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Author SHA1 Message Date
Eric
521e9da053 RNA-SeQC: Create new package (#6555) 
* RNA-SeQC: Create new package

* RNA-SeQC: Fix flake8 error

* RNA-SeQC: Fix Travis error
 2018-01-04 09:07:29 -06:00
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
Michael Kuhn
01bec7976b Fix HTML detection (#6394) 
Some servers report a content-type header instead of Content-Type.
 2018-01-02 21:21:36 -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
Adam J. Stewart
464ca87879 Add more unit tests for spack clean command (#6777) 2018-01-02 11:31:38 -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
Adam J. Stewart
05ce8407af Add unit tests for spack help command (#6779) 
* Add unit tests for spack help command
* Work around issue with using `spack help` twice in tests
 2017-12-30 22:55:49 -08:00
Adam J. Stewart
088c193a78 Update to the latest version of argparse (#6786) 
* Update to the latest version of argparse

* Re-add colified logic
 2017-12-30 16:08:35 -08:00