From 97f4f71eec204192cbcecd2dc0d7ef09e2bda213 Mon Sep 17 00:00:00 2001
From: Erin McAuley <erin@fulcrumgenomics.com>
Date: Tue, 14 Jan 2025 09:35:26 -0500
Subject: [PATCH 1/2] add install.rst and update index.rst

---
 docs/index.rst   |  1 +
 docs/install.rst | 43 +++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 44 insertions(+)
 create mode 100644 docs/install.rst

diff --git a/docs/index.rst b/docs/index.rst
index 34be8ae..7fae029 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -12,5 +12,6 @@ Documentation Contents
 .. toctree::
    :maxdepth: 2
 
+   install.rst
    api.rst
 
diff --git a/docs/install.rst b/docs/install.rst
new file mode 100644
index 0000000..3de91a5
--- /dev/null
+++ b/docs/install.rst
@@ -0,0 +1,43 @@
+============
+Installation
+============
+
+1. Install the environment manager :code:`mamba`
+2. Install the Python build tool :code:`poetry`
+
+3. Create an environment with Python, Cython, and Pysam:
+
+.. code-block:: bash
+
+   mamba env create -f pybwa.yml
+
+4. Activate the environment:
+
+.. code-block:: bash
+
+   mamba activate pybwa
+
+5. Clone the :code:`bwa` repo
+
+.. code-block:: bash
+
+   git clone https://github.com/lh3/bwa
+
+6. Configure poetry to install into pre-existing virtual environments:
+
+.. code-block:: bash
+
+    poetry config virtualenvs.create false
+
+7. Install :code:`pybwa` into the virtual environment:
+
+.. code-block:: bash
+
+    poetry install
+
+8. Check your build:
+
+.. code-block:: bash
+
+    poetry run pytest
+

From 4e9fd7606edbc920085fa02ef171ba61f50c78e5 Mon Sep 17 00:00:00 2001
From: Erin McAuley <erin@fulcrumgenomics.com>
Date: Tue, 14 Jan 2025 19:02:04 -0500
Subject: [PATCH 2/2] remove git clone bwa, but do add git clone pybwa

---
 docs/install.rst | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/docs/install.rst b/docs/install.rst
index 3de91a5..f2dd1a5 100644
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -2,26 +2,26 @@
 Installation
 ============
 
-1. Install the environment manager :code:`mamba`
-2. Install the Python build tool :code:`poetry`
-
-3. Create an environment with Python, Cython, and Pysam:
+1. Clone the :code:`pybwa` repo (note the :code:`--recurse-submodules` flag, as :code:`bwa` is a submodule)
 
 .. code-block:: bash
 
-   mamba env create -f pybwa.yml
+   git clone --recurse-submodules https://github.com/fulcrumgenomics/pybwa
+
+2. Install the environment manager :code:`mamba`
+3. Install the Python build tool :code:`poetry`
 
-4. Activate the environment:
+4. Create an environment with Python, Cython, and Pysam:
 
 .. code-block:: bash
 
-   mamba activate pybwa
+   mamba env create -f pybwa.yml
 
-5. Clone the :code:`bwa` repo
+5. Activate the environment:
 
 .. code-block:: bash
 
-   git clone https://github.com/lh3/bwa
+   mamba activate pybwa
 
 6. Configure poetry to install into pre-existing virtual environments: