Environment setup for REST Web Services - Job Dispatcher Sequence Analysis Tools - EMBL-EBI Skip to content Skip to breadcrumbs Skip to header menu Skip to action menu Skip to quick search Linked Applications Loading… EMBL-EBI Spaces Hit enter to search Help Online Help Keyboard Shortcuts Feed Builder What’s new Available Gadgets About Confluence Log in Job Dispatcher Sequence Analysis Tools Pages Blog Space shortcuts Your Privacy, Help & Support Page tree Browse pagesConfigureSpace tools Attachments (0) Page History Page Information Resolved comments View in Hierarchy View Source Export to PDF Export to Word Pages … Job Dispatcher Sequence Analysis Tools Home FAQ - Frequently Asked Questions Programmatic Access FAQ Skip to end of banner Jira links Go to start of banner Environment setup for REST Web Services Skip to end of metadata Created by Nandana Madhusoodanan, last modified by Fabio Madeira on Feb 28, 2020 Go to start of metadata Install web service Clients Clone the webservice-client repository (https://github.com/ebi-wp/webservice-clients) git clone https://github.com/ebi-wp/webservice-clients.git
cd webservice-clients Install Perl Windows Windows does not have Perl installed by default, so download and install Perl https://www.perl.org/get.html#win32 UNIX/LINUX Perl comes as default in Unix/Linux machines, type perl –v on command line to find which version is installed. If not installed, follow the instructions below : wget http://www.cpan.org/src//perl-.tar.gz
tar -xzf perl-.tar.gz
cd perl- To install Perl in a custom location, use prefix option as given below: ./Configure -des -Dprefix=$HOME/localperl
make
make test
make install MacOS Mac OS X already has Perl installed. Open a Terminal application and run perl -v to find out which version. If not installed by default, download from the below url : https://www.perl.org/get.html#osx Docker Ensure that docker installed properly, if not download and install https://www.docker.com/get-docker Once installed, go to terminal/command prompt and run docker run -it perl bash This will pull latest perl image from the docker hub, run the container and enter bash terminal interactively. Install Python Windows Windows does not have Python installed by default. So download and install Python https://www.python.org/downloads/windows/ Linux/Unix Python comes as default in Unix/Linux machines, type python -–version on command line to find which version. If not installed/get updated to newest version, follow the instructions below to get installed: Easiest way to install: sudo apt-get update
sudo apt-get install python Install from source : sudo apt-get update
sudo apt-get install build-essential
wget https://www.python.org/ftp/python//Python-.tar.xz
tar xf Python-.tar.xz
cd Python-
./configure --enable-optimizations
make -j 8
sudo make altinstall (altinstall will ensure that you don’t mess with the default system Python)
Invoke the new Python interpreter with:
python MacOS Mac OS X already has Python installed. Open a Terminal application and run python --version to find out which version. If not install by default, follow the instructions to get Python installed. https://www.python.org/downloads/mac-osx/ Docker Ensure that docker is installed in your machine, if not download and install https://www.docker.com/get-docker Once installed, get the required python image tag for the docker from the below url: https://hub.docker.com/_/python For Example, If the image tag is python:3.6-slim, docker run -it python:3.6-slim bash Install OpenJDK Java In order to run Java clients, Java (tested version 1.8.0.131_2") as well as ant (tested version 1.10.5), needs to installed. Note: Java 9 and above are currently not supported. Follow the below instructions to download and install OpenJDK Note: Supported versions- 1.8 https://openjdk.java.net/install/ Windows Download and install Java from the below url: https://openjdk.java.net/install/ Also make sure JAVA_HOME and PATH are properly set. Unix/Linux Download java from the below url: https://openjdk.java.net/install/ Installation instructions can be accessed via the below link: https://openjdk.java.net/install/ Mac Download and install java from the below url : https://openjdk.java.net/install/ Follow the installation instructions available at https://openjdk.java.net/install/ Docker Ensure that docker installed in your machine, if not download and install https://www.docker.com/get-docker Once installed, get the required python image tag for the docker from the below url: https://hub.docker.com/_/openjdk Install Dependencies Install dependencies associated with the client. This can be found in the service documentation page of each tool. e.g. WSDbfetch (Webform + REST) For Perl clients, Install the dependencies as given below: Perl For Perl clients, install dependencies as given below: sudo apt-get install build-essential
sudo apt install imagemagick
sudo apt install cpan
# then install dependencies
sudo cpan install LWP
sudo cpan install XML::Simple
sudo cpan install YAML::Syck
sudo cpan install JSON::XS
sudo cpan LWP::Protocol::https You might need to install additional operative system dependencies: sudo apt-get install libnet-ssleay-perl libio-socket-ssl-perl Python For Python clients, install dependencies as given below: pip install xmltramp2 requests If pip is not installed, follow the below commands(unix/linux): curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
python get-pip.py No labels Overview Content Tools Activity Powered by Atlassian Confluence 7.13.7 Printed by Atlassian Confluence 7.13.7 Report a bug Atlassian News Atlassian {"serverDuration": 87, "requestCorrelationId": "dc719b979da016c5"}
