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Author SHA1 Message Date
Eric
5a04ad1273 py-multiqc: Add version 1.5 (#7506) 2018-03-17 18:22:12 -05:00
Massimiliano Culpo
49feddf71e
py-performance: added package (#7500) 2018-03-17 20:33:13 +01:00
Massimiliano Culpo
e1290b438b
hwloc: constrain dependency on numactl (#7509) 
fixes #7505
 2018-03-17 18:18:35 +01:00
Massimiliano Culpo
cf4b3f2af6
hwloc: updated package (#7483) 
This includes:

* Added latest available versions (1.11.9, 2.0.0)
* Added variants to enable graphical output from lstopo
* Enabled build of the bundled netloc package if @2.0.0:
* Added dependency from numactl if @:1.11.9
* Added a constraint to avoid using  hwloc@2.0.0 with openmpi
 2018-03-15 10:16:33 +01:00
Robert Pavel
30b8dfbeba Added Tagged Release of ExaMiniMD (#7485) 2018-03-14 18:37:21 -06:00
Michael Kuhn
423f2341bc cube: Fix qt detection (#7242) 
cube's configure only recognizes qt versions with single digit version
components and breaks with qt 5.10. Patch the configure files directly
to avoid having to regenerate them.
 2018-03-14 09:01:11 +01:00
Levi Baber
1cde74656b phylip: new version (#7467) 2018-03-14 08:56:15 +01:00
Sinan
e378044f16 postgresql: add newest version 10.3 (#7455) 2018-03-14 08:54:02 +01:00
Federico Ficarelli
b5879d7d07 Fix extends('tcl') environment (#7473) 2018-03-14 07:02:50 +01:00
Matthias Diener
73dd58b68a Xterm: Fix URL (#7476) 2018-03-14 06:58:42 +01:00
Kelly (KT) Thompson
86f9c9fc73 Provide new package: mscgen. (#7477) 
Mscgen is a small program that parses Message Sequence Chart descriptions and
produces PNG, SVG, EPS or server side image maps (ismaps) as the output.

See http://www.mcternan.me.uk/mscgen/
 2018-03-14 06:56:11 +01:00
Yifan Zhu
5bd8ec8160 r-tfbstools: new package (#7243) 2018-03-13 12:40:41 +01:00
Stephen McDowell
6f76c2124a llvm 6.0.0 released as stable (#7459) 
Relase notes: http://releases.llvm.org/6.0.0/docs/ReleaseNotes.html
 2018-03-13 11:34:19 +01:00
Cyrus Harrison
f8d3a0225f add an option to build tbb statically (#7407) 2018-03-13 08:08:02 +01:00
f-sim
1329f3baca Fix dependency conflict in FEniCS. (#7404) 2018-03-13 08:04:09 +01:00
Federico Ficarelli
b594f89d5e Treat tcl as extendable (#7410) 
* Make tcl package extendable

* Let tk extend tcl

* Fix environment for Tcl extensions
 2018-03-13 10:31:03 +09:00
Denis Davydov
a4ed76c207 arpack-ng: add develop (#7458) 2018-03-12 09:06:37 +01:00
Levi Baber
39bfa12f22 astral: needs zip (#7443) 2018-03-10 10:56:59 +09:00
Patrick Gartung
82aa54151a Fix bug in lua package instroduced by PR #7434 (#7450) 
Fixes issue #7449
 2018-03-09 16:57:46 -08:00
Levi Baber
3945b2adb4 Augustus hash (#7447) 
* augustus: 3.3 package hash changed

* augustus: bamtools libraries now seem to be in lib64

* augustus: fix lib problem with older bamtools
 2018-03-09 16:05:39 -08:00
sknigh
9d3d7d3216 new package: tcptrace (#6993) 
Also added missing deps for libpcap: bison and flex
 2018-03-09 10:46:57 -08:00
Levi Baber
1eeb918f0d new package: cistem (#7438) 2018-03-09 10:19:10 -08:00
Eric
d2f0e57771 new package: py-bcbio-gff (#7129) 2018-03-09 10:14:53 -08:00
Eric
2f97aea4e4 new package: deconseq-standalone (#7290) 2018-03-09 10:13:41 -08:00
Axel Huebl
869c654c37 Boost: More Bintray (#7389) 
There are two additional releases moved to bintray.
Change to bintray for 1.64 and 1.65 as well since SF downloads are
too instable.
 2018-03-09 09:57:41 -08:00
Federico Ficarelli
8ad40babd6 cmake: new version (#7429) 2018-03-09 09:18:58 +01:00
Yifan Zhu
b6440fd10e r-cner: new package (#7228) 2018-03-09 08:36:26 +01:00
Patrick Gartung
331f5f27eb lua package: add lib64 to LUA_PATH and LUA_CPATH (#7434) 
This is needed when using system lua on RHEL and clones where lua
is installed in /usr/lib64. Note that the path entry for lua in
packages.yaml should specify the major/minor version of lua (since
this is used to calculate the lua lib directory)
 2018-03-08 20:18:55 -08:00
Michael Kuhn
74bb15285b json-c: Update to 0.13.1 (#7419) 
* json-c: Update to 0.13.1

0.12.1 does not compile with GCC 7.

* json-c: Add patch to make 0.12.1 build with gcc 7
 2018-03-08 14:25:29 -08:00
jthies
bcde37633d Added new package: ghost (#7362) 2018-03-08 11:16:51 +01:00
Brock Palen
732432df50 hoomd-blue version bump and compiler updated (#7021) 
updated hoomd-blue to latest tagged release in repo.  This version also supports newer gcc6 compilers, so added constraint for older version to avoid breaking existing installs.
 2018-03-08 09:35:59 +01:00
zenln
ad183f652f Added compiler conflict to prank (#7168) 2018-03-08 08:47:46 +01:00
Kelly (KT) Thompson
ac7fef3253 Help newer versions of trilinos/zoltan2 successfully configure. (#7059) 
+ Newer versions of zoltan2 are doing test compiles that link to parmetis.  If
  these checks don't find `metis.h`, the check fails.
+ This small tweak ensures that the zoltan2 configure step can find `metis.h`
  that is provided by spack.
 2018-03-08 08:39:35 +01:00
Yifan Zhu
66c46ae655 New package r-phangorn and its dependencies (#7034) 2018-03-08 08:30:02 +01:00
Levi Baber
98808196cb star: needs zlib (#7418) 2018-03-08 08:27:41 +01:00
Yifan Zhu
64f1fbb2e2 dislin: new package (#7305) 2018-03-08 06:38:17 +01:00
Robert Pavel
1cf451b62c Generalized ExaSP2 Install (#7422) 
Generalized ExaSP2 Install to use glob due to changes in naming
convention between previous release and current development branch
 2018-03-07 15:46:53 -08:00
Levi Baber
13e6fc730d cdbfasta: needs zlib (#7413) 2018-03-07 15:42:37 -08:00
snehring
cb64e32296 gcta: new package (#7425) 2018-03-07 15:40:51 -08:00
Jim Galarowicz
7f3a72fb33 OpenSpeedShop package: add support for building on cray (#7338) 2018-03-07 14:26:07 -08:00
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
healther
1ac0bce3e9 help gdb pick up python3 (#7104) 
* Update gdb to autotools package
* Help gdb find python libraries for python 3
 2018-02-28 23:13:06 -08:00
Omri Mor
b4b01b82ac mpich@develop: needs git submodules (#7357) 2018-02-28 19:48:57 -06:00
Eric
da2d6cccd6 new package: py-goatools (#7328) 2018-02-28 17:41:22 -08:00
Denis Davydov
98949bd79b change recurse into recursive in a few places (#7342) 2018-02-28 20:15:26 +01:00
Christoph Junghans
3089207ced minighost: fix build on Ubuntu (#7354) 
* minighost: fix build on Ubuntu

* minighost: append -lgfortran only for gcc
 2018-02-28 09:37:01 -08:00
Christoph Junghans
6c2fe27f41
examinimd: fix a typo (#7352) 2018-02-28 10:02:33 -07:00
healther
f302d64235 add package verilator (#7332) 
* add verilator package

* try to add environment variable and include folder

* manually install existing scripts and patch out spack's CXX wrapper

* added some comments

* make flake8 happy
 2018-02-27 23:46:02 -08:00
Mark C. Miller
0e326c9687 updating zfp version (#7304) 2018-02-27 21:49:04 +01:00
Robert Pavel
5689fd304c Added initial Spackage for examinimd (#7350) 2018-02-27 11:42:35 -07:00
Christoph Junghans
2244e43e2b minighost package: fixed a typo (#7349) 2018-02-27 10:23:33 -08:00