Files · 6e1b3f621dab240a5f26f649b4831310ddc9936b · eic_tools / Spack · GitLab

Snippets Groups Projects

Feature/add package for fastqc (#1573)

George Hartzell authored 8 years ago

* Add package for fastqc

This tool is a java mess.  Their Way To Do It is to just copy the entire
tree into it's final resting place, make the perl script at the top
level executable and take it from there.

Yuck.

This package assumes that `set_executable` actually sets all the user
bits.  If that change doesn't go in, then something equivalent needs to
be done.

* Use chmod to make fastqc executable

I haven't gotten any feedback on changing set-executable, so switch to
using chmod (from the cuda package).

* Flake8 cleanup

* Install files neatly, don't just copy top level of dir

Rather than blindly copying everything in the distribution, carefully
put the necessary bits into reasonable places.  Neatness counts, etc...

This requires patching the `fastqc` perl script, so this commit adds a
patch file.

* Additional pep8 cleanup

* Let dependency handle adding jdk to PATH

* Flake8 cleanup

* Ensure that java is on PATH

I thought that the run dependency on the jdk would put
java on my PATH, but it does not appear to work.

For now, do it by hand.

6e1b3f62

6e1b3f62 8 years ago

Name	Last commit	Last update
bin
etc/spack/defaults
lib/spack
share/spack
var/spack
.coveragerc
.flake8
.gitignore
.mailmap
.travis.yml
LICENSE
README.md

Spack is a package management tool designed to support multiple versions and configurations of software on a wide variety of platforms and environments. It was designed for large supercomputing centers, where many users and application teams share common installations of software on clusters with exotic architectures, using libraries that do not have a standard ABI. Spack is non-destructive: installing a new version does not break existing installations, so many configurations can coexist on the same system.

Most importantly, Spack is simple. It offers a simple spec syntax so that users can specify versions and configuration options concisely. Spack is also simple for package authors: package files are written in pure Python, and specs allow package authors to write a single build script for many different builds of the same package.

See the Feature Overview for examples and highlights.

To install spack and install your first package:

$ git clone https://github.com/llnl/spack.git
$ cd spack/bin
$ ./spack install libelf

Documentation

Full documentation for Spack is the first place to look.

We've also got a Spack 101 Tutorial, so you can learn Spack yourself, or teach users at your own site.

See also:

Technical paper and slides on Spack's design and implementation.
Short presentation from the Getting Scientific Software Installed BOF session at Supercomputing 2015.

Get Involved!

Spack is an open source project. Questions, discussion, and contributions are welcome. Contributions can be anything from new packages to bugfixes, or even new core features.

Mailing list

If you are interested in contributing to spack, the first step is to join the mailing list. We're using a Google Group for this, and you can join it here:

Spack Google Group

Contributions

Contributing to Spack is relatively easy. Just send us a pull request. When you send your request, make develop the destination branch on the Spack repository.

Your PR must pass Spack's unit tests and documentation tests, and must be PEP 8 compliant. We enforce these guidelines with Travis CI. To run these tests locally, and for helpful tips on git, see our Contribution Guide.

Spack uses a rough approximation of the Git Flow branching model. The develop branch contains the latest contributions, and master is always tagged and points to the latest stable release.

Authors

Many thanks go to Spack's contributors.

Spack was originally written by Todd Gamblin, tgamblin@llnl.gov.

Citing Spack

If you are referencing Spack in a publication, please cite the following paper:

Todd Gamblin, Matthew P. LeGendre, Michael R. Collette, Gregory L. Lee, Adam Moody, Bronis R. de Supinski, and W. Scott Futral. The Spack Package Manager: Bringing Order to HPC Software Chaos. In Supercomputing 2015 (SC’15), Austin, Texas, November 15-20 2015. LLNL-CONF-669890.

Release

Spack is released under an LGPL license. For more details see the LICENSE file.

LLNL-CODE-647188