lines=1,
+                        container=True,
+                        interactive=True
+                    )
+
+                    execute = gr.Checkbox(
+                        label="Execute Code",
+                        value=False,
+                        visible=True
+                    )
+
+                with gr.Row():
+                    example_button = gr.Button(
+                        value="Get an example",
+                        interactive=True,
+                        variant="primary"
+                    )
+
+                    upload_button = gr.Button(
+                        value="Run",
+                        interactive=True,
+                        variant="primary"
+                    )
+
+                    #clear = gr.Button("Restart")
+
+                with gr.Row():
+                    with gr.Column():
+                        gr.Markdown('### Check command line for realtime outputs')
+                        output_log = gr.TextArea(
+                            label="Check command line for realtime outputs",
+                            max_lines=5,
+                            container=True,
+                            lines=5,
+                        )
+
+        gr.Markdown("""This site was created by King Abdullah University of Science and Technology (KAUST).""")
+
+        click_event = upload_button.click(run,
+                            [input_file_path_description, input_outoput_path, input_goal, model_engine, openai_api,
+                             execute],
+                            [output_log])
+
+        example_button.click(get_an_example,
+                             [],
+                             [input_file_path_description, input_outoput_path, input_goal])
+
+    demo.launch(share=True, server_port=args.port, server_name='0.0.0.0')