Commit graph

6633 commits

Author SHA1 Message Date
Levi Baber
62208afdb9 py-multiqc: needs newer py-spectra (#9226) 2018-09-14 15:52:29 -07:00
Levi Baber
3c33b5efef py-networkx: new version (#9241) 2018-09-14 15:52:02 -07:00
Levi Baber
617ff8f125 py-decorator: new version (#9240) 2018-09-14 15:51:43 -07:00
Levi Baber
49aed4584b py-markdown: fix url and hashes (#9235) 2018-09-14 15:51:20 -07:00
Levi Baber
f52812e571 perl-gdgraph-histogram: new package (#9250) 2018-09-14 15:50:18 -07:00
Ken Raffenetti
881af613b3 bolt: new package starting at 1.0b1 (#9253) 2018-09-14 15:49:36 -07:00
Justin Stanley
31da752402 metasv: add required dependencies (#9254)
* add runtime deps
* revert to strict dep versions
2018-09-14 15:49:11 -07:00
Ken Raffenetti
17d4005a4f argobots: new package starting at 1.0b1 (#9238) 2018-09-14 15:48:40 -07:00
Justin Stanley
dda27fc0d1 rmats: new package starting at 4.0.2 (#9243)
* new package starting at 4.0.2
2018-09-14 14:54:26 -07:00
Douglas Duckworth
716ed92e32 motioncor2 - added version 1.1.0 and removed old, unlisted versions (#9229) 2018-09-14 13:57:22 -07:00
Matthias Diener
36f396ad5b gdb: add version 8.2 (#9246) 2018-09-14 13:56:15 -07:00
Justin Stanley
ff6b9b99fa gatk: new version (#9202)
* gatk: added 4.0.8.1, fixed binary install
* gatk: fix flake8 conflict
* gatk: improve comments and modify install
2018-09-14 13:55:52 -07:00
Justin Stanley
451328d6e6 mxnet: added 1.3.0 (#9236)
* add version 1.3.0
* change build parameters, install process
  * mxnet will not compile against spack's nnvm and dmlc so we must use
    the distributions provided by the source package.
* also removed 'bin' installation as mxnet is just a shared library.
* improve BLAS linking
* remove unnecessary args
* added variant for python bindings
2018-09-14 11:01:30 -07:00
sknigh
24dd24600c Added Kibana package, added Elasticsearch to 6.4.0 (#9239)
* Added kibana, updated elasticsearch
* Update elastic search to 6.4
2018-09-14 10:50:20 -07:00
Daniel Topa
056960870b Hwloc add update 2.0.2 (#9244)
Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2018-09-14 10:48:38 -07:00
Levi Baber
0ed58374e7 py-colormath: new version, requires newer networkx (#9237)
* py-colormath: new version requires newer networkx
2018-09-14 10:35:45 -07:00
Matthias Diener
466bc20874 cmake: add version 3.12.2 (#9248) 2018-09-14 09:36:39 -07:00
Neil Flood
1122fc3d1e r-nloptr: Explicit depends_on(nlopt). Previously there was a hidden d… (#9176)
* r-nloptr: Explicit depends_on(nlopt). Previously there was a hidden dependency, masked by the package's configure script.

* r-nloptr: Change spelling of variables to satisfy pyflake8

* r-nloptr: Break a long line to satisfy pyflake8

* r-nloptr: larger indent on continuation, to satisfy pyflake8

* r-nloptr: another attempt at larger indent on continuation, to satisfy pyflake8

* r-nloptr: now a smaller indent on continuation, to satisfy pyflake8

* r-nloptr: Another attempt at right amount of indent.

* r-nloptr: Another attempt at right amount of indent.

* Use the correct attributes for finding the nlopt includes and libs.

* Lines too long, split into pieces
2018-09-14 08:11:16 -05:00
Christoph Junghans
98d8c4d7ca
py-espresso: apply patch to v4.0.0 only (#9196) 2018-09-13 10:00:21 +00:00
Abhinav Bhatele
1e2b3b0768 AMG: update version (#9228) 2018-09-12 14:11:05 -06:00
Ricardo Silva
62977662e9 petsc: fix compilation with intel (#9198)
* mpiifort doesn't automatically link all run-time libraries
* scalapack was being picked up accidentaly if intel-mkl was in the spec
2018-09-12 11:18:41 -07:00
Abhinav Bhatele
ff13f3953e ecp-proxy-apps: update dependencies for release 1.0 and 1.1 (#9217) 2018-09-11 15:10:49 -06:00
Tristan Carel
6d0933b2a0 steps: new package starting at 3.3 (#9173) 2018-09-11 14:43:15 +02:00
Adam J. Stewart
ccbff6e0cd
Improve spec['python'].command support for bwpy (#9157) 2018-09-10 17:14:57 -05:00
Christoph Junghans
3dcbe50eb7 py-espresso: added v4.0.0 (#9192)
Added v4.0.0 and workaround for cmake bug
2018-09-10 08:55:32 +02:00
Satish Balay
a537d7b56e
trilinos: disable xlf_tpetra.patch for trilinos@develop (#9193)
This patch does not apply cleanly anymore and breaks clang/Mac builds

balay@asterix /home/balay/git-repo/github/trilinos (develop=)
$ patch -Np1 < /home/balay/git-repo/github/spack/var/spack/repos/builtin/packages/trilinos/xlf_tpetra.patch
can't find file to patch at input line 3
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|--- a/packages/tpetra/core/src/Tpetra_Details_libGemm.cpp
|+++ b/packages/tpetra/core/src/Tpetra_Details_libGemm.cpp
--------------------------
File to patch:
2018-09-08 23:51:16 -05:00
Satish Balay
8afc630e96
assimp: fix compile issues with intel compilers on knl/linux [a depen… (#9191)
* assimp: fix compile issues with intel compilers on knl/linux [a dependency for dealii]

Fixes issue #9189

* assimp: add variant 'shared' with default value 'True'
2018-09-08 16:18:37 -05:00
Denis Davydov
ffca064778 xsdk: disable assimp in deal.II (#9190) 2018-09-08 16:07:37 -05:00
Josh Deaton
7295c8aaad libMesh: New variant and updated recent versions. (#9186)
* libmesh: Added SLEPC eigensolver variant.

* libmesh: Added new versions.

* Corrected flake8 errors.

* Corrected SLEPc variant with proper config & conflicts.
2018-09-07 21:13:34 -07:00
Mike Pozulp
e678266550 Tanim (#9158)
* Added jdk version, added r-ks and r-multicool packages, made some r packages less conservative in their r version requirement

* flake8 fixes

* fix formatting in jdk version cmd

* Added type=('build', 'run') to some R package dependencies,
added some missing dependencies to r-ks. Thanks Adam.

* fix flake8 error
2018-09-07 16:00:52 -05:00
Denis Davydov
18ca196753 xsdk: add dealii (#7529) 2018-09-06 19:22:17 -05:00
Satish Balay
b6b8c7058a
Balay/xsdk trilinos develop (#9182)
* xsdk: update xsdk@develop dependency on trilinos@develop

* trilinos: enable tpetra, ifpack2, zoltan2, amesos2
2018-09-06 12:01:53 -05:00
Tristan Carel
733458347a gmodel: new package starting at 2.1.0 (#9170) 2018-09-06 10:48:08 +02:00
Tristan Carel
26b68a2bc5 gmsh: add git master and 4.0.0 versions (#9172) 2018-09-06 10:42:40 +02:00
Axel Huebl
901d76ef53 openPMD-api: ^py-numpy@1.15+ (#9178)
Due to an internal bug regarding the handling of scalars
(ndim must be 0) in numpy prior to 1.15.0, openPMD-api
will require the latest numpy 1.15+.

Since there is a small regression with datetime pickling in
1.15.0 from the required fix and spack only packages 1.15.1
currently, we depend on 1.15.1 in the recipe.
2018-09-06 10:41:45 +02:00
Tristan Carel
a779e87442 omega-h: add versions and variants (#9169)
* add 5 most recent versions and git master branch
* add trilinos, gmodel, throw, examples, optimize, symbols,
  and warnings variants
* disable XSDK so that Trilinos dependencies are found.
2018-09-05 11:01:45 -07:00
健美猞猁
501669faba Pack dlang's stdlib into dmd. (#9131)
* Update dmd.

* Build dmd and druntime.

* Build dmd.

* Restore edit.

* Flake8.
2018-09-04 14:49:28 -05:00
健美猞猁
8b9b89b931 Onedrive: a new package. (#9130)
* skilion-onedrive: a new package.

* Fix flake8 issues.
2018-09-04 14:35:49 -05:00
健美猞猁
9fe7000dda Bamdst: a new package. (#9113)
* Bamdst: a new package.

* Remove duplicate make() in install().
2018-09-04 14:35:33 -05:00
Levi Baber
5737155dd0 trinity: full dependencies (#9064) 2018-09-04 14:35:06 -05:00
Levi Baber
059daa2012 r-summarizedexperiment: new version (#9054)
* r-summarizedexperiment: new version

* r-summarizedexperiment: add ending range for r3.4 dep

* r-summarizedexperiment: fix range
2018-09-04 14:34:45 -05:00
Miles Perry
447db2fe8d Feature/py pycogent New-Version (#9095)
* added py-pycogent

* flake8 edits

* added type=('build', 'run') to deps, changed py-matplotlib and mpi4py

* changed python min version to 2.6

* fixed cython to py-cython dep

* fixed mpi4py to py-mpi4py

* fixed py-sqlalchemy

* added 1.5.3 version

* fixed version 1.5.3 install

* changed deps names to reflect convention

* added variants

* changed download URL and added SHA256 hash

* fixed deps

* added github url for 1.5.3

* removed unneeded deps

* doesn't require py-setuptools

* fixed url and added py-setuptools specific to version 1.9

* fixed variant names and changed cython to normal dependency instead of variant

* removed cython dep, failed to build when it was present. Changed variant name 'mpi4py' to 'mpi' and changed sqlalchemy variant name to mpi

* fixed dependencies and added py-pymysql dep

* added setup-environment step

* changed download url for 1.5.3 to pypi

* fixed flake8 issue

* updated

* added changes
2018-09-04 14:34:18 -05:00
Francesco Di Natale
e85f737d1f py-maestrowf: Addition of new releases. (#9135)
* Addition of latest maestrowf releases.

* Addition of filelock to dependencies.

* Addition of when clause to depends_on for filelock and tabulate.

* Correction of the tar url.
2018-09-04 14:33:55 -05:00
Levi Baber
3c9b0ee2ea r-genomicalignments: new version (#9055)
* r-genomicalignments: new version

* r-genomicalignments: ending range for r3.4 dep

* r-genomicalignments: fix range
2018-09-03 21:04:22 -05:00
Levi Baber
35d87bdf09 r-biomart: new version; (#9058)
* r-biomart: new version;

* r-biomart: ending range for r3.4 dep

* r-biomart: fix version range
2018-09-03 21:03:47 -05:00
Levi Baber
cb9a95fc37 r-deseq2: new version (#9062)
* r-deseq2: new version

* r-deseq2: fix r 3.4 dep range
2018-09-03 21:03:08 -05:00
Hadrien G
930e266a36 New package: AIDA (#9094)
* Trying to package old AIDA

* Document the incompleteness

* Install the jars too
2018-09-03 21:02:06 -05:00
Miles Perry
cb9e8eda8f Feature/py picrust New Package (#9096)
* added py-picrust

* flake8 edits

* fixed boilerplate, added type='build', 'run'

* fixed errors

* added deps

* fixed error

* fixed numpy max version

* fixed future version

* fixed version issues
2018-09-03 20:58:49 -05:00
Neil Flood
ee14d273e5 nlopt: Only support release>=2.5.0, since earlier release tarballs were actually AutoTools, not CMake. (#9110) 2018-09-03 20:56:48 -05:00
Miles Perry
ad8fbe3c7f aperture-photometry: new package (#9119) 2018-09-03 20:52:11 -05:00