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binder/CONTRIBUTING.md (3443, 2016-01-06)
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binder/app/.htaccess (140, 2016-01-06)
binder/app/Config/ (0, 2016-01-06)
binder/app/Config/CakePdf.php (379, 2016-01-06)
binder/app/Config/Schema/ (0, 2016-01-06)
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binder/app/Console/Command/AppShell.php (854, 2016-01-06)
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## OpenIAV (image annotation viewer) --- #### SIGNIFICANCE OpenIAV (image annotation viewer) is an open source Web-based image annotation platform for data share and archive in a biomedical laboratory. --- #### INTRODUCTION OpenIAV (image annotation viewer) is a Web-based image annotation tool. It can store a high-resolution figure, and view scale-free slide smooth. This tool includes a rich user interface for graphical annotation such as shape of a line, circle, rectangle, and color pallet. Additionally, you can describe a annotated information for an image as metadata. Detail information of this tools was provided at [RegMed project](https://regmed.hgc.jp/) .  --- #### NOTICE * This repository only distributes the source code of OpenIAV for a developer, if you are an end-user that need a detail information about usage, please visit our website. [RegMed project](http://regmed.hgc.jp) * We are distributing [the virtual container of OpenIAV on the Docker Hub](https://hub.docker.com/r/komiyama/binder/). --- #### INSTALL ##### Preparation of Docker for Mac OSX * M-1. Install "Command Line Tools for Xcode". ``` $ xcode-select --install ``` * M-2. Install a package management system of "Homebrew". ``` $ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" ``` * M-3. Update the package of Homebrew. ``` $ brew update $ brew upgrade ``` * M-4. Install application of "VirtualBox." * [https://www.virtualbox.org/wiki/Downloads](https://www.virtualbox.org/wiki/Downloads) * M-5. Install Boot2Docker and Docker. ``` $ brew install boot2docker docker ``` * M-6. Upgrade Boot2Docker. ``` $ boot2docker upgrade ``` * M-7. Check the IP address assigned using the command of Boot2Docker. ``` $ boot2docker ip ``` --- ##### Preparation of Docker for Windows * W-1. Install application of "Windows Docker Client". [https://docs.docker.com/installation/windows/](https://docs.docker.com/installation/windows/) [https://github.com/boot2docker/windows-installer/releases](https://github.com/boot2docker/windows-installer/releases) (Boot2Docker, Boot2Docker Management Tool, Docker, VirtualBox, msysGit are installed) * W-2. Start Boot2Docker from the start menu. * W-3. Make a note of the IP address of DOCKER_HOST displayed at the time of starting. --- ##### Preparation of Docker for Linux * LC-0. Install Docker from EPEL of Fedora in CentOS 6. (you do not need this process at after version 6.5) ``` $ sudo rpm -ivh http://ftp.riken.jp/Linux/fedora/epel/6/x86_64/epel-release-6-8.noarch.rpm ``` * LC-1. Update package of yum. ``` $ sudo yum update ``` * LC-2. Install Docker. ``` $ sudo yum install docker-io (in case CentOS 6) $ sudo yum install docker (in case CentOS 7) ``` * LC-3. Set up to start Docker at the time of boot of CentOS. ``` $ sudo chkconfig docker on ``` * LC-4. Start Docker service. ``` $ sudo /etc/rc.d/init.d/docker start ``` * LC-5. Inspect a host name, to access from a browser to a Web server. Please search an IP address with ifconfig --- ##### Install Image Annotation Viewer as common process * C-0. Register your account into Docker Hub. [https://registry.hub.docker.com/](https://registry.hub.docker.com/) (Link to other Website) * C-1. If you encounter the message of "Cannot connect to the Docker daemon. Is 'docker -d' running on this host?" then you execute next command. ``` $ export $(boot2docker shellinit) ``` * C-2. login to Docker Hub. ``` $ docker login ``` * C-3. Pull container image of Image Annotation Viewer from Docker Hub. ``` $ docker pull komiyama/binder ``` * C-4. Check an information of container image. ``` $ docker images ``` * C-5. Start a container as a daemon and assign HTTP port to the container. ``` * $ docker run -t -i -d -p 80:80 --name binder komiyama/binder ``` * C-6. Check a started container. ``` $ docker ps -a ``` * C-7. Access http://HOSTNAME:PORT/binder/login/ via a browser. * C-8. Default user accounts were registered as each user roles. ``` Administrator: (ID:admin, Password:adminadmin) User: (ID:user1, Password:useruser) Supervisor: (ID:demo1, Password:demodemo) ``` * C-9. Set up the CONTAINER ID into a stop option of Docker at the termination of a container. ``` $ docker stop CONTAINER_ID ``` --- ##### Common process of local installation for Image Annotation Viewer from Docker Images of TAR file * C'-1. If you encounter the message of "Cannot connect to the Docker daemon. Is 'docker -d' running on this host?" then you execute next command. ``` $ export $(boot2docker shellinit) ``` * C'-2. Download the TAR file of container image of annotation image viewer from our Web site. * https://regmed.hgc.jp/docker/ImageAnnotationViewer_latest.tar.gz * C'-3. Load the TAR file in to your docker. ``` $ docker load -i /YOUR/FILE/PATH/AnnotationImageViewer_latest.tar.gz ``` * C'-4. Check an information of container image. ``` $ docker images ``` * C'-5. Set a human readable tag to the loaded IAV image. ``` $ docker tag IMAGE_ID komiyama/binder:latest ``` * C'-6. Start a container as a daemon and assign HTTP port to the container. ``` $ docker run -t -i -d -p 10080:80 --name binder komiyama/binder ``` * C'-7. Check a sturted container. ``` $ docker ps -a ``` * C'-8. Access http://DOCKER_HOST:PORT/binder/login/ via a browser. Example: http://192.168.59.103:10080/binder/login/ * C'-9. Default user accounts were registered as each user roles. Administrator: (ID:admin, Password:adminadmin) User: (ID:user1, Password:useruser) Supervisor: (ID:demo1, Password:demodemo) * C'-10. Set up the CONTAINER ID into an option parameter of docker stop command at the termination of a container. ``` $ docker stop CONTAINER_ID ``` --- #### USAGE ##### Usage and detail information Please visit [the RegMed project Web site](https://regmed.hgc.jp/aiv.html) .

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