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5210 commits

Author SHA1 Message Date
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