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[Installing With Docker *\*(RECOMMENDED)\**](#installing-with-docker)<br>
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[Installing Natively](#installing-natively)<br>
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[Customization](#customization)<br>
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[Migration](#migration)<br>
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[Citation](#citation)<br>
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[Troubleshooting](#troubleshooting)<br>
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## Hardware Requirements
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FORCAST can be installed on any machine running a [docker-compatible operating system](https://docs.docker.com/install/). Alternately, to run FORCAST natively, Ubuntu 16.04 is required.
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In either case, a minimum of 8GB of RAM and 100GB of hard disk space is recommended.
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## Installing with Docker
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*\*RECOMMENDED OPTION\**
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For first time users, and those using personal computers, this is the recommended way to install FORCAST.
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First, install the [docker engine](https://docs.docker.com/install/). If using Linux, also install [docker compose](https://docs.docker.com/compose/install/) (this is included by default in Mac and Windows installations of docker).
Navigate to the `FORCAST` directory. The `sample.env` file defines yeast (*Saccharomyces_cerevisiae*) as the organism of interest with genome assembly R64-1-1:
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```
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ORGANISM=Saccharomyces_cerevisiae
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ASSEMBLY=R64-1-1
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```
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-[Hardware Requirements](#hardware-requirements)
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Rename the file to `.env` and change these defaults to your desired organism/genome build if they are different. A full list of available genomes can be found at [ftp://ftp.ensembl.org/pub/current_fasta](ftp://ftp.ensembl.org/pub/current_fasta).
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-[Installing with Docker](#installing-with-docker)
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From within the `FORCAST` directory, build the docker container:
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-[Customization](#customization)
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```docker-compose up```
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-[Migration](#migration)
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Depending on the size of your organism, it may take several hours to download the genome and build the index files. Once the setup is complete, the message: ` * Starting Apache httpd web server apache2 * ` will be displayed. FORCAST should now be available via web browser at your server's domain address (or at localhost if running locally on your personal computer).
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-[Citation](#citation)
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Once you're finished using FORCAST, it can be shut-down by typing Ctrl-C and typing ```docker-compose down``` on the command-line. Your guides and primers will be saved to the ```/mongo``` folder and the indexed genome files saved to the ```/jbrowse``` folder for the next time you start up FORCAST (again via ```docker-compose up```).
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-[Troubleshooting](#troubleshooting)
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## Installing Natively
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(Requires `sudo` privileges and a machine running Ubuntu 16.04)
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## Hardware Requirements
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Install git and apache2:
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```
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sudo apt-get update
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sudo apt-get install -y git apache2
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```
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Navigate to a folder where you would like to install FORCAST. It must be a folder that can be served by apache2 (i.e. `var/www/html`) and remove the index.html file if it exists
Storage should expand as needed to store however many genome assemblies you wish to work with.
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Then, run the installation script using the command below
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```
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cd FORCAST/src/installation
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./install.sh /var/www/html/FORCAST
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```
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## Installing with Docker
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If the installation process halts with a message ```Default Kerberos version 5 realm:```, press Enter
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On the host computer or server, install the [Docker Engine](https://docs.docker.com/install/) and additionally
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[Docker Compose](https://docs.docker.com/compose/install/) on Linux. Note the licensing requirements for
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Docker Desktop, though the Docker Engine and Compose for Linux remain free and open source.
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After the installation step is completed, start the mongodb server: `systemctl start mongod`
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Clone this repository. Note: an image will be provided at a later date, and cloning will not be required.
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Then, navigate to the `src/setup` folder under the root directory (e.g.`/var/www/html/FORCAST/src/setup`), and run the following command to setup Jbrowse, the BLAST database and mongodb.
Replace the default organism (*Saccharomyces_cerevisiae*) and its genome build (**R64-1-1**) with your organism and build of interest. A full list of available genomes can be found at [ftp://ftp.ensembl.org/pub/release-98/fasta](ftp://ftp.ensembl.org/pub/release-98/fasta/).
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Navigate to the cloned repository folder, build the Docker image, and start the service container.
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Now, run the script to grant apache the correct file permissions.
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```
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cd /var/www/html/FORCAST/src/installation
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./setPermissions.sh
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```bash
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docker-compose up
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```
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Next, the apache server needs to be configured to make the tool web accessible.
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FORCAST should now be available on `localhost:80`, or port 80 of the hosting machine.
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Open the file ```/etc/apache2/sites-available/000-default.conf```, and modify the DocumentRoot to the location where FORCAST was installed, and add this section below:
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```
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DocumentRoot /var/www/html/FORCAST
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<Directory '/var/www/html/FORCAST'>
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Options +ExecCGI
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AddHandler cgi-script .py
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Allow from all
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</Directory>
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```
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Genomes are downloaded from Ensembl. For a full list from the current release, see [Ensembl](https://ftp.ensembl.org/pub/current_fasta/).
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Not all of these have been tested with FORCAST. Please keep in mind the Ensembl release version
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(106, as of writing), the species of organism, and the assembly name for the following step to
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download the assembly and install for FORCAST. This performs all steps necessary to index the
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assemblies and load tracks into JBrowse. Depending on the size of the genome, this could take
FORCAST should now be accessible from your browser at ```http://<your servers address>```. For example if your VM's IP address is ```172.20.20.20```, you can type : ```http://172.20.20.20``` in your browser to access FORCAST.
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**Tested examples**
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To enable In Silico PCR tool [Dicey](https://github.com/gear-genomics/dicey) (a.k.a. [Silica](https://www.gear-genomics.com/silica/)), run the ```enable_dicey.sh``` script. Again provide your organism of interest and genome assembly in place of *Saccharomyces_cerevisiae* and R64-1-1:
Which will fetch and name the index files if they're available.
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If you want your installation of FORCAST to be secured by https, please refer to apache2's documentation on how to enable https module.
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_Drosophila melanogaster_ is known to not install properly due to using a different naming scheme.
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## Customization
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@@ -154,7 +104,7 @@ After modifying the `rgens.json` file, you can run the `load_RGENs.py` script in
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## Migration
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If using a previous version of FORCAST, existing Primers and Guides can be migrated to the new version by performing the following steps:
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1) Navigate to the _existing_ FORCAST installation and make copies of the collections to migrate. Replace mm10 with your genome version, if it is different, and define a directory where the database files should be output.
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1) Navigate to the _existing_ FORCAST installation and make copies of the collections to migrate. Replace mm10 with your genome version, if it is different, and define a directory where the database files should be output.
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