From 134f1593247eca248b0878630be2618f39cf90b2 Mon Sep 17 00:00:00 2001
From: Jenny Wong <jnywong.pro@gmail.com>
Date: Mon, 22 Jan 2024 10:13:07 +0000
Subject: [PATCH] Genomics config

---
 environment.yml  | 10 ++++++++++
 requirements.txt | 15 +--------------
 2 files changed, 11 insertions(+), 14 deletions(-)
 create mode 100644 environment.yml

diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..e69e370
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,10 @@
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - fastqc=0.11.9
+  - trimmomatic=0.39
+  - bwa=0.7.17=ha92aebf_3
+  - samtools=1.9=h8ee4bcc_1
+  - bcftools=1.9
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index 7978335..8125b99 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,14 +1 @@
-jupyterlab==3
-numpy
-matplotlib
-jupyter-book
-jupyterlab-iframe
-jupyterlab-git 
-jupyterlab_myst
-jupyter-server-proxy
-ghp-import
-sphinx-autobuild
-sphinxcontrib-mermaid
-docutils==0.17.1  # see https://jupyterbook.org/en/stable/content/citations.html?highlight=docutils#citations-and-bibliographies
-nox
-gh-scoped-creds
+igv-notebook
\ No newline at end of file