From dfe2d29d6a039967b5d16947ff71a48167f7592c Mon Sep 17 00:00:00 2001
From: Neurodesk Github Action Runner <mail.neurodesk@gmail.com>
Date: Tue, 19 Nov 2024 05:20:02 +0000
Subject: [PATCH] might already work

---
 recipes/palmettobug/README.md | 20 +++++++++++++++++
 recipes/palmettobug/build.sh  | 41 +++++++++++++++++++++++++++++++++++
 recipes/palmettobug/test.sh   |  2 ++
 3 files changed, 63 insertions(+)
 create mode 100644 recipes/palmettobug/README.md
 create mode 100755 recipes/palmettobug/build.sh
 create mode 100644 recipes/palmettobug/test.sh

diff --git a/recipes/palmettobug/README.md b/recipes/palmettobug/README.md
new file mode 100644
index 00000000..e615eff2
--- /dev/null
+++ b/recipes/palmettobug/README.md
@@ -0,0 +1,20 @@
+
+----------------------------------
+## palmettobug/0.0.1 ##
+CIPHER is a pure-python GUI in customtinker that, along with its sister package isoSegDenoise, can preprocess, segment, and analyze high-dimensional image or flow cytometry data, especially mass cytometry / imaging mass cytometry data
+
+Example: 
+```
+palmettobug
+```
+
+More documentation can be found here: https://github.com/immunecells/CIPHER/tree/main
+
+Citation:
+```
+TBD
+```
+
+To run container outside of this environment: ml palmettobug/0.0.1
+
+----------------------------------
diff --git a/recipes/palmettobug/build.sh b/recipes/palmettobug/build.sh
new file mode 100755
index 00000000..5e075b15
--- /dev/null
+++ b/recipes/palmettobug/build.sh
@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+set -e
+
+# this template file builds tools required for dicom conversion to bids
+export toolName='palmettobug'
+export toolVersion='0.0.1'    # Don't forget to update version change in README.md!!!!!
+
+
+if [ "$1" != "" ]; then
+    echo "Entering Debug mode"
+    export debug=$1
+fi
+
+source ../main_setup.sh --reinstall_neurodocker=false
+
+neurodocker generate ${neurodocker_buildMode} \
+    --pkg-manager apt \
+    --base-image ubuntu:24.04 \
+    --env DEBIAN_FRONTEND=noninteractive \
+    --run="printf '#!/bin/bash\nls -la' > /usr/bin/ll" \
+    --run="chmod +x /usr/bin/ll" \
+    --run="mkdir -p ${mountPointList}" \
+    --install ca-certificates wget unzip libx11-6 fontconfig libgles2 \
+    --workdir /opt \
+    --miniconda version=latest \
+                conda_install="python=3.9" \
+    --run="wget https://object-store.rc.nectar.org.au/v1/AUTH_dead991e1fa847e3afcca2d3a7041f5d/build/CIPHER-main.zip \
+      && unzip CIPHER-main.zip \
+      && rm -rf CIPHER-main.zip \
+      && cd CIPHER-main \
+      && pip install . \
+      && cd .. \
+      && rm -rf CIPHER-main" \
+    --env DEPLOY_BINS=palmettobug \
+    --copy README.md /README.md \
+  > ${imageName}.${neurodocker_buildExt}
+
+
+if [ "$1" != "" ]; then
+   ./../main_build.sh
+fi
\ No newline at end of file
diff --git a/recipes/palmettobug/test.sh b/recipes/palmettobug/test.sh
new file mode 100644
index 00000000..812acae9
--- /dev/null
+++ b/recipes/palmettobug/test.sh
@@ -0,0 +1,2 @@
+python3 --version #should be 3.9
+palmettobug
\ No newline at end of file