Add brkraw (#602)

recipes/brkraw/README.md

@@ -0,0 +1,88 @@
+[![DOI](https://zenodo.org/badge/245546149.svg)](https://zenodo.org/badge/latestdoi/245546149)
+[![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/BrkRaw/tutorials/master)
+
+## BrkRaw: A comprehensive tool to access raw Bruker Biospin MRI data
+#### Version: 0.3.11
+
+### Description
+
+The ‘BrkRaw’ is a python module designed to provide a comprehensive tool to access raw data acquired from 
+Bruker Biospin preclinical MRI scanner. This module is also compatible with the zip compressed data 
+to enable use of the archived data directly.  
+The module is comprised of four components, including graphical user interface (GUI), command-line tools, 
+high-level and low-level python APIs.
+- For the GUI, we focused on improving convenience for checking metadata and previewing the reconstructed image.
+- For the command-line tool, we focused on providing tools for converting, organizing, archiving, and managing data.
+The command-line tool also provides easy-to-use function to convert large set of raw data into organized structure
+according to [BIDS](https://bids.neuroimaging.io).
+- For the high-level python API, we focused on enhancing the accessibility of reconstructed image data with 
+preserved image orientation and metadata for the image analysis. 
+It compatible users' convenient objects type ([nibabel](https://nipy.org/nibabel/) or 
+[SimpleITK](https://simpleitk.readthedocs.io/en/master/gettingStarted.html#python-binary-files)) 
+without the conversion step. 
+- For the low-level python API, we focused on providing a consistent method to access raw Bruker data including 
+parameter and binary files with the python compatible datatype while keeping the sake of simplicity.
+
+#### Conversion reliability
+![Robust Orientation](imgs/bruker2nifti_qa.png)
+We've tested our converter using the sample dataset from [Bruker2Nifti_QA](https://gitlab.com/naveau/bruker2nifti_qa) 
+and the results showed correct geometry and orientation for all datasets.
+We are still looking for more datasets showing orientation issue, 
+**if you have any shareable dataset, please contact the developer.**
+
+### Website
+For more detail information including installation, usage and examples, 
+please visit our [GitPage](https://brkraw.github.io).
+
+- [Installation](https://brkraw.github.io/docs/gs_inst.html)
+- [Command-line tool usage examples](https://brkraw.github.io/docs/gs_nii.html)
+- [Converting dataset into BIDS](https://brkraw.github.io/docs/gs_bids.html)
+- [Python API usage examples](https://brkraw.github.io/docs/ap_parent.html)
+- [GUI](https://brkraw.github.io/docs/gs_gui.html)
+- [Interactive Tutorial](https://mybinder.org/v2/gh/BrkRaw/tutorials/ac95b2c87b05664cb678c5dc1a930641397130ed)
+
+
+### Credits:
+##### Authors
+- SungHo Lee ([email protected]): main developer
+- Woomi Ban ([email protected]): sub-developer who tested and refined the module structure
+- Jaiden Dumas: proofreading of documents and update contents for the user community.
+- Dr. Gabriel A. Devenyi: The vast contributions to refinement of module functionality and troubleshooting.
+- Yen-Yu Ian Shih ([email protected]): technical and academical advisory on this project (as well as funding)
+##### Contributors
+- Drs. Chris Rorden and Sebastiano Ferraris: The pioneers related this project who had been inspired the developer
+ through their great tools including [dcm2niix](https://github.com/rordenlab/dcm2niix) and 
+ [bruker2nifti](https://github.com/SebastianoF/bruker2nifti), as well as their comments to improve this project. 
+- Dr. Mikael Naveau: The publisher of 
+[bruker2nifti_qa](https://gitlab.com/naveau/bruker2nifti_qa), the set of data 
+to help benchmark testing of Bruker converter.
+
+
+### License:
+GNU General Public License v3.0
+
+### How to get Support
+If you are experiencing any problem or have questions, please report it through 
+[Issues](https://github.com/BrkRaw/bruker/issues)
+
+### Citing BrkRaw
+Lee, Sung-Ho, Ban, Woomi, & Shih, Yen-Yu Ian. (2020, June 4). BrkRaw/bruker: BrkRaw v0.3.3 (Version 0.3.3). 
+Zenodo. http://doi.org/10.5281/zenodo.3877179
+
+
+**BibTeX**
+```
+@software{lee_sung_ho_2020_3907018,
+  author       = {Lee, Sung-Ho and
+                  Ban, Woomi and
+                  Shih, Yen-Yu Ian},
+  title        = {BrkRaw/bruker: BrkRaw v0.3.4},
+  month        = jun,
+  year         = 2020,
+  publisher    = {Zenodo},
+  version      = {0.3.4},
+  doi          = {10.5281/zenodo.3907018},
+  url          = {https://doi.org/10.5281/zenodo.3907018}
+}
+```

recipes/brkraw/brkraw.pkg

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+pkgdef pip {
+    require distro/ubuntu
+
+    pkg pkg:pip
+
+    env append PATH /usr/local/bin
+}
+
+pkgdef tzdata {
+    require distro/ubuntu
+
+    exec tzdata {
+        apt update
+        DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt -y install tzdata
+    }
+}
+
+pkgdef python3-tkinter {
+    require distro/ubuntu
+
+    pkg tzdata
+
+    pkg pkg:python3-tk
+}
+
+pkgdef brkraw {
+    pkg pip
+
+    pkg python3-tkinter
+
+    exec brkraw {
+        pip install bruker'[SimpleITK]'
+    }    
+}

recipes/brkraw/build.sh

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+#!/usr/bin/env bash
+set -ex
+
+export toolName='brkraw'
+export toolVersion='0.3.11'
+
+if [ "$1" != "" ]; then
+    echo "Entering Debug mode"
+    export debug=$1
+fi
+
+source ../main_setup.sh
+
+echo "EXPERIMENTAL: using tinyrange"
+
+$TINYRANGE login \
+    --size lg \
+    --package-path brkraw.pkg \
+    --pkg ubuntu \
+    --pkg brkraw \
+    --exec "whoami" \
+    --pull-snapshot brkraw.tar.gz
+
+neurodocker generate ${neurodocker_buildMode} \
+    --base-image ubuntu:22.04 \
+    --pkg-manager apt \
+    --run="printf '#!/bin/bash\nls -la' > /usr/bin/ll" \
+    --run="chmod +x /usr/bin/ll" \
+    --run="mkdir -p ${mountPointList}" \
+    --add ./brkraw.tar.gz / \
+    --env PATH='$PATH':/usr/local/bin/ \
+    --copy README.md /README.md \
+> ${imageName}.${neurodocker_buildExt}
+
+if [ "$1" != "" ]; then
+   ./../main_build.sh
+fi

recipes/main_setup.sh

@@ -55,6 +55,8 @@ export imageName=${toolName}_${toolVersion}
 # If TinyRange exists in the expected location then enable it.
 if test -f /storage/tinyrange/tinyrange; then
        export TINYRANGE=/storage/tinyrange/tinyrange
+elif command -v tinyrange &> /dev/null; then
+       export TINYRANGE=tinyrange
 fi
 
 echo "building $imageName in mode $buildMode"