Denis Davydov
4b5fe75bc3
add OctavePackage ( #6746 )
...
* add OctavePackage
1. remove import CudaPackage which is not needed anymore
2. mention CudaPackage and OctavePackage in packaging guide
3. adjust OctavePackageTemplate
4. add clue file for Octave build
5. sanity check on self.prefix
* use setup_environment
2018-01-02 20:03:27 -06:00
Feiyi Wang
fd6b9ac3af
py-xattr: a python interface to access extended file attribute ( #6747 )
...
* py-xattr: a python interface to access extended file attribute
* py-xattr: style fix
2018-01-02 20:02:03 -06:00
Brian Van Essen
a92268d62a
Lbann update ( #6751 )
...
* Added a package for the MDAnalysis toolkit.
* Updated the LBANN recipe to use the revised cmake environment being
rolled out.
* Flake8 errors
2018-01-02 20:01:23 -06:00
Denis Davydov
3d257e8280
likwid: add stable 4.3.0 ( #6761 )
2018-01-02 19:59:14 -06:00
Denis Davydov
cc74da5aab
mesa: disable binutils on macOS ( #6763 )
2018-01-02 19:58:38 -06:00
Levi Baber
353870fe50
jags: lapack fix ( #6764 )
...
* jags: fixing openblas thows a lapack error when compiling. atlas works. other lapack providers may work. also adding tags
* changing blas/lapack reference
* removing openblas conflict
* jags: whitespace cleanup for flake8
2018-01-02 19:57:54 -06:00
Milton Woods
6922ea5889
Esmf fixes for Cray, OSX and mpich ( #6768 )
...
* esmf: put .mod files in the spack compiler search path
* esmf: allow building with Cray mpi
* esmf: create run-path dependent libraries on osx
* esmf: link fortran interface libraries when building with mpich
2018-01-02 19:43:55 -06:00
Jon Rood
e1e24ff80e
Adding option to build Nalu with Hypre support. ( #6782 )
2018-01-02 19:42:47 -06:00
peetsv
fef93d2221
perl-xml-libxml: adding perl module ( #6783 )
...
* perl-xml-libxml: adding perl module
* line length change
2018-01-02 19:42:09 -06:00
Sinan
7f319b9f84
create perl-file-which package ( #6800 )
...
* create perl-file-which package
* trivial edits for package.py so
trivial edits for package.py so that flake8 will not complain
2018-01-02 19:36:59 -06:00
stefanosoffia
2aaba189ed
Updated 'nginx' from v1.12.0 to v1.13.8. ( #6810 )
...
This fixes build issues with most recent gcc versions.
See issue #6252 .
2018-01-02 19:29:47 -06:00
Eric
958abe5b29
py-pyani: Create new package ( #6811 )
2018-01-02 19:27:42 -06:00
Eric
7db7b5b596
MinCED: Create new package ( #6815 )
2018-01-02 19:25:08 -06:00
Levi Baber
08ea9808c6
adding specific version url for augustus 3.3 due to old folder structure ( #6813 )
2018-01-02 19:24:28 -06:00
Jon Rood
285538a78d
Tioga package: Explicitly list MPI compilers for Cmake ( #6741 )
2018-01-02 13:14:22 -08:00
Jon Rood
2812644ed7
paraview package: Explicitly specify MPI compilers in Cmake ( #6738 )
2018-01-02 13:06:25 -08:00
Milton Woods
5dd5dc01c2
new package: Pfunit: unit testing framework for Fortran ( #6795 )
2018-01-02 12:18:08 -08:00
Eric
e483f9297a
new package: DIAMOND ( #6793 )
2018-01-02 12:03:45 -08:00
Eric
8271f0e271
new package: tantan ( #6792 )
2018-01-02 12:00:13 -08:00
Adam J. Stewart
b10098dc53
Cython only needed for develop version of mpi4py ( #6780 )
2018-01-02 11:34:24 -08:00
Eric
9ac9017589
new package: py-rseqc ( #6773 )
2018-01-02 11:10:55 -08:00
Eric
e8b1e79fbf
package py-biopython: remove py-mx dependency ( #6772 )
2018-01-02 10:59:21 -08:00
Eric
caa39d08d4
package r-rcurl: boilerplate cleanup ( #6771 )
2018-01-02 10:58:03 -08:00
Eric
c3b003e698
bamtools: Add version 2.5.1 ( #6770 )
2018-01-02 10:55:07 -08:00
Axel Huebl
da93c9b870
Add: lines-are-beautiful ( #6784 )
...
Adds the C++ File API library "lines-are-beautiful" for the
reMarkable e-ink tablet.
2017-12-30 12:29:27 -08:00
Nichols A. Romero
24743b7e5a
QMCPACK package: update blas/lapack detection ( #6753 )
...
* Fix detection of blas and lapack: provide libraries/includes as
arguments to CMake rather than using CMake's auto-detection.
This includes a patch to QMCPACK's CMake files to refer to
Spack-built blas/lapack implementations. This also includes
special-case logic for the intel-mkl implementation of blas/lapack
* Break up unit tests and short tests. Only hard failure if the unit
tests fail, if short tests fail issue a warning only.
* Add QMCPACK 3.3.0, get rid of 3.0.0
2017-12-22 16:47:49 -08:00
Denis Davydov
f764ac4573
dealii: support 64bit BLAS ( #6758 )
2017-12-22 15:55:04 +01:00
Andrey Prokopenko
937f68c359
clang,flang: update CC, CXX environment in installation module ( #6737 )
2017-12-22 07:32:10 +01:00
peetsv
d1786779c4
gmap-gsnap: adding version 2014_12_28 ( #6720 )
2017-12-22 06:56:58 +01:00
Levi Baber
f2e061debf
Feature/fasttree ( #6227 )
...
* fasttree: new package
* fasttree: better version handling
* fixing line length for flake8
2017-12-20 19:10:24 -08:00
Mark Olesen
ef2e51571d
ENH: better handling of mpich for openfoam packages
...
- define MPICH_SKIP_MPICXX, link libmpich instead of libmpi
(as per disussion in PR #4990 )
ENH: more flexible editing/patching of openfoam env files
CONFIG: comment out requirement for openmpi+thread_multiple
- was originally slated for the 1712 release and beyond, but there are
reportedly unstable version/network combinations.
Leave as comment for future reference, since it may be arise again.
STYLE: renamed openfoam-site.patch as 1706-site.patch (and reformatted)
- to preserve against impending changes in the layout of
config.{csh,sh}/settings
2017-12-20 11:32:33 -08:00
Mark Olesen
235c3c1025
ENH: improved openfoam module creation (issue #4942 )
...
- post-install module settings for openfoam-com and foam-extend.
2017-12-20 11:32:33 -08:00
Eric
6ea4614dbd
picard: Add version 2.17.0 ( #6729 )
2017-12-20 13:28:37 +01:00
Denis Davydov
ea5f8c7382
octave: add optim and struct packages ( #6733 )
2017-12-20 13:27:50 +01:00
Gregory Lee
241ea77229
sqlite package: apply B0 patch to additional versions ( #6728 )
2017-12-19 11:06:39 -08:00
Denis Davydov
0ef741d291
slepc: add 3.8.2 ( #6724 )
2017-12-19 15:40:30 +01:00
Denis Davydov
e462d39afe
intel-tbb: add 2018.2 ( #6725 )
2017-12-19 15:39:42 +01:00
Denis Davydov
98f220b304
hypre: add 2.13.0 ( #6726 )
2017-12-19 15:39:27 +01:00
Denis Davydov
599094abbd
suite-sparse: add 5.1.0 ( #6727 )
2017-12-19 15:39:12 +01:00
Jack Morrison
720ad57bcd
Added GDB verison 8.0 ( #6704 )
2017-12-19 09:54:18 +01:00
peetsv
d0a10edb67
nextflow: adding version 0.21.0 ( #6722 )
2017-12-19 09:07:33 +01:00
Peter Doak
d4c84be91b
Emacs: added gnutls variant (tested on Centos 7) ( #6711 )
2017-12-19 08:36:54 +01:00
Denis Davydov
69f959ec0b
gmsh: add 3.0.6 ( #6718 )
2017-12-19 08:31:23 +01:00
junkudo
d69d692203
CoinHSL : Prevent CoinHSL from building in parallel ( #6715 )
...
CoinHSL does not seem to be able to be built in parallel. This commit forces serial compilation.
2017-12-19 08:30:39 +01:00
Denis Davydov
548c225d45
dealii: add GMSH, add CMAKE_FIND_APPBUNDLE to CMakePackage ( #6723 )
...
* dealii: add GMSH dependency
* CMakePackage: add CMAKE_FIND_APPBUNDLE to prevent picking up binaries from /Applications
2017-12-19 08:28:55 +01:00
peetsv
e8de22ce46
lftp: adding version 4.6.4 ( #6721 )
2017-12-19 08:19:33 +01:00
Mark Olesen
b3e9192d18
openfoam-org: new version ( #6686 )
...
Add new version with a patch.
2017-12-18 19:47:49 -08:00
peetsv
f7a5a27138
IGV: new package ( #6710 )
2017-12-18 19:37:09 -08:00
Benedikt Riedel
36fa574779
globus-toolkit: add version and openssl dependency ( #6617 )
2017-12-18 15:23:56 -08:00
Douglas Duckworth
d3519af7de
relion - added new stable version 2.1 ( #6706 )
2017-12-18 10:38:20 -08:00
healther
0cff0fba73
fix post install method for py3 in mercurial ( #6497 )
...
* fix post install method for py3 in mercurial
* Update package.py
* Update package.py
* use print_str instead of manual print detection
* Update package.py
* use only depends_on
* Update package.py
* Update package.py
State py3 compatibility for @4.3: according to setup.py from the 4.3.tar.gz from pypi
2017-12-17 12:00:58 -06:00
Sergey Kosukhin
576ef5e2b3
Package 'cdo': get rid of unnecessary dependency on MPI C++ library. ( #6632 )
2017-12-16 19:48:56 -07:00
nshtg
2a639097b0
Add new package signify ( #6645 )
...
OpenBSD tool to sign and verify signatures on files.
See https://github.com/aperezdc/signify
2017-12-16 19:47:59 -07:00
Eric
7d800a0fc2
breseq: Create new package ( #6648 )
2017-12-16 19:47:11 -07:00
fpruvost
6c81cf1a78
build lapacke with tmg ( #6654 )
2017-12-16 19:43:46 -07:00
David Orman
7b8d889d31
bwa: added version 0.7.16a and checksum ( #6658 )
2017-12-16 19:43:02 -07:00
Jack Morrison
d4cc1ac86b
Hadoop: Replace broken url ( #6671 )
2017-12-16 19:42:03 -07:00
David Böhme
3467c207c8
Caliper update, add version 1.6.0 ( #6680 )
2017-12-16 19:39:52 -07:00
Eric
dac09dd5fb
py-bx-python: Create new package ( #6672 )
2017-12-16 19:38:59 -07:00
Eric
d08dc0c019
py-tetoolkit: Create new package ( #6673 )
2017-12-16 19:38:36 -07:00
Eric
d3545ed1b3
py-pandas: add versions 0.19.2 and 0.21.1 ( #6687 )
2017-12-16 19:38:02 -07:00
Paschalis Korosoglou
a69cfd5f78
Add petsc version 3.8.3 ( #6688 )
2017-12-16 19:37:35 -07:00
Paschalis Korosoglou
61dbd3182d
Add clanguage variant for petsc ( #6689 )
2017-12-16 19:37:20 -07:00
Eric
87420dccee
bedtools2: Add version 2.27.1 ( #6693 )
2017-12-16 19:36:35 -07:00
peetsv
5d0e7abcc5
MetaSV: adding new package ( #6691 )
2017-12-16 19:36:11 -07:00
Eric
5539c94e67
PANDAseq: Create new package ( #6694 )
2017-12-16 19:35:48 -07:00
Eric
554d4045fa
DeNovoGear: Create new package ( #6699 )
2017-12-16 19:34:53 -07:00
lingnanyuan
34cf796b54
mefit: Create new package. ( #6700 )
2017-12-16 19:34:30 -07:00
Denis Davydov
f78418d8bb
moltemplate: add new package ( #6702 )
2017-12-16 19:33:28 -07:00
David Orman
176b518d4b
new package: gatk ( #6674 )
2017-12-15 11:00:55 -08:00
Jon Rood
7369ba21bf
new package: Percept ( #6636 )
...
This also adds the 'exception' boost library to the set of default
libraries built by boost.
2017-12-14 18:11:47 -08:00
Douglas Duckworth
1aed3f7c01
added breakdancer ( #6319 )
2017-12-14 14:43:32 -07:00
Massimiliano Culpo
6c1fa37e3d
fftw: added version 3.3.7 ( #6678 )
2017-12-14 21:38:33 +01:00
Jon Rood
b447c2ba51
Add TIOGA package and optional dependency of Nalu on TIOGA ( #6638 )
2017-12-14 11:46:25 -08:00
Scott Wittenburg
ce832fca59
libharu: Make dependencies on zlib and libpng explicit ( #6682 )
2017-12-14 08:58:42 +01:00
Douglas Duckworth
5a66065dfa
relion: add version and cuda arch variant ( #6317 )
...
Add preferred version 2.0.3. Added beta version. Added conflict with
gcc versions >= 5 when building with cuda@8 (which is currently the
only supported cuda version). Added cuda architecture variant. Added
comment about current lack of cuda@9 support.
2017-12-13 10:30:38 -08:00
Denis Davydov
c0aa12111b
tasmanian: add new package ( #6659 )
2017-12-13 16:01:51 +01:00
Axel Huebl
836bf65250
CUDA: 9.1 ( #6663 )
...
Add the latest CUDA release, 9.1
2017-12-13 14:43:40 +01:00
peetsv
2e4c9e47a8
py-pysam: adding old version 0.7.7 ( #6675 )
2017-12-13 09:01:45 +01:00
Eric
5fa9e61321
SPAdes: add version 3.11.1 ( #6668 )
2017-12-13 08:57:29 +01:00
David Orman
c5cb8ae159
picard: added version 2.13.2 ( #6669 )
2017-12-13 08:57:06 +01:00
Audrey Thoma
45784af7f2
new packages: biopieces and dependencies ( #6478 )
...
This also adds the tcl, tk, and libx11 dependencies to ruby. All other
changes are new packages.
2017-12-12 18:35:13 -08:00
Christoph Junghans
27be66420a
laghos: inject CXX ( #6664 )
2017-12-12 17:26:02 -07:00
Christoph Junghans
e80a27d713
swfft: inject CC/CXX ( #6666 )
2017-12-12 17:25:48 -07:00
Satish Balay
80284617a5
xsdk: update xsdk@develop to use sundials, plasma, magma ( #6649 )
...
Also update xsdk@0.3.0 to use a fixed version of magma
2017-12-12 09:31:08 -08:00
nshtg
e831ecbf3a
Add new package minisign ( #6644 )
...
A dead simple tool to sign files and verify signatures.
See https://jedisct1.github.io/minisign
2017-12-11 17:27:40 -07:00
nshtg
45e8e4b4fb
libsodium: Update to 1.0.15 ( #6643 )
2017-12-11 17:27:09 -07:00
nshtg
25aa21a7a7
git: Update to 2.15.1 ( #6642 )
2017-12-11 17:26:53 -07:00
nshtg
74938f58d2
openssl: Update to 1.0.2n ( #6641 )
...
From 07.12.2017, fixes CVE-2017-3737
2017-12-11 17:26:37 -07:00
Brian Van Essen
6fec473e9e
Py h5py update ( #6635 )
2017-12-11 17:26:13 -07:00
健美猫
e19aa80734
intel-parallel-studio: restrict patch to versions > 2016 ( #6523 )
...
Fixes #6522
Patch psxevars.sh and psxevars.csh only when year > 2016.
pxevars.csh does not exist for versions before 2017. psxevars.sh
does not appear to require this patch for versions before 2017.
2017-12-11 13:14:24 -08:00
Johann Klähn
e83c3d1b6a
bazel: include SPACK_DEBUG_LOG_ID in environment ( #6562 )
...
Fixes #6521 .
Bazel's build system filters environment variables, including those
set by Spack for use by its compiler wrapper. This updates the patch
to include the SPACK_DEBUG_LOG_ID variable added in #5837 .
2017-12-11 10:34:06 -08:00
Satish Balay
53b2ec356b
disable plasma in xsdk 0.3.0 ( #6621 )
2017-12-10 17:51:54 -08:00
Adam J. Stewart
f41a263a28
Fix reference to self.versions in neovim package ( #6639 )
2017-12-10 21:43:49 +01:00
Cyrus Harrison
95a384f051
updates to conduit and ascent packages (new PR) ( #6584 )
...
* optional path to use spacks py-site-pkgs, install host-cfg for provenance
* add more comments and address review requests
* only use st-pkgs-dir when +python
* ascent does not need doxygen
* capture mpiexec if it exists
* added missing import
* flake8 fix
* default adios variant to False
* ascent develop now reqs conduit master
* optional path to use spacks py-site-pkgs, install host-cfg for provenance
* add more comments and address review requests
* only use st-pkgs-dir when +python
* ascent does not need doxygen
* capture mpiexec if it exists
* added missing import
* flake8 fix
* default adios variant to False
* ascent develop now reqs conduit master
* conduit: use hdf5 1.8 for wider output compat
2017-12-08 13:43:12 -08:00
Chris Green
e279299b9b
Relax restriction on lua version. ( #5886 )
2017-12-08 20:52:00 +01:00
Thilina Rathnayake
c1bc1be2a7
Add NekCEM package to spack ( #6509 )
2017-12-08 10:30:42 -07:00
Thilina Rathnayake
d6db532095
Update the Nekbone package ( #6508 )
2017-12-08 10:29:58 -07:00
healther
4c02e7e9f4
add restriction to py-setuptools dependency on py-flake8 ( #6589 )
2017-12-08 10:22:52 -07:00
Eric
bb8e7ee023
Perl-statistics-descriptive: Create new package ( #6588 )
2017-12-08 10:22:16 -07:00
