Development Container

Overview

In the BV-BRC project we employ an opinionated build system that is centered around what we call a "dev container", short for development container. This is not a container in the sense of a Docker or Singularity container (we started using the terminology before this technology was commonplace); rather it is a container directory for code and other resources that are components of a larger build.

The build system uses the dev container as a wrapper around a set of modules; typically each of these modules is maintained as a github repository. The dev container provides an overall Makefile and set of inclusions for the module Makefiles to support both of the following:

• Development builds such that when the dev container user environment shell include file (user-env.sh) is sourced by the developer, all executable scripts are included in the user's path and do not need to be invoked with either the language interpreter (e.g. python or perl) and do not have to have a full path specified. When changes are made to either scripts or included libraries no rerun of the build process is required to see the changes take effect. Of course if there are modules that use compiled languages such as C++ or Java, a build step is required.
• Production deployments where all required assets are copied to a production deployment directory and are executable without access to the original source directory.

This infrastructure enables the entire application development process to be performed on the developer's own environment with a solid expectation that when the code is deployed in a production environment no issues will arise in the transition from development to production.

The dev container model assumes that there is a runtime directory available that includes all the third-party software and language interpreters that are required for the development work. On a Linux development machine with a full installation of software installed it may be possible to use the /usr directory on Linux as a runtime. However, it is likely that the required language interpreters and the corresponding libraries are not available there. For work on the BV-BRC system we typically use a runtime environment that is built from source, using a runtime build system found at https://github.com/BV-BRC/runtime_build.

Inside the dev container is a directory called modules. This directory will hold the modules that are to be included in the container build.

There is a set of standard modules that are required for each standard BV-BRC build. They include the following:

Module	Purpose
p3_auth	User authentication support
app_service	Utilities related to application submission
p3_cli	BV-BRC command line scripts
p3_core	Key common core BV-BRC code modules
sra_import	Code for SRA import utilities
p3_deployment	BV-BRC deployment support routines
typecomp	BV-BRC RPC type compiler
Workspace	BV-BRC Workspace code support
seed_gjo	Bioinformatics utilities from the SEED project
seed_core	Bioinformatics utilities from the SEED project

The Github repository paths for these modules may be found in the file core-modules.

Configuring a Development Container

The workflow for setting up a dev container for the purpose of working on BV-BRC code development is as follows:

• Clone the dev_container repository. It isn't necessary to fork the module for this work; since the dev_container repository contains the build boilerplate you won't need to make any changes to that need to persist.
• Determine the set of modules needed to clone into the dev_container. The core-modules file discussed above is a good starting pont.
• Clone each of those modules into the modules directory
• In the root of the dev_container directory, run the bootstrap script to link the configuration of the dev container to the runtime and set up configuration files
• Source the user-env.sh script to initialize the user environment to use this dev container.
• Run make to perform the initial build.

Setup Examples

We will work through several examples of configuring a development container.

Linux, with a runtime in the shared filesystem

In the BV-BRC project development environment, we maintain a build of the BV-BRC standard runtime in a shared NFS volume called /vol/patric3/cli/ubuntu-runtime. We'll set a shell variable to store that value so that if you are working through this example on your own system you can just redefine that variable to the correct value for your environment

RT=/vol/patric3/cli/ubuntu-runtime

Now we can check out the dev container and the standard set of modules:

$ mkdir brc-work
$ cd brc-work
$ git clone https://github.com/BV-BRC/dev_container
Cloning into 'dev_container'...
remote: Enumerating objects: 1339, done.
remote: Counting objects: 100% (222/222), done.
remote: Compressing objects: 100% (81/81), done.
remote: Total 1339 (delta 146), reused 198 (delta 141), pack-reused 1117
Receiving objects: 100% (1339/1339), 175.69 KiB | 2.31 MiB/s, done.
Resolving deltas: 100% (818/818), done.
$ cd dev_container/
$ ./checkout-bvbrc-modules

The checkout-bvbrc-modules script simply clones each of the modules in the core-modules file into the modules subdirectory of the dev container:

$ ls modules
app_service  p3_auth  p3_cli  p3_core  p3_deployment  README  sra_import  typecomp

Now we may do the bootstrap and build:

$ ./bootstrap $RT
$ source user-env.sh
$ make
if [ ! -d bin ] ; then mkdir bin ; fi
if [ ! -d cgi-bin ] ; then mkdir cgi-bin ; fi
[[ much more output]]

With the build complete, we can run standard BV-BRC programs:

$ p3-login olson
Password: *********
Logged in with username [email protected]
$ p3-ls /[email protected]/home
[[ my home directory]]
$ p3-echo 83332.12 | p3-get-genome-data --attr genome_name
id	genome.genome_name
83332.12	Mycobacterium tuberculosis H37Rv

At this point you can check out the set of modules you need to work on for your development work. For example, if you wish to work on the fastq utilities module you would run the following:

pushd modules
git clone https://github.com/BV-BRC/p3_fqutils
popd

If you add new modules to the modules directory, you will need to rerun the bootstrap to inform the dev container that its configuration changed and then reload the user-env.sh so your shell environment contains the corresponding changes. It is also best to clear out the contents of the toplevel bin directory so that any changes to the environment are propagated there.

$ ./bootstrap
$ rm bin/*
$ source user-env.sh
$ make
[output]

Linux, using a BV-BRC Singularity container

The standard BV-BRC deployment utilizes a Singularity container that holds a standard BV-BRC runtime. We can utilize this to create a dev container environment. It is essentially the same process as above, only we need to bind our work directory into the Singularity container when we start it up.

This example will use a one-liner to find the latest development version of the BV-BRC Singularity container inside the BV-BRC development system environment.

$ LATEST_SIF="$(ls -t /vol/patric3/production/containers/bvbrc-dev-*.sif | head -n 1)"
$ echo $LATEST_SIF
/vol/patric3/production/containers/bvbrc-dev-389.sif
$ singularity shell --bind `pwd` $LATEST_SIF
Singularity> git clone https://github.com/BV-BRC/dev_container
[clone output]
Singularity> cd dev_container/
Singularity> ./checkout-bvbrc-modules
[clone output]
Singularity> RT=/opt/patric-common/runtime
Singularity> ./bootstrap $RT
Singularity> source user-env.sh
Singularity> make

At this point you can use this configuration as in the prior section.

MacOS, using the BV-BRC Command Line Interface release

The BV-BRC project makes available MacOS builds of the BV-BRC toolkit, including a runtime. For development where the tools included in that release are sufficient (due to space considerations, there is not a complete set of the third-party bioinformatics tools included in the MacOS release) this is a good option for local development.

To start with this, install the command-line interface package using the instructions found at the BV-BRC Command Line Interface github repository.

All that is required to use this version is to run the bootstrap script with the appropriate runtime.

RT=/Applications/BV-BRC.app/runtime

The rest of the linux instructions will work as described above.

Usage

1. Shell into a container with a recent development image.

   LATEST_SIF="$(ls -t /vol/patric3/production/containers/bvbrc-dev-*.sif | head -n 1)"
   echo shelling into $LATEST_SIF
   singularity shell --bind /disks/tmp:/tmp,/vol,/home,/homes $LATEST_SIF

2. Clone this repository onto your development host.

   git clone https://github.com/BV-BRC/dev_container
   cd dev_container

3. Clone "module repositories" into the modules directory. If you have a common set of modules you often need, you can create a script to clone all of those first, like checkout-p3-modules. You could add an additional helper script like that to include any modules you need for current development. Otherwise just manually clone the addition(s). E.g.:

    ./checkout-p3-modules
    # Manual clone
    pushd modules
    git clone [email protected]:PATRIC3/p3_fqutils.git
    popd

4. Run the bootstrap script with the path to a "runtime directory" as the first argument. Here we will use the one provisioned inside the sif image. The following DEPLOY_RUNTIME variable also appears to be relevant for the deployment targets in the Makefile. E.g.:

    export DEPLOY_RUNTIME="/opt/patric-common/runtime"
    KB_IGNORE_MISSING_DEPENDENCIES=1 ./bootstrap $DEPLOY_RUNTIME

5. Source the user-env.sh script in the "development directory". This file is created during the bootstrap script step.

source user-env.sh

6. Build the modules. The current Makefile default target (all) runs the build_modules target.

   # if these steps were run before, start with an empty bin dir
   rm /bin/*
   make
   # same as . . .
   # make build_modules

7. Optional: Deploy. The "deployment directory" needs to be a directory where you have permissions to write. By default, this is a directory called /kb/deployment. If you have sufficient permissions to create this directory, then you may skip this step. To override that default set in the Makefile, you can set your own TARGET. E.g.:

   export TARGET="deployment"

   . . . with the path to where you would like to deploy.

If no modules have been cloned into the modules sub directory, this will create directories and files in the deployment directory for every module. It might be best to skip this step right now, as the current Makefile appears to not work.

    make deploy

8. Develop and test (a) module(s). Repeat steps 4 - 6. (7?) as necessary.
   • Any new scripts in any module script directories will require a make run for/in that module. This would always be the case when a new module is added.
   • Re-run the bootstrap and user-env.* sourcing when adding modules to modules.
   • Note: Run any module scripts using their generated wrapper, which should be in the executable PATH. E.g. run-me.pl should be run with run-me. This will test the intended call stack, as well as testing this make machinery. Apparently this is required, as well: export KB_INTERACTIVE=1

Definitions

• runtime directory: This is a directory that contains "bin", "lib", "man", "etc" subdirectories containing third*party software that BV-BRC repositories depend upon (default: /kb/runtime). E.g. a perl binary and Perl modules. See the bootstrap repository for what normally goes here.

• deployment directory: This is the directory that contains "bin", "lib", "man", "etc" subdirectories for BV-BRC developed code.

• development directory: This is the directory where new code is written and developed. It is customary for modules to be cloned from the git repository into the modules directory of the development directory. As code is modified, it is pushed back to the git repository.