Skip to main content

How to install myChEMBL using two Vagrant commands

 

 

 

TL;DR

  1. install Vagrant and VirtualBox
  2. run vagrant init chembl/myChEMBL && vagrant up
  3. wait a bit...
  4. go to http://127.0.0.1:8000/
  5. enjoy!

What have I just done?


Vagrant is a tool for building and deploying complete development environments and myChEMBL 18 now supports installation via Vagrant. We achieved this by first creating a myChEMBL Vagrant Box, which we then register on the Vagrant Cloud. This then allows users to install myChEMBL on there local system using two simple commands*:

vagrant init chembl/myChEMBL
vagrant up


*assumes you have vagrant installed

It's that simple! After you type this into your system console, the expected output should be similar to the one below:




What are those two commands doing?


The first command initializes the current directory to be a Vagrant environment by creating an initial Vagrantfile and prepopulates the config.vm.box setting in the created Vagrantfile. This happens immediately. This command should be executed only once.

The second one, when executed for the first time, downloads myChEMBL box file from the public repository, unpacks it and store downloaded files into a dedicated directory on your machine, so you won't have to download it again. Then, it configures myChEMBL virtual machines and runs it using VirtualBox. The box file is big (7GB) so it will take some time to download and uncompress, but this will happen only once.

OK, so I've executed them successfully, now what?


Just open your favorite browser and type this URL: http://127.0.0.1:8000/. You should see the my ChEMBL LaunchPad (We have seen apache take a little while to fire up, so if you do not see LaunchPad straight away give a couple more minutes).

Can I ssh into the machine?

 

Yes, just type:

vagrant ssh

and you are there. You are logged in as a special 'vagrant' user with root privileges and no password. If you prefer to work as a standard 'chembl' user just type:

sudo su - chembl

Great, now how can I switch the machine off?


Do it by typing:

vagrant halt

You can bring it up anytime using already known command:

vagrant up

which should execute very fast for the second time as everything is already downloaded.

Are there any software dependencies?


Yes, but not many. In order to use Vagrant you should install it. Our configuration currently supports only VirtualBox as a provider so you should install it as well.

What advantages does the myChEMBL Vagrant install offer over the standard myChEMBL installation?

  1. First of all, you don't have to remember the download URL of where the myChEMBL Vagrant box lives. All you need to know is a box name: 'chembl/myChEMBL'.   
  2. You don't have to think about any configuring VirtualBox image (e.g. network settings), as all of the configuration is stored in a Vagranfile prepared by us.
  3. Using command line interface it is easy to deploy myChEMBL on multiple machines automatically. You can run it easily on your headless server.
  4. The download is smaller, so it will download faster. The box file size is 7.1GB compared to 8.5 GB of standard myChEMBL-18_0-disk1.vmdk file.
If future, we plan to support more providers, in particular Amazon Web Services and Docker.
We also plan to make provisioning more flexible so if needed you will be able to choose what Linux distribution should be used as a base for your myChEMBL (Red Hat and CentOS are the most important distros we would like to support).

Bugs and help


We've found a couple of minor bugs since the release of myChEMBL 18. They are all fixed now and mychembl vagrant box includes all the fixes. If you happen to find any other issue, related to myChEMBL or specific to our vagrant distribution, please report it to mychembl[at]ebi.ac.uk.

You can always check for new updates using following command:

vagrant box outdated

In case new updated are available you can update the box by running:

vagrant box update

Just please remember that updating the box means downloading it from remote repository so it will take some time. Also note that this command will not magically update running Vagrant environments. If a Vagrant environment is already running, you'll have to destroy and recreate it to acquire the new updates in the box.

In our next myChEMBL related blog post we will tell you how to install myChEMBL on local VM or 'metal' machine running Ubuntu (Hint: have a look at this file).

Comments

Popular posts from this blog

A python client for accessing ChEMBL web services

Motivation The CheMBL Web Services provide simple reliable programmatic access to the data stored in ChEMBL database. RESTful API approaches are quite easy to master in most languages but still require writing a few lines of code. Additionally, it can be a challenging task to write a nontrivial application using REST without any examples. These factors were the motivation for us to write a small client library for accessing web services from Python. Why Python? We choose this language because Python has become extremely popular (and still growing in use) in scientific applications; there are several Open Source chemical toolkits available in this language, and so the wealth of ChEMBL resources and functionality of those toolkits can be easily combined. Moreover, Python is a very web-friendly language and we wanted to show how easy complex resource acquisition can be expressed in Python. Reinventing the wheel? There are already some libraries providing access to ChEMBL d

ChEMBL 29 Released

  We are pleased to announce the release of ChEMBL 29. This version of the database, prepared on 01/07/2021 contains: 2,703,543 compound records 2,105,464 compounds (of which 2,084,724 have mol files) 18,635,916 activities 1,383,553 assays 14,554 targets 81,544 documents Data can be downloaded from the ChEMBL FTP site:   https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_29 .  Please see ChEMBL_29 release notes for full details of all changes in this release: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_29/chembl_29_release_notes.txt New Deposited Datasets EUbOPEN Chemogenomic Library (src_id = 55, ChEMBL Document IDs CHEMBL4649982-CHEMBL4649998): The EUbOPEN consortium is an Innovative Medicines Initiative (IMI) funded project to enable and unlock biology in the open. The aims of the project are to assemble an open access chemogenomic library comprising about 5,000 well annotated compounds covering roughly 1,000 different proteins, to synthesiz

Identifying relevant compounds in patents

  As you may know, patents can be inherently noisy documents which can make it challenging to extract drug discovery information from them, such as the key targets or compounds being claimed. There are many reasons for this, ranging from deliberate obfuscation through to the long and detailed nature of the documents. For example, a typical small molecule patent may contain extensive background information relating to the target biology and disease area, chemical synthesis information, biological assay protocols and pharmacological measurements (which may refer to endogenous substances, existing therapies, reaction intermediates, reagents and reference compounds), in addition to description of the claimed compounds themselves.  The SureChEMBL system extracts this chemical information from patent documents through recognition of chemical names, conversion of images and extraction of attached files, and allows patents to be searched for chemical structures of interest. However, the curren

Julia meets RDKit

Julia is a young programming language that is getting some traction in the scientific community. It is a dynamically typed, memory safe and high performance JIT compiled language that was designed to replace languages such as Matlab, R and Python. We've been keeping an an eye on it for a while but we were missing something... yes, RDKit! Fortunately, Greg very recently added the MinimalLib CFFI interface to the RDKit repertoire. This is nothing else than a C API that makes it very easy to call RDKit from almost any programming language. More information about the MinimalLib is available directly from the source . The existence of this MinimalLib CFFI interface meant that we no longer had an excuse to not give it a go! First, we added a BinaryBuilder recipe for building RDKit's MinimalLib into Julia's Yggdrasil repository (thanks Mosè for reviewing!). The recipe builds and automatically uploads the library to Julia's general package registry. The build currently targe

New Drug Warnings Browser

As mentioned in the announcement post of  ChEMBL 29 , a new Drug Warnings Browser has been created. This is an updated version of the entity browsers in ChEMBL ( Compounds , Targets , Activities , etc). It contains new features that will be tried out with the Drug Warnings and will be applied to the other entities gradually. The new features of the Drug Warnings Browser are described below. More visible buttons to link to other entities This functionality is already available in the old entity browsers, but the button to use it is not easily recognised. In the new version, the buttons are more visible. By using those buttons, users can see the related activities, compounds, drugs, mechanisms of action and drug indications to the drug warnings selected. The page will take users to the corresponding entity browser with the items related to the ones selected, or to all the items in the dataset if the user didn’t select any. Additionally, the process of creating the join query is no