Merge pull request #15 from philipmac/main

Adds IMOD Dockerfile & "how to contribute" section

README.md

@@ -1,2 +1,50 @@
 # image_portal_workflows
 Workflows related to project previously referred to as "Hedwig"
+
+
+# How to contribute:
+For a more detailed example, see: https://docs.github.com/en/github/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request
+Broadly speaking the below should be close to what you'll need to do.
+
+- Fork niaid repo into your gh account via web interface.
+- Clone your repo to local machine, e.g.:
+
+	`git clone git@github.com:philipmac/nih_3d_workflows.git`
+
+- Set `upstream` as niaid repo.
+
+	`git remote add upstream git@github.com:niaid/nih_3d_workflows.git`
+
+- ensure origin and upstream look something like this:
+  ```
+  $ git remote -v
+  origin	git@github.com:philipmac/image_portal_workflows.git (fetch)
+  origin	git@github.com:philipmac/image_portal_workflows.git (push)
+  upstream	git@github.com:niaid/image_portal_workflows.git (fetch)
+  upstream	git@github.com:niaid/image_portal_workflows.git (push)
+  ```
+- Make changes to local copy.
+- Run `flake8` linter (see https://pypi.org/project/flake8/):
+
+	`flake8 . --max-line-length=127`
+
+- Run `black` formatter (see https://pypi.org/project/black/).
+
+	`black .`
+
+- Ensure neither `black` nor `flake8` are complaining.
+
+- Commit your local work, ensure you're up to date with `upstream`, and push to `origin`.
+
+	```
+	git commit -m "Fixes issue 123, ..."
+	git fetch upstream
+	git rebase upstream/master
+	git push origin branch_with_fix
+	```
+
+- Initiate creation the Pull Request (PR) via your fork into niaid/nih-3d-main using the web interface.
+- Look at your changes, ensure *only* those changes are included in your PR.
+- Submit PR with some helpful English. See: https://git-scm.com/book/en/v2/Distributed-Git-Contributing-to-a-Project
+- Feel free to let niaid repo admin (currently Philip MacM) know there's a PR waiting for review.
+- Thanks! :)

utils/imod/Dockerfile

@@ -0,0 +1,12 @@
+FROM centos:8
+
+ENV IMOD=imod_4.11.11_RHEL7-64_CUDA10.1.sh
+
+RUN yum install -y wget file python38
+RUN  wget https://bio3d.colorado.edu/imod/AMD64-RHEL5/${IMOD} && \
+     sh ${IMOD} -yes && \
+     rm -f ${IMOD}
+
+
+ENV IMOD_DIR=/usr/local/IMOD
+ENV PATH=$IMOD_DIR/bin:$PATH