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Author SHA1 Message Date
健美猫
708fe9f676 Add a new pacakage: HiC-Pro. (#7858) 
* HiC-Pro: a new package.

* Flake8.

* Update.

* Remove nektar.
 2018-04-21 13:08:56 -05:00
健美猫
b91b4a6c4d A new pacakge: IMP. (#7859) 2018-04-21 13:08:44 -05:00
lingnanyuan
f939895b1b py-mg-rast-tools: Create new package and its dependencies. (#7816) 
* r-matr: Create new package.

* shocklibs: Create new package.

* r-biom-utils: Create new package.

* r-mgraster: Create new package

* py-poster: Create new package.

* py-requests-toolbelt: Create new package.

* perl-libwww-perl: Create new package.

* py-mg-rast-tools: Create new package.

* mg-rast-tools: Fix version constraints for dependencies.

* Change dependency type of py-setuptools.
 2018-04-21 10:28:44 -05:00
Levi Baber
3274f16780 py-pymol: new package (#7823) 
* py-pymol: new package

* py-pymol: needs python+tk
 2018-04-21 10:28:09 -05:00
healther
8cc24fa20b add variant htmlreport to package cppcheck (#7824) 
Change-Id: I31766d3ceb4fa8852b9bdc82444e36514e760f4b
 2018-04-21 10:26:37 -05:00
Denis Davydov
5794f432a9 gnuplot: add 5.2.2 (#7831) 2018-04-21 10:24:36 -05:00
Denis Davydov
2dfd61080b dealii: disable +slepc with ~petsc (#7832) 2018-04-21 10:22:10 -05:00
Eric
a808553fa1 DIAMOND: Add version 0.9.20 (#7847) 
* DIAMOND: Add version 0.9.20

* DIAMOND: add version 0.9.21
 2018-04-21 09:57:06 -05:00
Levi Baber
5ae960c476 jellyfish: fixing url for v2 package retrieval (#7849) 2018-04-21 09:56:38 -05:00
健美猫
c8e3c94c6f self has no attribute named satisfies. (#7826) 2018-04-19 12:43:12 -05:00
Axel Huebl
26e9b3b74d openPMD-api (#7765) 
* openPMD-api

Add a new package for openPMD-api.

openPMD is a meta-data standard (markup, schema) for hierarchical,
scientific particle and mesh based data.

openPMD-api is a library wrapping the underlying backends (HDF5,
ADIOS, ...) into a single, object-aware API.

* Repository: https://github.com/openPMD/openPMD-api
* Project: https://github.com/openPMD http://www.openPMD.org

* mpi variant forwarding: fix concretization
 2018-04-19 09:04:07 -05:00
Levi Baber
d65fbf4c68 libxml2: adding subdir to cpath for deps (#7819) 
* libxml2: adding subdir to cpath for deps

* libxml2: no join_path

* libxml2: fix cpath for run_env

* libxml2: typo
 2018-04-19 09:01:11 -05:00
Levi Baber
7219f4a2aa freetype: adding subdir to cpath for deps (#7818) 
* freetype: adding subdir to cpath for deps

* freetype: no join_path

* freetype: fix cpath for run_env
 2018-04-19 09:00:49 -05:00
Kelly (KT) Thompson
4869b7312a Suite-sparse: provide patch to fix builts with clang@6.0.0. (#7811) 
+ I am unable to build suite-sparse@5.2.0 with clang@6.0.0.  The build fails
  with the error:

```
     2397    [ 99%] Linking C executable wildtype_demo
     2398    make[4]: Leaving directory
  `/tmp/kellyt/spack-stage/spack-stage-w0XYhK/SuiteSparse/GraphBLAS/build'
  >> 2399    libgraphblas.so.2.0.1: undefined reference to `__fpclassify'
  >> 2400    clang-6.0: error: linker command failed with exit code 1 (use -v to
  see invocation)
  >> 2401    make[4]: *** [wildtype_demo] Error 1
```

+ This error appears because libgraphblas.so requires `-lm`, but that link
  dependency is not explicitly listed in GraphBLAS\CMakeLists.txt.
+ A patch file is provided to add this dependency.  The patch is only applied
  when the compiler is `%clang`.
 2018-04-19 08:59:55 -05:00
healther
6d1097f99b add variants and conflicts for curl (#7804) 
* add variants and conflicts for curl

* darwinssl - Apple's SSL/TLS implementation
* libssh    - use libssh implementation
* add darwin conflict for libssh{,2}
* add linux conflict for darwinssl

* remove openssl when +darwinssl

* Update package.py

* Update package.py

* Update package.py

* Update package.py
 2018-04-19 07:23:16 -05:00
Levi Baber
4ed613d7e1 freeglut: new package (#7820) 2018-04-18 19:49:42 -05:00
Levi Baber
ecdb3065ed glew: adding gl dependency (#7817) 2018-04-18 17:58:45 -05:00
Jim Galarowicz
0fc51a9c3e Simple updates to the Krell Institute OpenSpeedShop and CBTF components build package files. (#7812) 2018-04-18 14:05:53 -05:00
Levi Baber
5d39e76353 xrandr: needs randrproto (#7814) 
* xrandr: needs xrandrproto

* xrandr: fix typo
 2018-04-18 14:02:04 -05:00
Axel Huebl
5f73c2759d ADIOS 1.13.1 & SZ 1.4.12.3 (#7808) 
* ADIOS 1.13.1

ADIOS 1.13.1 fixes several issues with zero-sized block
reading and writing when compression transports are used.

* SZ 1.4.12.3

Add the lastest SZ release used in ADIOS1.
 2018-04-18 10:52:13 -05:00
Matteo Guglielmi
247f24e015 bcl2fastq2: package update (#7794) 
* bcl2fastq2: package update

* package/bcl2fastq2: homepage fix

* package/bcl2fastq2: glob fix

* package/bcl2fastq2: code clean up

* package/bcl2fastq2: code clean up #2
 2018-04-18 10:11:44 -05:00
Loic Hausammann
87747b888f Add grackle 3.1 (#7805) 2018-04-18 07:23:09 -05:00
Matthias Diener
d950aeee09 cmake: update version (#7802) 2018-04-17 17:26:03 -05:00
Eric
1b32a4e3a5 DIAMOND: add zlib dependency (#7801) 2018-04-17 15:59:23 -05:00
Adam J. Stewart
5854acd233 Add latest version of cURL (#7800) 2018-04-17 14:33:08 -06:00
Eric
b84424e879 bismark: Create new package (#7795) 
* bismark: Create new package

* bismark: fix dependency types
 2018-04-17 14:45:10 -05:00
Yifan Zhu
b4bdf0db80 psmc: new package (#7773) 
* psmc: new package

* psmc: changed version number

* psmc: overwrite build phase
 2018-04-17 13:30:30 -05:00
Eric
8e58bf21cf perl-statistics-pca: Create new package (#7796) 
* perl-statistics-pca: Create new package

* perl-statistics-pca: fix dependency types
 2018-04-17 13:30:12 -05:00
Matteo Guglielmi
8afdf3d148 r-biomart: package update (#7787) 2018-04-17 12:55:36 -05:00
Matteo Guglielmi
65da62751f r-delayedarray: package update (#7788) 2018-04-17 12:55:20 -05:00
Eric
d49182cb7a DIAMOND: add versions 0.9.19, 0.8.38, 0.8.26 (#7789) 2018-04-17 12:55:08 -05:00
Matteo Guglielmi
abbd51cd21 r-summarizedexperiment: package update (#7790) 2018-04-17 12:54:56 -05:00
Matteo Guglielmi
02181c951a r-genomicalignments: package update (#7791) 2018-04-17 12:54:36 -05:00
Matteo Guglielmi
025e608fd5 r-bsgenome: package update (#7792) 2018-04-17 12:54:04 -05:00
Matteo Guglielmi
7171f31425 r-topgo: package update (#7793) 2018-04-17 12:53:37 -05:00
Matteo Guglielmi
c392bfc7d6 r-s4vectors: package update (#7779) 
* r-s4vectors: package update

* r-s4vectors: dependencies fix
 2018-04-17 10:04:37 -05:00
Matteo Guglielmi
5272ed5ad0 r-biobase: package update (#7785) 2018-04-17 10:04:24 -05:00
Matteo Guglielmi
8907161c93 Package/r-iranges (#7780) 
* r-iranges: package update

* r-iranges: package update

* r-iranges: dependencies fix
 2018-04-17 09:36:12 -05:00
Matteo Guglielmi
c2559bdef3 r-genomicranges: package update (#7782) 
* r-genomicranges: package update

* r-genomicranges: dependencies fix
 2018-04-17 09:33:24 -05:00
Matthias Maiterth
ed4d0c5a87 Package/geopm (#7560) 
* geopm: Added initial files for package geopm
and py-natsort dependency

* geopm: Updated variants for hwloc and mpi defaults

* geopm: Cleaned up unwanted hyphenation in description.

* geopm: updates according to change request.

* geopm: Updated minor change requests.

Clarification for ruby-ronn dependency included as a TODO.
This requires changes in the current configure and build process
which will be changed in a future version.

* geopm: changed to AutotoolsPackage and fixed hwloc

The changes for hwloc required to add a specific version bc of a
conflicting version of openmpi's hwloc dependency being below
1.99. This works but updates to this package should check if this
restriction is still required. (Thus TODO added)

* geopm: Added link dependencies (thanks for pointing this out).

Also removed empty line below class definition.

* geopm: Fixed depends_on according to package guide.

Removed wrong type 'run' and removed types for numactl, mpi and hwloc
to use default build & link type.

* geopm: Fixed and updated +doc dependencies

new pacakge ruby-ronn (package specified as in ruby-narray package)
Updated second +doc dependency doxygen.

* geopm: Changed args for Autotools specific feature.

Added enable_or_disable and with_or_without instead of if cascade.
Added overhead variant.
Also added missing dependency (default: build&link) for json-c).
 2018-04-17 07:51:56 -05:00
Geoffrey Oxberry
40f0305bfa glvis@3.3: new package (#7166) 
* glvis@3.3: new package

* mesa-glu: now provides 'glu' (GL Utility library)

* openglu: add package, provides glu

* [GLVis] Use MakefilePackage as base. Add 'develop' version.

Small tweaks in the makefile arguments.

* [GLVis] Locate the X11, GL and GLU libraries within their respective
prefixes. Set the C compiler in the makefile arguments.

* [GLVis] Fix a bug: the same variable was used for two different things.

* [libx11] Add the libs property

* [OpenGL] Add the libs property

* [OpenGLU] Add the libs property

* [GLVis] Use the libs properties of libx11, opengl, and openglu
 2018-04-17 07:48:48 -05:00
Matteo Guglielmi
07ebcb7f6b r-biocgenerics: package update (#7778) 2018-04-17 07:43:26 -05:00
Matteo Guglielmi
f4cc57261b r-genomeinfodb: package update (#7781) 2018-04-17 07:43:11 -05:00
Matteo Guglielmi
1c8df39024 r-htmltable: package update (#7767) 
* r-htmltable: package update

* r-htmltable: dependency fix

* r-htmltable: dependency fix #2

* r-htmltable: dependency fix #3
 2018-04-17 07:26:37 -05:00
Christoph Junghans
b6d3feba20
ospac: fix compiler usage and install (#7776) 2018-04-16 15:56:37 -06:00
Yifan Zhu
e94808a560 miniasm: new package (#7772) 2018-04-16 16:06:09 -05:00
Yifan Zhu
625ead40e3 fermikit: new package (#7775) 2018-04-16 15:54:05 -05:00
Matteo Guglielmi
385a209ff9 r-limma: package update (#7763) 
* r-limma: package update

* r-limma: dependency fix
 2018-04-16 11:49:40 -05:00
Michael F. Herbst
61b3e60f1f Add libcint version 3.0.11 (#7764) 2018-04-16 11:49:13 -05:00
Matteo Guglielmi
63d8f87f54 r-hmisc: package update (#7766) 2018-04-16 10:16:00 -05:00
Matteo Guglielmi
be934c5781 r-data-table: package update (#7768) 2018-04-16 10:14:20 -05:00
Matteo Guglielmi
3ae6dd9f64 r-matrix: package update (#7769) 2018-04-16 10:14:00 -05:00
Matteo Guglielmi
33f2200bf7 r-deseq2: package update (#7770) 2018-04-16 10:13:45 -05:00
healther
d0c388ca68 add version 2.0.9 to py-slurm-pipeline (#7771) 
Change-Id: I6b597076b0740d65b8aeaebf95f459745b1b1503
 2018-04-16 10:13:06 -05:00
Christoph Junghans
826c1f88a3
votca-moo: removal (#7762) 
votca-moo is now part of votca-ctp (see votca/ctp#93)
 2018-04-14 16:18:11 -06:00
Christoph Junghans
dae4653920 eospac: initial commit (#7761) 
* eospac: initial commit

* eospac: add stable version
 2018-04-14 14:14:38 -05:00
Eric
c8f78676eb perl-moose: Add versions 2.2007,2.2009,2.2010 (#7758) 2018-04-13 19:08:13 -05:00
Eric
1d0ecce49f perl-devel-overloadinfo: Add version 0.005 (#7754) 2018-04-13 16:58:50 -05:00
Eric
b6a130703d prank: Add version 170427 (#7755) 2018-04-13 16:58:39 -05:00
Eric
d602d04d46 tcl: Add version 8.6.8 (#7756) 2018-04-13 16:58:25 -05:00
Eric
eaaf1666ba tk: Add version 8.6.8 (#7757) 2018-04-13 16:58:13 -05:00
Massimiliano Culpo
94fbd7b60d
flux: changed default value for doc variant to False (#7749) 
fixes #2095
 2018-04-13 15:58:58 +02:00
Raghu Raja
ef253f9db4 libfabric: added v1.6.0 and v1.5.3 (#7742) 2018-04-13 09:09:54 +02:00
Adam J. Stewart
b9b19e1660 Fix www.example.com homepages (#7744) 2018-04-13 07:08:10 +02:00
Eric
21914d36be py-illumina-utils: Create new package (#7745) 
* py-illumina-utils: Create new package

* fix dependency types
 2018-04-12 22:45:21 -05:00
Eric
0091fda57b perl-contextual-return: Create new package (#7741) 
* perl-contextual-return: Create new package

* perl-contextual-return: Fix homepage url
 2018-04-12 15:56:07 -05:00
Yifan Zhu
7d8e6b2eda New package r-tmixclust (#7658) 
* r-tmixclust: new package

* r-cluster: hash changed

* r-cluster: removed 2.0.6 and added the latest 2.0.7-1
 2018-04-12 14:51:51 -05:00
Howard Pritchard
f5e4befcac UCX: update for release 1.3.0 (#7740) 
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
 2018-04-12 14:51:25 -05:00
Eric
11cbee6e92 perl-perlio-utf8-strict: Create new package (#7738) 2018-04-12 14:02:37 -05:00
Yifan Zhu
fde1e0ecb8 supernova: new package (#7719) 
* runing a test

* supernova: new package

* removed with working_dir line
 2018-04-12 13:31:18 -05:00
Eric
89b5403b79 perl-text-simpletable: Create new package (#7739) 2018-04-12 13:29:51 -05:00
Yifan Zhu
8a4268837e New package r-spem (#7657) 
* r-truncnorm: new package added

* r-solnp: new package added

* r-spem: new package added

* r-truncnorm: removed dependency r-testthat
 2018-04-12 12:55:10 -05:00
Eric
61875784df perl-math-matrixreal: Create new package (#7737) 2018-04-12 12:53:53 -05:00
healther
bc379ab919 fix dependencies for matplotlib@2.2.2 (#7735) 2018-04-12 12:53:30 -05:00
Eric
41867cf007 perl-want: Create new package (#7734) 2018-04-12 12:24:28 -05:00
Geoffrey Oxberry
bbdf586d14 glu: new virtual package; openglu: new package (#7162) 
* mesa-glu: now provides 'glu' (GL Utility library)

* openglu: add package, provides glu

* openglu: add custom fetcher, remove nonsense url

Change openglu package to look like the opengl package in GitHub PR

* [OpenGLU] Fix a typo
 2018-04-12 07:16:16 -07:00
Geoffrey Oxberry
0e4e7d05e4 opengl: make error throw on install, not fetch (#7063) 
* opengl: make error throw on install, not fetch

* opengl: add configuration advice for darwin

* opengl: add more versions of GL/OpenGL

* opengl: improve documentation in comments

* [OpenGL] Fix formatting
 2018-04-12 07:14:38 -07:00
healther
3608c4d3b5 add package py-gdbgui (#7715) 
* add package py-gdbgui

Change-Id: I553e1e4c4f6385348190817199e05b25522b57b4

* fix alignment

* add setuptool runtimedependency

* add gdb run dependency
 2018-04-11 21:30:23 -05:00
healther
3b44a2ff40 Add package py-slurm-pipeline (#7681) 
* add package py-slurm-pipeline

Change-Id: Iade405a7e96f04e476cea76e460cac2ebdf21f95

* add missing py-six dependency

Change-Id: I382fa4139880c1a61af3f314c74ed6e7c2e88c5b

* Update package.py

* Update package.py

* Update package.py

* fix flake8
 2018-04-11 14:25:08 -05:00
Simon Flood
ed5f68211e Add ANTs package (#7717) 
* Add ants package

Add a package for ANTs (version 2.2.0)

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py
 2018-04-11 14:22:23 -05:00
healther
a23e319dac add package py-python-socketio (#7721) 
* add package py-python-socketio

* fix indention

* add description to eventlet variant

* fix dependencies

Change-Id: I425ae165dfcce30df6cbbd671cd6ef1bef5078dc

* Update package.py

* Update package.py

* Update package.py

* Update package.py
 2018-04-11 14:21:37 -05:00
peetsv
af13236d68 py-cnvkit: add new package (#7688) 
* py-cnvkit: add new package

* updating dependencies

* correcting flake8 error

* adding py-setuptools dependency
 2018-04-10 20:25:32 -05:00
healther
9ba7ecb1de add package py-gevent (#7712) 
* add package py-gevent

Change-Id: I49722e02a961f20b9177ae8575b78b42bf6c01c9

* fix alignment

* add cffi dependency
 2018-04-10 20:24:11 -05:00
healther
4eeec729ea add package py-eventlet (#7722) 2018-04-10 20:22:45 -05:00
healther
70754c5d21 add package py-greenlet (#7720) 
* add package py-greenlet

* remove optional setuptools dependency
 2018-04-10 20:22:28 -05:00
healther
6508a2c3d3 add package py-python-engineio (#7723) 
* add package py-python-engineio

* flake8 fix
 2018-04-10 20:21:57 -05:00
Christoph Junghans
45ddfe83ef lammps: add v20180316 (#7725) 
* lammps: add v20180316

* add latte@1.1.1 and make lammps use it
 2018-04-10 20:21:35 -05:00
Daniel Topa
dbb7f8e13a hwloc: add v 2.0.1 (#7724) 
Signed-off-by: Dan Topa <dantopa@lanl.gov>
 2018-04-10 20:20:09 -05:00
Michael Kuhn
e7760f1f59 go: Update to 1.10.1 (#7708) 
Also update go-bootstrap to the 20171003 snapshot.
 2018-04-10 14:41:52 -05:00
healther
8dac669a87 add package py-pygdbmi (#7711) 
* add package py-pygdbmi

Change-Id: I9850ccecebb1d46e983cda39c371caab23ad61e9

* add runtime setuptools dependency (from distutils import)

* remove unnecessary run dependency
 2018-04-10 14:35:26 -05:00
thecorkscrew
3bd74f1858 Added C-Lime Package (#7707) 
* Added C-Lime Package

* Small fix
 2018-04-10 12:05:05 -05:00
healther
f278f512cc add py-cython@0.28.1 (#7709) 
Change-Id: I7e3931f8224a367ce1657256b3100139abcc4f86
 2018-04-10 12:03:51 -05:00
healther
ab7e2a5c9e add py-flask@0.12.2 (#7710) 
Change-Id: I51887f661e6dd896a9f740b51f4e81bdf532f9b4
 2018-04-10 12:03:17 -05:00
healther
a59aef7c78 add package py-flask-compress (#7713) 
* add package py-flaks-compress

Change-Id: Ia67f292364f339907c7c0a5bd707a7a1e69877be

* fix alignment

* linebreak to make flake8 happy
 2018-04-10 11:58:35 -05:00
healther
431a3068b6 add package py-flask-socketio (#7714) 
* add package py-flask-socketio

Change-Id: Ib9bb41b9c3de06f07ffb47449edf02476827b610

* fix alignment

* add missing werkzeug dependency
 2018-04-10 11:57:06 -05:00
peetsv
f8765593e0 Perl file copy recursive 0.40 (#7718) 
* perl-file-copy-recursive: add newer version v0.40
 2018-04-10 11:48:02 -05:00
Adam J. Stewart
eac2defed5
Add latest versions of libxcb and xcb-proto (#7650) 2018-04-10 11:47:02 -05:00
Adam J. Stewart
69f94f18a3
Fix GCC 6/7 build on APFS (#7696) 2018-04-10 11:46:44 -05:00
lingnanyuan
ecc481a9a7 fermi: Create new package. (#7702) 
* fermi: Create new package.

* fermi: Add missing dependency.

* fermi: Change dependency type of perl to run.
 2018-04-10 08:52:21 -05:00
lingnanyuan
dc8c8311c6 wgsim: Create new package. (#7674) 
* wgsim: Create new package.

* fix flake8 error.

* wgsim: change cc compiler to spack_cc.

* add missing dependency.
 2018-04-09 14:23:11 -05:00