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5549 commits

Author SHA1 Message Date
lingnanyuan
f393a2c146 orthofinder: Create new package. (#7364) 2018-03-07 20:45:45 +01:00
Federico Ficarelli
ef310d9f66 fmt: add version (#7415) 2018-03-07 13:59:20 +01:00
simo-tuomisto
da48d3113c py-gpaw package with variants for MPI, FFTW and ScaLAPACK (#7373) 2018-03-07 09:30:47 +01:00
Douglas Duckworth
0f114d9718 Relion 2.1 - Using CudaPackage class (#6707) 2018-03-07 07:45:48 +01:00
Christoph Junghans
95b2738549 lammps: add version 20180222 (#7408) 2018-03-07 06:32:06 +01:00
Christoph Junghans
360feb4193
minighost: rework link logic (#7402) 2018-03-06 15:51:12 -07:00
Mike Pozulp
b0795d84c7 adds patches required to build hdf5 1.8.10 (#7386) 
For hdf5 `1.8.10` and some compilers, the hdf5 build system adds the
'-ansi' flag. hdf5 1.8.10 is not actually ansi compliant so this
adds a patch to modify the places where it violates ansi
compatibility (which ends up being a few comments).
 2018-03-06 12:49:36 -08:00
Eric
ea7879bce5 bowtie2: Add version 2.3.4.1 (#7252) 2018-03-06 18:48:48 +01:00
Geoffrey Oxberry
5ed6e6f184 pnmpi@1.7: new package (#7051) 
Add PnMPI, a dynamic MPI tool infrastructure that builds on top of the
PMPI interface.
 2018-03-06 18:48:28 +01:00
健美猫
c0f6cb5393 Add the libssh2 variant for curl. (#6980) 2018-03-06 18:41:22 +01:00
Eric
2be8712406 perl-net-scp-expect: Create new package (#7028) 2018-03-06 18:39:13 +01:00
Christoph Junghans
274036bfed gromacs: add v2018 (#7050) 2018-03-06 18:37:45 +01:00
Simon Flood
fa5911af83 Update package.py (#7327) 
Add versions released after 3.5.0 (3.4.3, 3.5.1, and 3.6.x)
 2018-03-06 18:28:02 +01:00
peetsv
d649fda48a py-crossmap: adding new package (#7108) 2018-03-06 18:27:03 +01:00
Sergey Kosukhin
8d6738a3e6 Setup dependent environment for pkgconf. (#7102) 2018-03-06 18:25:00 +01:00
Elizabeth Fischer
02bed55007 py-rasterio: Added with dependencies. (#7156) 2018-03-06 18:21:34 +01:00
Geoffrey Oxberry
45e78a42cf sosflow: add missing dependencies (#7182) 
SOSflow depends on MPI and pkg-config, but neither of these
dependencies are currently in the spack package, so this commit adds
them.
 2018-03-06 18:17:49 +01:00
Paschalis Korosoglou
ceb8963362 Add cmor version 3.3.0 (#7197) 2018-03-06 18:16:52 +01:00
Eric
d77a2eecbe perl-graph-readwrite: Create new package (#7284) 2018-03-06 18:12:06 +01:00
mcneish1
642484caeb Add sqlite 3.22.0 (#7335) 2018-03-06 18:09:09 +01:00
healther
b106c86fa3 Fix apr pick up of log4cxx (#7347) 2018-03-06 18:08:51 +01:00
Michael Kuhn
17772fcd43 likwid: Fix build (#7244) 
likwid uses the current directory when building the paths to its
internal libraries. Spack overwrites PWD, causing likwid to not find
hwloc.h.
 2018-03-06 18:07:37 +01:00
Veselin Dobrev
65a1655022 mumps: add the libs property (#7264) 2018-03-06 18:05:58 +01:00
Ricardo Silva
4a54178ff8 Make neuron package more generic (#7393) 
Make neuron package more generic

* find the bin directory dynamically for use in run_env and spack_env
* replace filter_compilers after install with filter_compiler_wrappers
* update checksum for _current_ 7.5 version
* make +python conflict with ~shared
* prepend the architecture specific lib directory to the LD_LIBRARY_PATH

Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>
 2018-03-06 16:31:28 +01:00
Matthias Diener
8f350d0002 Colordiff: new package (#7070) 2018-03-06 13:14:29 +01:00
Eric
bcae9c3506 py-bitstring: Create new package (#7190) 2018-03-06 13:04:16 +01:00
Veselin Dobrev
7482cf1d9f suite-sparse: add a package-specific 'libs' property (#7269) 2018-03-06 10:09:20 +01:00
Yifan Zhu
9c828f3068 trnascan-se: new package (#7351) 2018-03-06 09:58:05 +01:00
Axel Huebl
c7a8c4a44c libSplash 1.7.0: Root Fix (#7368) 
Fix installs as "root" user for the last libSplash release.
Missing quoting of string compares resulted in a CMake error
when run as root (e.g. in a Docker build).
 2018-03-06 09:38:40 +01:00
lingnanyuan
7aff7cbaec snpEff: Create new package. (#7382) 2018-03-06 09:34:22 +01:00
Eric Müller
2f06292abc mosh build depends on pkg-config (#7365) 2018-03-06 09:34:00 +01:00
Eric
c2d1344c51 perl-file-slurper: Create new package (#7378) 2018-03-06 09:28:37 +01:00
Christoph Junghans
ca367b4de3 exasp2: add v1.0 (#7398) 2018-03-06 09:01:53 +01:00
Yifan Zhu
d90b03db09 braker: added list_url (#7058) 2018-03-06 08:51:43 +01:00
Yifan Zhu
4a7e88cc71 r-sf: new package (#6547) 
* r-sf: new package

* r-sf: added version requirements for dependencies
 2018-03-05 23:45:19 -06:00
Christoph Junghans
96f9576426
minighost: another Ubuntu fix (#7359) 2018-03-05 17:39:21 -07:00
Christoph Junghans
94c8299a1e
minismac2d: fix build with external Debian MPI (#7318) 2018-03-05 16:07:41 -07:00
Eric
35115127bc perl-extutils-depends: Create new package (#7376) 2018-03-05 21:32:22 +01:00
Federico Ficarelli
fa442ed61a rapidjson: new package (#7391) 2018-03-05 21:10:02 +01:00
Mario Melara
ccb24b1438 Fix pkgconf on Crays (#7171) 
This updates Cray.setup_platform_environment to use cray-specific
pkgconfig paths so that all providers of 'pkgconfig' have access
to them (previously the 'pkg-config' provider had this but the
'pkgconf' provider did not).
 2018-03-05 12:08:11 -08:00
Adam J. Stewart
89a591eb3b Fix version-specific URLs for Python packages (#7394) 2018-03-05 12:00:49 -08:00
Veselin Dobrev
e4597f09be openmpi: add package-specific 'headers' property (#7267) 
* [OpenMPI] Add the 'headers' property. This removes some redundant
headers from sub-directories, returned by the default '.headers'
handler.

* [OpenMPI] In the .headers property, add a fallback to search all of
prefix for the mpi.h header. Recommended by @junghans to support some
external configurations, see #7268.
 2018-03-05 12:53:36 -07:00
Federico Ficarelli
3cf2cda4ec tclap: new package (#7390) 2018-03-05 14:53:42 +01:00
Eric
ca336b60fa bracken: Create new package (#7375) 2018-03-05 14:16:27 +01:00
Mike Pozulp
90c8243113 add -ldl to silo ldflags when building with static hdf5 in order to fix #7384 (#7385) 2018-03-05 13:28:37 +01:00
Cyrus Harrison
d59ee8d07d update for conduit 0.3.1 release (#7344) 2018-03-05 11:04:21 +01:00
Eric Müller
1a77884c07 fix ruby build on gcc >= 7 (#7387) 
* pkgconfig fixes a "libffi.a requires -fPIC" build error
* the patches solve the mentioned problem on GCC 7.x
 2018-03-05 10:01:23 +01:00
Axel Huebl
189d9ec138 Rsync package: Fix Src Link (#7367) 
Fix the source link to rsync downloads.

The old link only contained the latest release, the new link
contains all.
 2018-03-01 22:42:26 -08:00
junkudo
6213463aeb new package: hiop (#7039) 2018-03-01 15:26:28 -08:00
Eric
86afd0e851 new package: perl-parallel-forkmanager (#7049) 2018-03-01 12:37:16 -08:00