From 5e961fa687795d08203aacc3cc75887fb5142063 Mon Sep 17 00:00:00 2001
From: Will Tackett <will.s.tackett@gmail.com>
Date: Wed, 28 Aug 2019 15:09:33 -0400
Subject: [PATCH] re-upload :/

---
 .dockerignore                  |  1 +
 Dockerfile                     |  0
 create_archive_fw_heudiconv.py |  0
 docker-env.sh                  |  4 ++++
 manifest.json                  | 34 +++++++++++++++++++---------------
 neurodebian.gpg                |  0
 readme.md                      |  8 --------
 report.py                      |  0
 requirements.txt               |  0
 run.sh                         |  4 ++--
 10 files changed, 26 insertions(+), 25 deletions(-)
 mode change 100644 => 100755 Dockerfile
 mode change 100644 => 100755 create_archive_fw_heudiconv.py
 create mode 100644 docker-env.sh
 mode change 100644 => 100755 manifest.json
 mode change 100644 => 100755 neurodebian.gpg
 delete mode 100644 readme.md
 mode change 100644 => 100755 report.py
 mode change 100644 => 100755 requirements.txt
 mode change 100644 => 100755 run.sh

diff --git a/.dockerignore b/.dockerignore
index 973aa3e..b1a6f61 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -5,3 +5,4 @@ venv
 .idea
 .gitignore
 readme.md
+.git
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
old mode 100644
new mode 100755
diff --git a/create_archive_fw_heudiconv.py b/create_archive_fw_heudiconv.py
old mode 100644
new mode 100755
diff --git a/docker-env.sh b/docker-env.sh
new file mode 100644
index 0000000..459430d
--- /dev/null
+++ b/docker-env.sh
@@ -0,0 +1,4 @@
+export HOME="/root"
+export FLYWHEEL="/flywheel/v0"
+export PATH="/opt/miniconda-latest/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
+export CONDA_DIR="/opt/miniconda-latest"
diff --git a/manifest.json b/manifest.json
old mode 100644
new mode 100755
index a52e76c..b20ff44
--- a/manifest.json
+++ b/manifest.json
@@ -1,21 +1,25 @@
 {
-	"name": "presurgical_report",
-	"label": "Presurgical Report Generator",
+	"name": "y",
+	"label": "y",
 	"description": "Generates a report from an fmri scan of an epilepsy patient",
+	"version": "0",
+	"inputs": {
+		"fmriprep_dir": {
+			"base": "file",
+			"description": "Full path to directory containing fmriprep results"
+		}
+	},
+	"config": {},
+	"command": "./report.py",
 	"author": "Will Tackett",
-	"maintainer": "Will Tackett <william.tackett@pennmedicine.upenn.edu>",
+	"maintainer": "Will Tackett",
+	"license": "BSD-3-Clause",
 	"source": "none",
 	"url": "none",
-	"version": "3.1.1",
-	"license": "BSD-3-Clause",
-	"inputs": {
-		"fmriprep_dir": {
-			"description": "Full path to directory containing fmriprep results",
-			"base": "file"
-		},
-		"config": {},
-		"command": "./report.py",
-		"author": "Will Tackett",
-		"maintainer": "Will Tackett"
+	"custom": {
+		"gear-builder": {
+			"category": "analysis",
+			"image": "report"
+		}
 	}
-}
\ No newline at end of file
+}
diff --git a/neurodebian.gpg b/neurodebian.gpg
old mode 100644
new mode 100755
diff --git a/readme.md b/readme.md
deleted file mode 100644
index 0a28f01..0000000
--- a/readme.md
+++ /dev/null
@@ -1,8 +0,0 @@
-# presurgical-report
-*started August 13, 2019*
-
-presurgical-report is a nipype-based program for automatically generating a report of a patients' presurgical fMRI. The report contains resulting activation maps and ROI statistics. It was originally designed for presurgical epilepsy patients who receive an fMRI to lateralize language function. 
-
-The algorithm is Dockerized with the intent of turning it into a gear for the Flywheel neuroinformatics platform. 
-
-The program takes a BIDs dataset and fMRIPREP results as inputs. It does a general linear model (GLM) analysis of the preprocessed BOLD time series images to create activation maps using FSL commands wrapped in nipype.  From these results, it generates an html report using jinja-based templating. 
diff --git a/report.py b/report.py
old mode 100644
new mode 100755
diff --git a/requirements.txt b/requirements.txt
old mode 100644
new mode 100755
diff --git a/run.sh b/run.sh
old mode 100644
new mode 100755
index 5000a73..90c56cf
--- a/run.sh
+++ b/run.sh
@@ -13,7 +13,7 @@ mkdir -p ${OUTPUT_DIR}
 CONTAINER='[flywheel/presurgicalreport]'
 #cp ${FLYWHEEL_BASE}/fmriprep_dir ${INPUT_DIR}/bids_dataset/derivatives/fmriprep/fmriprep_dir
 
-
+echo "test"
 # CREATE A BIDS FORMATTED DIRECTORY
 #   Use fw-heudiconv to accomplish this task
 /opt/miniconda-latest/bin/python3 ${FLYWHEEL_BASE}/create_archive_fw_heudiconv.py
@@ -34,4 +34,4 @@ fi
 # Show the contents of the BIDS directory
 ls -R ${BIDS_DIR}
 
-python report.py /flywheel/v0/bids_dataset /flywheel/v0/bids_dataset/derivatives/fmriprep/ /flywheel/v0/outputs
\ No newline at end of file
+/opt/miniconda-latest/bin/python3 report.py /flywheel/v0/bids_dataset /flywheel/v0/bids_dataset/derivatives/fmriprep/ /flywheel/v0/outputs