From 1e3e759891dd7f945a1850e5232331bec4686907 Mon Sep 17 00:00:00 2001
From: Cade Mirchandani <cade@ucsc.edu>
Date: Tue, 10 Jan 2023 23:08:32 +0000
Subject: [PATCH 1/2] add build dockerfile

---
 Dockerfile | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100644 Dockerfile

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..26834e7
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,11 @@
+FROM ubuntu:18.04
+RUN apt-get update -y && apt-get install -y autoconf build-essential libboost-all-dev zlib1g-dev libbz2-dev libcurl4-openssl-dev liblzma-dev samtools cmake python3 python3-pip libjpeg-dev
+RUN pip3 install --upgrade pip setuptools wheel
+RUN pip3 install matplotlib
+RUN apt-get install -y python curl bzip2 && apt-get autoclean && rm -rf /var/lib/apt/lists/*
+RUN curl -L https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17_x64-linux.tar.bz2 | tar -jxvf -
+ENV PATH="${PATH}:/minimap2-2.17_x64-linux"
+COPY . /workdir
+WORKDIR /workdir
+RUN mkdir build && cd build && cmake .. && make -j 4
+ENV PATH="${PATH}:/workdir/build"
\ No newline at end of file

From a09d8f88dfb4e68f83b420891152b34c08fd49bf Mon Sep 17 00:00:00 2001
From: Cade Mirchandani <cade@ucsc.edu>
Date: Wed, 11 Jan 2023 04:31:29 +0000
Subject: [PATCH 2/2] add argparse for parsing input paths and labels

---
 scripts/plot_matrix.py | 43 +++++++++++++++++++++++++++++++-----------
 1 file changed, 32 insertions(+), 11 deletions(-)

diff --git a/scripts/plot_matrix.py b/scripts/plot_matrix.py
index 2f81350..26c65f0 100644
--- a/scripts/plot_matrix.py
+++ b/scripts/plot_matrix.py
@@ -2,7 +2,7 @@
 from matplotlib import cm
 import matplotlib.colors as colors
 import numpy
-
+import argparse
 A,C,G,T = 0,1,2,3
 
 # Index key for storing base data in matrix form
@@ -148,17 +148,38 @@ def main():
 
     # ------------------------------------------------------------------------------------------------------
 
-    paths = [
-        "/home/ryan/code/runlength_analysis_cpp/build/output/rle_test/length_frequency_matrix_nondirectional.csv",
-        "/home/ryan/code/runlength_analysis_cpp/build/output/rle_test/length_frequency_matrix_nondirectional.csv",
-        ]
-
-    labels = [
-        "test",
-        "test",
-    ]
-
+    # paths = [
+    #     "/home/ryan/code/runlength_analysis_cpp/build/output/rle_test/length_frequency_matrix_nondirectional.csv",
+    #     "/home/ryan/code/runlength_analysis_cpp/build/output/rle_test/length_frequency_matrix_nondirectional.csv",
+    #     ]
 
+    # labels = [
+    #     "test",
+    #     "test",
+    # ]
+    
+    # quick cli for workflow use from https://stackoverflow.com/questions/32761999/how-to-pass-an-entire-list-as-command-line-argument-in-python
+    CLI=argparse.ArgumentParser()
+    CLI.add_argument(
+        "--paths",  # name on the CLI - drop the `--` for positional/required parameters
+        nargs="*",  # 0 or more values expected => creates a list
+        type=str,
+        default=[],  # default if nothing is provided
+    )
+    CLI.add_argument(
+        "--labels",
+        nargs="*",
+        type=str,  # any type/callable can be used here
+        default=[],
+    )
+
+    # parse the command line
+    args = CLI.parse_args()
+    # access CLI options
+    print("paths: %r" % args.paths)
+    print("labels: %r" % args.paths)
+    paths = args.paths
+    labels = args.labels
     figure,axes = pyplot.subplots(ncols=len(paths), nrows=1)
     colormap = pyplot.get_cmap("viridis")
     # colormap = truncate_colormap(colormap, max=0.5)