From ae134c50da806636f2f8b6c6dbf66c12c0763e04 Mon Sep 17 00:00:00 2001
From: Austin Macdonald <austin@dartmouth.edu>
Date: Fri, 28 Apr 2023 17:21:44 -0400
Subject: [PATCH 1/2] Lets keep the script out of the container

---
 code/opfvta-images/Containerfile      | 3 ---
 code/opfvta-images/Containerfile.base | 9 ---------
 2 files changed, 12 deletions(-)
 delete mode 100644 code/opfvta-images/Containerfile.base

diff --git a/code/opfvta-images/Containerfile b/code/opfvta-images/Containerfile
index acab7d4d..f2a8fa21 100644
--- a/code/opfvta-images/Containerfile
+++ b/code/opfvta-images/Containerfile
@@ -30,6 +30,3 @@ RUN echo "sci-biology/opfvta_bidsdata-2.0" > /etc/portage/profile/package.provid
 
 RUN pushd /var/db/repos/local_opfvta/sci-misc/opfvta; ebuild opfvta-99999.ebuild manifest; popd
 RUN emerge -v opfvta --autounmask-continue
-RUN source /etc/profile
-
-ENTRYPOINT ["/opfvta/produce.sh"]
diff --git a/code/opfvta-images/Containerfile.base b/code/opfvta-images/Containerfile.base
deleted file mode 100644
index 8bdef3dc..00000000
--- a/code/opfvta-images/Containerfile.base
+++ /dev/null
@@ -1,9 +0,0 @@
-# based on stage3 image
-# FROM gentoo/stage3:amd64-hardened-20200905
-FROM gentoo/stage3:latest
-
-# copy the entire portage volume in
-COPY --from=portage /var/db/repos/gentoo /var/db/repos/gentoo
-
-RUN emerge -v --noreplace dev-vcs/git
-RUN emerge -v1u portage

From 474a1c5caf97415c5dd384deb6b3ffce8799974c Mon Sep 17 00:00:00 2001
From: Austin Macdonald <austin@dartmouth.edu>
Date: Fri, 28 Apr 2023 17:44:05 -0400
Subject: [PATCH 2/2] cleanup

---
 Makefile                         | 19 +++++--------------
 code/opfvta-images/Containerfile |  3 +++
 code/produce-analysis.sh         |  2 ++
 3 files changed, 10 insertions(+), 14 deletions(-)
 create mode 100644 code/produce-analysis.sh

diff --git a/Makefile b/Makefile
index d1bd7069..cd7d67df 100644
--- a/Makefile
+++ b/Makefile
@@ -26,24 +26,15 @@ push:
 	podman push ${FQDN_IMAGE}
 
 run:
-	# TODO
-	ifndef OPFVTA_SCRATCH_DIR
-	$(error OPFVTA_SCRATCH_DIR is not set)
-	endif
+	ifeq ($(OPFVTA_SCRATCH_DIR),)
+	echo "OPFVTA_SCRATCH_DIR must be set to a directory with at least 200Gb of space."
+	else
 	podman run \
 		-it \
 		--rm \
 		-v inputs/opfvta-bids:/usr/share/opfvta_bidsdata \
 		-v inputs/mouse-brain-templates-0.5.3:/usr/share/mouse_brain_atlases \
+		-v outputs/:/outputs
 		-v ${OPFVTA_SCRATCH_DIR}:/root/.scratch
 		${FQDN_IMAGE}
-
-# Use this to run a shell
-handtest:
-	podman run \
-		-it \
-		-v input_data:/usr/share/opfvta_bidsdata \
-		-v reference_data:/TODOWHEREDOESTHISGO \
-		-v output:/root/.scratch \
-		${FQDN_IMAGE} \
-		/bin/bash
+	endif
diff --git a/code/opfvta-images/Containerfile b/code/opfvta-images/Containerfile
index f2a8fa21..9f76b2c0 100644
--- a/code/opfvta-images/Containerfile
+++ b/code/opfvta-images/Containerfile
@@ -11,6 +11,9 @@ ARG gentoo_hash=0f6aa0646baad09881e581250e24a4e018e14abc
 ARG science_hash=3f2aee8f5efbcf9301c98133bf56daaf2767ded6
 ARG FEATURES="-ipc-sandbox -network-sandbox -pid-sandbox"
 
+# This will be bound, and contents available outside of container
+RUN mkdir /outputs
+
 COPY code/opfvta /opfvta
 COPY code/opfvta/.gentoo/portage/ /etc/portage/
 COPY code/opfvta/.gentoo/overlay/ /var/db/repos/local_opfvta/
diff --git a/code/produce-analysis.sh b/code/produce-analysis.sh
new file mode 100644
index 00000000..bfa64248
--- /dev/null
+++ b/code/produce-analysis.sh
@@ -0,0 +1,2 @@
+make data
+make all