Update the samtools package to support v1.3.1, which
- now uses configure script; and
- now depends on external htslib package.
The dependency on mpc seems to have been bogus, it's never linked in,
nor is it mentioned in the source tree. I *do* have a version in
/usr/lib64, but ldd does not sure it being linked in either....
By depending on 'ncurses' I can do away with the need for the patch.
- It's not really a circular dependency -- git is a run dependency of gettext
- We can revert this change when Spack is smart enough to make git a run
dependency and build it.
+ Always depend on the gettext package. This simplifies the logic and I no
longer need to 'import sys'
+ Only apply the patch for the older version of glib.
Add py-meep package and dependencies
Merging to add the gettext support, will submit a separate issue for the LD_LIBRARY_PATH issue with MPI and py-meep
Before I learned that I was stumbling over a real but (#1308), I thought
I needed to arrange for the fetcher to skip the unpack step.
This commit removes the useful `def unpack`.
Use the resource machinery to fetch/cache/unpack/... the App::cpanminus
tarball.
- this hardcodes the version, I can't figure out how to use a variant to
hold/set the value and access it in the resource().
- change up the install to use the `with working_dir()` meme.
Make running perl's tests conditional, one must now specify the
`--run-tests` flag to the `spack install` command in order to run the
tests.
On one system (8 core, 16GB Digital Ocean Droplet), installing without
tests takes 3 minutes, with tests takes 16 minutes.
Rather than hard-coding the verison of `cpanm` that's [optionally]
installed into the core, make it a variant with a default value of
'1.7042'.
Also discovered that `prefix + 'bin'` is the same as `prefix.bin`, so
embetter that bit of code.
Add perl package, based on [work by
justintoo](https://github.com/LLNL/spack/pull/105). He had too many
things pulled into that pull request, this just adds a perl package.
Support the current releases on the past three minor branches.
Run perl's tests before installing.
Install cpanm into the core (makes building on top of this perl *much*
simpler). Controlled by a variant.
I cargo culted that from my *nextflow* package. I [thought I] needed it
to work around Spack trying to use tar to unpack something that was
neither a tar ball nor unpackable.
This package works fine without it. In retrospect, the error that I was
seeing in the *nextflow* package was probably this problem #1308.
