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Add Blast+ package. (#3562)

George Hartzell authored 8 years ago

* Add Blast+ package.

Adds support for NCBI's blast+@2.6.0.  I'll be adding a few historical versions in the near future.

It's a fairly direct transliteration of the [Homebrew Science recipe][hbs].

I skipped the mysql support.

There is a problem with HDF5 support.  Blast's configure script test program defines a macro 'HOST' to a string value and one of the HDF5 bits has an variable named 'HOST'.  Fun things happen.   I've disabled support for now.

I've run very very basic tests.  I'll get this out to my users and ensure that it works and fine tune the options and etc....

[hbs]: https://github.com/Homebrew/homebrew-science/blob/master/blast.rb

* Flake8 fixes

* Update w.t.r. mamelara's PR and cleanup

Add paths to things in the --with-* config args

Add add'l config flags from #3394.

Update patch to no-op and add comment.

Add add'l dependencies after studying `configure --help`.

* Flake8 cleanup

* Add support for blast+@2.2.30

Need to work around a configure bug.  See https://github.com/Homebrew/homebrew-science/issues/2337#issuecomment-170011511.

* Re-wrap comment, line length not a problem.

I'd broken a comment across to line in a fit of flake8
induced fear.  Adam pointed out that it's ok.

* Remove explicit prefix config

Remove explicit prefix config, the autotools package does it for us.

f5bc42f2

f5bc42f2 8 years ago

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

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