sjackman
commented
8 years ago @acabunoc Hi, Abigail. I'm available electronically both days 9–5 to answer questions. I'll be available in person in Vancouver Thu 9–12 and Fri 9–5.
Open abbycabs opened 8 years ago
sjackman
commented
8 years ago @acabunoc Hi, Abigail. I'm available electronically both days 9–5 to answer questions. I'll be available in person in Vancouver Thu 9–12 and Fri 9–5.
eronisko
commented
8 years ago Hi @sjackman, is this sprint project about working through the issues in the repo or do you have any other plans?
sjackman
commented
8 years ago Hi, Ernest. I'd like to build precompiled binary bottles of bioinformatics formula for Linuxbrew. My field is bioinformatics, but someone else could tackle the same project for their area of interest. Outside of this bottling effort, tackling the existing backlog of issues would be great. Last year I helped people create formulas for software they use that did not yet have a formula. I'd be happy to do that again.
sjackman
commented
8 years ago
[ Project Lead ] @sjackman [ GitHub Repo ] https://github.com/Linuxbrew/homebrew-science [ Track ] Tools: you are building a tool others can help you build [ Level ] Intermediate [ Timezone ] PDT
Description
Installing software is at best a tedious experience, and is often a distressing experience. Each operating system (OS) provides its own package manager to install software and manage dependencies: for example, apt-get and yum for the various distributions of Linux, and Homebrew is popular for Mac OS. Using the package manager provided by the system is not however without its own set of challenges. The system's package manager may require administrator access to the machine, which is typically not available on high performance computing clusters. It installs versions of software from the era of the OS, and clusters are notorious for running ancient distributions of Linux. Current bioinformatics software is often not yet packaged and provided only as source. Compiling software from source can vary from difficult to impossible, for example when the compiler and libraries provided by the operating system are a decade old. Manually navigating the recursive dependency chain of the tool and its dependencies, and their dependencies, can feel like a labyrinth with no end, and can even result in conflicting dependencies that are mutually exclusive and impossible to satisfy.
Linuxbrew is a package manager for Linux derived from Homebrew, the Mac OS package manager. It is a cross-platform utility, compatible with any distribution of Linux and version of Mac OS released in the last decade, allowing you to use the same package manager on both your Linux server and your Mac laptop. It can be installed in your home directory, and does not require administrator access. Using Linuxbrew, challenging tasks are made easy; for example installing a modern compiler in your home directory takes a few minutes, even on an ancient distribution of Linux.
Homebrew-Science is a collection of scientific software packages installable by either Linuxbrew or Homebrew. With nearly 600 software packages available, over 200 of those are bioinformatics tools. Software packages are maintained up-to-date by a fervent community of over 400 contributors.
Linuxbrew eliminates the hassle of installing software, and enables reproducible science by facilitating reproducible installations of the software used for an analysis.
Want to Contribute?
Join us at the Global Sprint June 2-3. Leave a comment in this issue to let the project lead know you're interested in contributing during #mozsprint 2016!
Note to the Project Lead
Congrats, @sjackman! This is your official project listing for the Mozilla Science Global Sprint 2016. To confirm your submission, please complete the following:
Do you want to become a featured project? :tada:
Here are some exercises that will help your project be more inviting to new contributors. We hope you'll try to complete some of these as you prepare for #mozsprint.
If you complete all the exercises, your project will be eligible to be featured in our collection of open source science projects! Once you've finished this list, contact @acabunoc to submit your project for review.