From 64a7431fa5c8a011abee4eee6f75e88974222d74 Mon Sep 17 00:00:00 2001
From: Michael Joseph <josephmje.22@gmail.com>
Date: Thu, 12 Aug 2021 11:10:28 -0400
Subject: [PATCH] update binder environment

---
 README.md              |  2 +-
 binder/apt.txt         |  1 +
 binder/environment.yml | 22 ++++++++++++++++++++++
 binder/postBuild       |  4 ++++
 4 files changed, 28 insertions(+), 1 deletion(-)
 create mode 100644 binder/apt.txt
 create mode 100644 binder/environment.yml
 create mode 100644 binder/postBuild

diff --git a/README.md b/README.md
index cb26ae21..6be26b55 100644
--- a/README.md
+++ b/README.md
@@ -92,7 +92,7 @@ To cite this lesson, please consult with [CITATION](CITATION)
 [slack_channel_status]: https://img.shields.io/badge/Slack_Channel-neuroimaging-E01563.svg
 [slack_channel_url]: https://swcarpentry.slack.com/messages/CCJBHKCHZ
 [binder_svg]: https://mybinder.org/badge_logo.svg
-[binder_url]: https://mybinder.org/v2/gh/carpentries-incubator/SDC-BIDS-dMRI/main
+[binder_url]: https://mybinder.org/v2/gh/carpentries-incubator/SDC-BIDS-dMRI/main?urlpath=lab/tree/code
 [episode01]: https://carpentries-incubator.github.io/SDC-BIDS-dMRI/introduction/index.html
 [episode02]: https://carpentries-incubator.github.io/SDC-BIDS-dMRI/preprocessing/index.html
 [episode03]: https://carpentries-incubator.github.io/SDC-BIDS-dMRI/local_orientation_reconstruction/index.html
diff --git a/binder/apt.txt b/binder/apt.txt
new file mode 100644
index 00000000..5c62b5aa
--- /dev/null
+++ b/binder/apt.txt
@@ -0,0 +1 @@
+tree
diff --git a/binder/environment.yml b/binder/environment.yml
new file mode 100644
index 00000000..6b3e2370
--- /dev/null
+++ b/binder/environment.yml
@@ -0,0 +1,22 @@
+name: dc-dmri
+
+channels:
+  - default
+  - conda-forge
+
+dependencies:
+  - python=3.8.*
+  - pip
+  - git
+  - dipy=1.3.0
+  - fury=0.6.1
+  - matplotlib
+  - nibabel
+  - nilearn=0.7.0
+  - numpy
+  - osfclient
+  - pandas
+  - seaborn
+
+  - pip:
+      - pybids
diff --git a/binder/postBuild b/binder/postBuild
new file mode 100644
index 00000000..a6eaafce
--- /dev/null
+++ b/binder/postBuild
@@ -0,0 +1,4 @@
+# download pre-processed dMRI data
+osf -p cmq8a fetch ds000221_subject/ds000221_sub-010006.zip data/ds000221_sub-010006.zip
+unzip data/ds000221_sub-010006.zip -d data
+rm data/ds000221_sub-010006.zip