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Author SHA1 Message Date
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
Axel Huebl
5bf19a9d84 Fix AstroPy: Missing Markupsafe (#6630) 
`py-markupsafe` was missing during `spack install` as a build error.
 2017-12-08 10:21:46 -07:00
Axel Huebl
353ea07040 Add: Py-Plotly (#6628) 
* Add: Py-Plotly

The requirements of py-plotlit are rather strict fixed to specific
versions, so I did not add an "upper versions" `:` to the constrains.
See
  https://github.com/plotly/plotly.py/blob/master/requirements.txt

* Py-Requests, Py-Six, Py-Pytz: Older Versions

Add two older versions of requests, pytz and six for plotly.
 2017-12-08 10:21:28 -07:00
Paschalis Korosoglou
5e8139cbd1 Fix in download url for package libaio (#6616) 2017-12-08 10:20:14 -07:00
nshtg
e283a79da6 Update zsh to 5.4.2 (#6609) 2017-12-08 10:19:40 -07:00
lingnanyuan
3474dd5d40 r-tidycensus: Create new package. (#6595) 2017-12-08 10:18:45 -07:00
lingnanyuan
cc20ad0eec r-rgdal: Create new package. (#6593) 2017-12-08 10:18:29 -07:00
lingnanyuan
85c4224474 r-tigris: Create new package. (#6591) 2017-12-08 10:18:11 -07:00
nshtg
173236dacf Update openSSL to 1.0.2m/1.1.0g (#6596) 2017-12-08 10:13:58 -07:00
nshtg
fd764b9946 Update openSSH to 7.6p1 (#6598) 2017-12-08 10:13:41 -07:00
nshtg
1954075091 Update tmux to 2.6 (#6597) 2017-12-08 10:13:22 -07:00
Tzanio Kolev
2343e5185d Updated hash for v1.0 tag of Laghos (#6626) 2017-12-08 10:12:33 -07:00
Sergey Kosukhin
bd92cc0a1a Package 'openjpeg': set INSTALL_NAME_DIR on MacOS for old versions. (#6603) 2017-12-08 13:36:20 +01:00
Paschalis Korosoglou
1bdea98978 r-rhtslib: added build dependency on autoconf (#6627) 2017-12-08 11:18:25 +01:00
Eric
1c72a5da3a py-cogent: Create new package (#6624) 2017-12-08 10:38:37 +01:00
Denis Davydov
23d56a75ab dealii: update boost dependency (#6586) 
(i) blacklst 1.65.0 due to issues on Ubuntu with gcc 5.4.0
(ii) add a patch for 1.65.1 to fix serialization
(iii) simplify boost's depends_on()
 2017-12-08 10:37:54 +01:00
lingnanyuan
96476a32e5 py-htseq: Create new package. (#6623) 2017-12-08 10:36:57 +01:00
Brian Van Essen
20fc7d56d7 Candle benchmarks update (#6619) 
Added a dependency on HDF5 support for the CANDLE benchmarks.
 2017-12-08 10:34:49 +01:00
Benedikt Riedel
df184c707a Adding openssl dependency to xrootd. Closes #6601 (#6618) 2017-12-08 10:33:08 +01:00
nshtg
17692d6c05 Update vim to 8.0.1376 (#6599) 2017-12-08 10:29:50 +01:00