lingnanyuan
414287a52e
r-rgeos: Create new package. ( #6592 )
2018-01-04 09:01:17 -06:00
Denis Davydov
cef711458e
qt: add 5.10.0, fix macOS build, clean-up comments/TODOs ( #6766 )
...
* qt: add 5.10.0, fix macOS build, clean-up comments/TODOs
* qt: fix pkgconfig files
* qt: restore-pc-files.patch
* add version constraint to the patch
* qt: adjust url_for_version for 5.10.0
2018-01-04 09:00:01 -06:00
Milton Woods
70d589a14e
xios: I/O management for climate models ( #6796 )
...
* xios: XML-IO-SERVER library for IO management of climate models
* xios: install to prefix directory
* xios: add a test case
* xios: define versions to use cache and mirror directories
* xios: use proper svn URL for version 910
* xios: package url must be defined, otherwise uninstall fails
* xios: add trunk version to allow building latest revision
* xios: enable parallel build
* xios: allow installation with mpif90 compiler wrappers
* xios: use mpi variants of dependencies
* xios: allow user to specify MPI launcher via MPIRUN environment variable
* xios: prefer spack versions of blitz and boost (needed for gcc@7)
* xios: enable builds with clang+gfortran on OSX
* xios: use numeric versions for releases, @develop for trunk
* xios: different patches required for @1.0 and @develop
* xios: patch function for clang works across revisions
* xios: link blitz library
* xios: workaround bug 17782 in llvm
* xios: whitespace adjustments for flake8
* xios: avoid bare except clause
* xios: netcdf-fortran inherits ^netcdf+mpi from xios dependencies
2018-01-04 08:58:24 -06:00
Eric
75f1a91821
py-umi-tools: Create new package ( #6823 )
...
* py-umi-tools: Create new package
* py-umi-tools: fix dependencies
2018-01-04 08:55:37 -06:00
Loikki
229db0f1c7
Update grackle ( #6822 )
2018-01-03 21:35:17 +01:00
Mark Olesen
f07ce6094e
package openfoam-com: add version 1712 and update patches ( #6820 )
...
* combine all patches for 1612 into a single file, with additional
comments to explain the rational.
* Add kahip decomposition variant.
* Add support for ARM64 architecture.
* filter instead of patching etc/config.*/settings. This eliminates
patch files for 1706, perhaps for the future as well.
* URLs at or before version 1612 have a different structure, so
provide a url_for_version implementation to handle this
2018-01-03 11:30:10 -08:00
Sinan
2f551908b8
package/r-rjags: create new package ( #6804 )
...
* package/r-rjags: create new package
* fix typo
fix typo
* package/r-rjags small fix to pass flake8 tests
* package/r-rjags: more fixes to satisfy flake8 tests
2018-01-03 10:17:15 -06:00
健美猫
34c9f08c2c
fltk depends on libx11. ( #6816 )
2018-01-03 10:14:51 -06:00
健美猫
ce317674bf
Add a new version and runtime dependency for MotionCor2. ( #6817 )
...
* Update motioncor2 to 1.0.4 and add libtiff dependency.
* Add comments for libtiff dependency in MotionCor2.
2018-01-03 10:03:35 -06:00
健美猫
ec2c0b3e65
Add libtiff@3. ( #6818 )
2018-01-03 10:02:45 -06:00
Denis Davydov
e623bbb679
suite-sparse: support 64bit BLAS ( #6767 )
...
* suite-sparse: support 64bit BLAS
* use double quotes instead of escaped quotes
2018-01-03 09:58:19 -06:00
stefanosoffia
2ed914aa1b
Flex v2.6.4 conflicts with gcc@7.2.0 ( #6819 )
2018-01-03 09:46:57 -06:00
Douglas Duckworth
d466d8f3d3
singularity - added master branch ( #6631 )
...
* singularity - added master branch as this has latest fixes - 2.4 does not compile on centos 6 without use of this branch
* renamed to develop
* added master branch properly
2018-01-02 21:47:21 -06:00
Axel Huebl
5d2f752c1b
New Package: py-adios ( #5686 )
...
The ADIOS1 numpy bindings depend on an installed, fully loaded
ADIOS C library + its config tools to build properly.
2018-01-02 21:37:59 -06:00
Brian Van Essen
3c63710532
Intel mkl dnn ( #6268 )
...
* Added a package for the MDAnalysis toolkit.
* Added a package for the Intel MKL-DNN project.
* Fixed flake8 errors.
* Fixed Flake8
2018-01-02 21:27:34 -06:00
Eric
d2c3b3884b
rsem: update version 1.3.0 md5sum ( #6650 )
2018-01-02 21:15:40 -06:00
Michael Kuron
2c5c7a37cb
atom-dft: new package plus dependencies ( #6653 )
...
* atom-dft: new package plus dependencies
* Indentation fix
* Use the compiler wrappers
* Pass variables instead of using FileFilter
2018-01-02 20:32:37 -06:00
Jimmy Tang
ea6b6ef1ff
Install all the cli tools from all the sub-directories ( #6705 )
...
* Install all the cli tools from all the sub-directories
* Satisfy pep8
2018-01-02 20:14:39 -06:00
Feiyi Wang
8ed1c84539
py-lrudict: a LRU-based cache dictionary ( #6734 )
...
* add py-lrudict
* style fix
* style fix: add blank lines
2018-01-02 20:10:49 -06:00
Feiyi Wang
8221265c3c
py-scandir: a better directory iterator, backport to 2.7 ( #6739 )
2018-01-02 20:08:58 -06:00
Levi Baber
59cd2db8f3
gatk: boilerplate cleanup ( #6744 )
2018-01-02 20:05:04 -06:00
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