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Author SHA1 Message Date
George Hartzell
0c3f220fb1 Disallow bcl2fastq2 on OS X (#9966) 
* Disallow bcl2fastq2 on OS X

[Illumina's computing requirements][reqs] claim support for RHEL/CentOS and
go on to say:

> May be possible to install and run on other 64-bit Linux distributions or Unix variants.

The sufficient issue is its reliance of malloc.h.  There may be more.

[reqs]: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software/computing-requirements.html

* Add an informative msg for the user
 2018-12-04 13:44:15 +01:00
Neil Flood
e3d204cb8f Expand dependency on qt to allow qt4 (#9964) 2018-12-04 13:37:37 +01:00
Satish Balay
808c2ea5ce petsc: when petsc is built with fortran [default in spack] its best to use hdf5+fortran (#9986) 2018-12-04 13:32:30 +01:00
Neil Flood
47b7016ea7 r-optparse: new package (#9967) 2018-12-04 13:20:08 +01:00
Nick Forrington
9551b34cb5 pgi: Add checksum for PGI 18.10 (#9985) 2018-12-04 13:12:20 +01:00
Matthias Diener
dfb02fd078 cmake: add version 3.13.1 (#9983) 2018-12-04 13:09:49 +01:00
Levi Baber
27e8fcb945 abyss: new version (#9981) 2018-12-04 13:02:36 +01:00
sknigh
a9695bac50 Added missing libtool dependencies to libvterm and unibilium (#10007) 2018-12-04 13:01:37 +01:00
Robert Maynard
0d033a042c Download CMake sources from the Github releases (#10003) 
Now that CMake is providing CMake release artifacts on github,
we should prefer those as they have better download speeds and
uptime.
 2018-12-03 12:35:51 -06:00
jthies
3a2045b7c0 Phist 1.7.4 (#9996) 
* packages/phist: new version 1.7.4 with new variant 'host' to enable/disable host-specific optimizations.
 2018-12-03 09:40:51 -06:00
HAOCHENG LIU
66a62d82c4 Bump vtkm to version 1.3 and add new features (#9968) 
This commit allows users to enable openmp, rendering, logging and mpi
in vtkm. Meanwhile, it adds support for cuda architecture selection.

[VTK-m 1.3 Release notes](https://gitlab.kitware.com/vtk/vtk-m/tags/v1.3.0)
 2018-11-30 19:48:22 -08:00
Mark W. Krentel
cc5446f25c hpctoolkit: overhaul to use spack dependencies (#9946) 
Overhaul hpctoolkit to AutotoolsPackage and to build its dependencies
directly from spack instead of using hpctoolkit-externals.

Remove hpctoolkit-externals since it's no longer needed.
 2018-11-30 18:11:12 -08:00
jwallior
930debcf35 New versions for a few python modules (#9969) 
* py-jupyter-console: Add version 5.2.0

* py-jupyter-core: add version 4.4.0

* py-lxml: add version 4.2.5

* py-zmq: add version 17.1.2

* py-terminado: add version 0.8.1

* py-pexpect: add version 4.6.0

* py-pytables: add version 3.4.4
 2018-11-28 21:44:15 -06:00
Piotr Luszczek
8375b5b571 Add PLASMA version 18.11.0 and Lua variant (#9689) 
* Add PLASMA 18.11.1 with optional Lua and test for headers
 2018-11-28 16:59:05 -06:00
Ondřej Čertík
62f1cf3678 Add f18 package (#9183) 
* Add f18 package

* Fix flake8 errors

* Install the f18 binary into prefix.bin by hand

* Add spack-build into the path

* Fix the license header
 2018-11-28 14:13:30 -06:00
Massimiliano Culpo
e998a399da Injected flags have a consistent order (#9960) 
Fixes #9908

Spack was assembling flags in a manner that could in different
orderings for repeated concretizations of the same spec and config
 2018-11-28 10:23:38 -08:00
Michael Kuhn
5cea4a75d7 glib: disable SELinux explicitly (#9956) 2018-11-28 10:06:17 +01:00
George Hartzell
e4e980ee97 bcl2fastq2 package: recursively delete after copy (#9959) 
Fixes #9944

73c978d replaced a move with a copy, which cased rmdir to fail (as
it expects an empty directory). This switches to use `shutil.rmtree`
instead.
 2018-11-27 17:22:14 -08:00
Scott Wittenburg
33b112a60d Expose option to save all dependencies when writing spec.yaml (#9965) 2018-11-27 17:13:39 -08:00
Jon Rood
4c3091b05e Fixing problems with lammps dependencies voropp and latte (#9909) 
* Fixing problems with lammps dependencies voropp and latte.

* Always replacing CFLAGS in voropp and specifying voropp+pic dependency in lammps.
 2018-11-27 16:55:21 -07:00
Matthias Diener
2164181d0a git: add version 2.19.2 (#9961) 
Also fixes instructions for new releases
 2018-11-27 16:32:22 -06:00
Neil Flood
8a78c9c6bc Rename py-proj to py-pyproj, consistent with Spack's current naming conventions (#9962) 2018-11-27 16:31:30 -06:00
thelfer
2e04f3daab new package: add support for the tfel package (#9930) 2018-11-27 07:16:55 +01:00
Michael Kuhn
16d3e44515 py-pygobject: add missing pkgconfig dependency (#9955) 2018-11-26 21:41:44 -06:00
Axel Huebl
b26c85301d OpenMPI: Prefer Last 3.X (#9945) 
The latest OpenMPI release, v4.0.0, does not build with many GCC
variants. Since this is our default, a lot of users get hit.

Let's wait for some point releases.
 2018-11-26 16:46:04 -06:00
Eric
20a6dde10b GATK: Add version 4.0.11.0 (#9953) 2018-11-26 14:54:05 -06:00
Eric
d9046e70c1 minced: Add version 0.1.6 (#9951) 2018-11-26 14:22:17 -06:00
Matthias Diener
bab3d7734a hdf5: add version 1.8.21 (#9952) 2018-11-26 12:56:44 -06:00
Michael Kuhn
7df14134c1 go: add 1.11.2 (#9948) 2018-11-26 11:33:55 -06:00
Eric
5cd8233139 metabat: Add version 2.11.2 (#9950) 2018-11-26 11:32:14 -06:00
Miles Perry
28e93a7a79 Feature/gatk (#9872) 
* added 3.8-1 version

* fixed flake8 stuff
 2018-11-26 11:30:21 -06:00
Adam J. Stewart
06dcf72f14 Uncomment dependencies previously disallowed by concretizer (#9942) 2018-11-26 09:11:16 +01:00
Sinan
096922c39d Package/py scikit learn (#9843) 
* add v0.20 specific dependency versions, also add cython and py-test as dependencies

* make flake8 happy

* make cython a build-only dependency
 2018-11-24 19:03:30 -06:00
Neil Flood
4c1733bff4 py-pygresql: new package (#9922) 
* py-pygresql: new package

* Added dependency on py-setuptools, as the build will use it if present
 2018-11-24 17:45:27 -06:00
Neil Flood
e3e01ab3d7 py-psycopg2: new package (#9926) 
* py-psycopg2: new package

* Added dependency on py-setuptools, as the build will use it if present
 2018-11-24 17:45:16 -06:00
Denis Davydov
058a772a52 p4est: fix a typo (#9932) 2018-11-24 17:45:04 -06:00
Matthias Diener
9d2ea84112 mc: add version 4.8.21 (#9943) 2018-11-24 17:42:46 -06:00
Matthias Diener
e86a28aff7 intel-parallel-studio: add missing updates to 2019.1 (#9941) 2018-11-24 15:44:57 -06:00
Neil Flood
9945a59c47 py-geopandas: New package. (#9919) 
* py-geopandas: New package, including packages for its dependencies

* Trailing whitespace removed, etc

* One more trailing whitespace

* Removed some extraneous dependencies. No idea why I thought I needed them, but it now builds fine without them.

* Added a variant +plotting, to include the dependencies required for plotting, as these are large-ish if not being used.

* Added explicit dependency on py-matplotlib
 2018-11-24 15:44:44 -06:00
Matthias Diener
25b9938ad1 cmake: add version 3.13.0 (#9940) 2018-11-24 14:23:10 -06:00
Neil Flood
a0fc573ff4 r-geor: new package, and a couple of its dependencies (#9920) 
* r-geor: new package, and a couple of its dependencies

* Update to new copyright header

* Include the list_url for the R package archive dir

* Added explicit version ranges on dependencies, as per the relevant CRAN pages

* Correct dependency types in r-splancs.
 2018-11-24 14:21:54 -06:00
Andreas Baumbach
862d1799fb new version 18.1 for py-pip (#9938) 
Change-Id: Ie462e802049dd6150767dc555fb5708999e081ec
 2018-11-23 18:09:20 -06:00
Neil Flood
2e510413c3 r-compositions: new package, including its dependencies (#9921) 
* r-compositions: new package, including its dependencies

* Include the list_url for the R package archive dir

* Added explicit version ranges on dependencies, as per the relevant CRAN pages
 2018-11-23 18:06:57 -06:00
Neil Flood
3557b6e149 libspatialite: new package (#9923) 2018-11-22 13:54:52 -06:00
Nicholas Labello
13f2e68688 munge: update versions and url format to reflect switch to .xz format… (#9916) 
* munge: update versions and url format to reflect switch to .xz format in recent releases

* package:munge remove unneeded version-specific urls
 2018-11-22 13:13:40 -06:00
Eric
be92d46962 minced: add version 0.3.2 and fix install paths (#9918) 2018-11-22 13:13:06 -06:00
Neil Flood
c42ceb886c qca: new package (#9924) 2018-11-22 12:45:42 -06:00
Neil Flood
b6e664846a qjson: new package (#9925) 2018-11-22 12:45:17 -06:00
Denis Davydov
0f6f3ece95 p4est: apply patches to 2.0 only (#9928) 2018-11-22 12:40:22 -06:00
Michael Kuhn
f7a445e4b0 multitime: new package (#9929) 2018-11-22 12:39:51 -06:00