Installation from the Docker repository

We recommend to use our Docker repository to avoid conflicts.

Install Docker program

The getting started guide on Docker has detailed instructions for setting up Docker on Mac, Linux and Windows.

Running APPRIS-Docker container

You are going to run an APPRIS container (with an Ubuntun linux) on your system and get a taste of the docker run command.

To get started, let's run the following in our terminal:

$ docker pull appris/core

The pull command fetches the appris image from the Docker registry and saves it in our system. You can use the docker images command to see a list of all images on your system.

$ docker images
REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
appris/core       latest              84a2cef92a68        45 minutes ago      3.224 GB
appris/core       2017_08.v24         12c4188c29c7        50 minutes ago      3.224 GB

Great! Let's now run a APPRIS-Docker container based on this image. To do that you are going to use the docker run command.

Create a working directory

Create a working directory where the input file for APPRIS, and the results from APPRIS will be locate (with read/write permissions)

$ mkdir ${working_dir} && chmod -R og+w ${working_dir}

Download databases for APPRIS code

Download the database files that the code needs into the working directory

WARNING: The database file is quite big (around 35Gb). Take care!

$ cd ${working_dir} && \
  wget http://apprisws.bioinfo.cnio.es/archives/db/appris_db_archives.${appris_version}.tar.gz && \
  tar -xf appris_db_archives.${appris_version}.tar.gz

In windows, the symbolic links don't work. For that reason, you have to change them:

Delete the symbolic links:

$ cd db
$ rm firestar
$ rm pdb_{version}

Rename the files

$ mv firestar_{version} firestar
$ mv pdb_{version}.emptySeqs.fa pdb_{version}

WARNING: Docker in Windows is limited to c:\Users folder. If you want to create a volume using a directory outside of c:\Users try this (ref):

In windows 7, I used docker toolbox. It used Virtual Box. 1. Open virtual box 2. Select the machine (in my case default). 3. Right clicked and select settings option 4. Go to Shared Folders 5. Include a new machine folder. For example, in my case I have included: Name: e:{working_dir} Path: e/{working_dir} 6. Click and close 7. Open "Docker Quickstart Terminal" and restart the docker machine. Use this command: $ docker-machine restart ... $ docker-machine env

Create/Download the features input files

Create (or download) the input data files.

Note: For more information, read the FEATURES readme file

Running APPRIS-Docker container

The next step is to run the appris/core image mounting the database directory and the working directory

$ docker run -itd \
    -v ${database_dir}:/opt/appris/db \
    -v ${working_dir}:/home/appris/ws \
    appris/code

Now, we run APPRIS commands in a running container with appris user.

$ docker exec --user appris -it {CONTAINER_ID} \
    bash -c "source /opt/appris/conf/apprisrc.docker && \
            appris_run_appris \
                -c /home/appris/ws/test.ws.env \
                -m firestar,matador3d,matador3d2,spade,corsair,thump,crash,proteo,appris \
                -l info"

Note: For more detail, read the related section in the DOCKER readme file

Installation from Scratch

Requirements

Ubuntu Linux x86_64 machine
Softwares:
```
 - gawk
 - git
 - npm
 - nodejs
```

Perl requirements (recommendation, use [CPAN] (https://www.perl.org/cpan.html)):

 - FindBin
 - Getopt::Long
 - Config::IniFiles
 - Bio::SeqIO
 - Bio::SearchIO
 - File::Temp
 - File::Basename
 - Data::Dumper
 - JSON
 - DBI
 - DBD::mysql
 - POSIX
 - IO::String
 - Statistics::Descriptive
 - Moose
 - Class::Load
 - Data::OptList
 - Module::Implementation
 - Class::Load::XS
 - MRO::Compat
 - Data::Printer
 - IPC::Run
 - CGI
 - HTTP::Status
 - Email::Valid
 - MIME::Lite
 - Parse::RecDescent
 - XML::DOM

Note: See the lib/appris_perllib/Makefile.PL file

[MySQL Client] (http://dev.mysql.com/doc/refman/5.7/en/linux-installation.html)
[BioPerl] (http://bioperl.org/) (at least, 1.2.3)
[Ensembl API] (http://www.ensembl.org/info/docs/api/api_installation.html)

Installation

Steps you have to do to acquire APPRIS system

Clone APPRIS code:

git clone https://github.com/appris/appris.git

Setting up the environment variables:
1. Add in your bash profile the following lines:
```
export APPRIS_HOME="APPRIS HOME"
source ${APPRIS_HOME}/conf/apprisrc
source ${APPRIS_HOME}/conf/apprisrc.WS
```
2. Setting up the environment variables for each execution in the sample configuration file "${APPRIS_HOME}/conf/scripts/apprisrc.*"

Download databases for APPRIS code:

wget http://apprisws.bioinfo.cnio.es/archives/db/appris_db_archives.${appris_version}.tar.gz && \
tar -xf appris_db_archives.${appris_version}.tar.gz

wget
cd ${APPRIS_HOME}
tar -xf appris_local_db.${date_version}.tar.gz

Setting up 'firestar' method:

Create FireDB database:

mysql> create user 'firedb'@'localhost';
mysql> grant all on FireDB.* to 'firedb'@'localhost';
mysql> create database FireDB;

Import FireDB database:

mysql FireDB -h localhost -u firedb < ${APPRIS_HOME}/db/FireDB_*.sql

Setting up the environment variables in the file "${APPRIS_HOME}/conf/code/firestar.ini":
1. Include database variables:
```
database: FireDB
user: firedb
pwd:
```
2. Change the env vars:
```
[PATHS]
	home
	DB
	tmp
	AFM
[CLUSTER_PATHS]
	home
	root
	dir
	DB
```

Take into account the temporal files coming for "${APPRIS_HOME}/code/opt" programs SignalP and TargetP (DEPRECATED):
```
cd signalp-3.0/tmp and targetp-1.1/tmp
chmod -R +t tmp
chmod -R 777 tmp
```
Setting up the variables for Ensembl database in the "${APPRIS_HOME}/conf/code/ensembldb.ini" (DEPRECATED):
```
ENSEMBL_CORE_REGISTRY, ENSEMBL_COMPARA_REGISTRY
```

Build the images of APPRIS

Build the image of APPRIS/core

Now that you have your Dockerfile, you can build your image. The docker build command does the heavy-lifting of creating a docker image from a Dockerfile.

$ docker build -t appris/core -f build/appris_core.dockerfile .

The following files are required:

build/appris_core.dockerfile
build/setup.sh
build/entrypoint.sh
build/FireDB_{data_version}.sql.gz

Build the image of APPRIS/server

Now that you have your Dockerfile, you can build your image. The docker build command does the heavy-lifting of creating a docker image from a Dockerfile.

$ docker build -t appris/server -f build/appris_server.dockerfile .

Download data files for APPRIS server that server needs into the {data_directory}

We have to ways to obtain the data files:

Download the data files from external repository

$ wget http://apprisws.bioinfo.cnio.es/archives/data/appris_data_archives.${appris_version}.tar.gz && \
  tar -xf appris_data_archives.${appris_version}.tar.gz

WARNING: The data file is quite big (around 7Gb). Take care!

Where appristools saves the annotations

Import databases of APPRIS annotations

Run the appris/server image mounting the data directory

$ docker run -itd \
    -v ${data_dir}:/opt/appris/data \
    appris/server

Eg.
$ docker run -itd \
    -v /home/{user}/projects/APPRIS/data/2017_08.v24:/opt/appris/data \
    appris/server

Import the databases files within the Docker image

WARNING: You will need around 50Gb in the system to import database files. Think on that!

2.1 Run a *_bash_* in the running *__appris/server__* container
```
$ docker exec --user appris -it {CONTAINER_ID} bash
```

2.1 Import databases
```
$ docker exec --user appris -it {CONTAINER_ID} \
    bash -c "source /opt/appris/conf/apprisrc.docker && \
            perl /opt/appris/docker/scripts/import_appris_dbs.pl \
                -c /opt/appris/conf/config_{appris_version}.json \
                -d /opt/appris/data \
                -l info"
```
```
Eg.
$ docker exec --user appris -it {CONTAINER_ID} \
    bash -c "source /opt/appris/conf/apprisrc.docker && \
        perl /opt/appris/docker/scripts/import_appris_dbs.pl \
            -c /opt/appris/conf/config_2017_08.v24.reduced.json \
            -d /opt/appris/data \
            -l info"
```

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

INSTALL.md

INSTALL.md

Installation from the Docker repository

Install Docker program

Running APPRIS-Docker container

Create a working directory

Download databases for APPRIS code

Create/Download the features input files

Running APPRIS-Docker container

Installation from Scratch

Requirements

Installation

Build the images of APPRIS

Build the image of APPRIS/core

Build the image of APPRIS/server

Download data files for APPRIS server that server needs into the {data_directory}

Import databases of APPRIS annotations

Files

INSTALL.md

Latest commit

History

INSTALL.md

File metadata and controls

Installation from the Docker repository

Install Docker program

Running APPRIS-Docker container

Create a working directory

Download databases for APPRIS code

Create/Download the features input files

Running APPRIS-Docker container

Installation from Scratch

Requirements

Installation

Build the images of APPRIS

Build the image of APPRIS/core

Build the image of APPRIS/server

Download data files for APPRIS server that server needs into the {data_directory}

Import databases of APPRIS annotations