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5854 commits

Author SHA1 Message Date
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
Sinan
c1e3e5de5c new package "DSRC" (bioinformatics) (#7680) 
* new package "DSRC" (bioinformatics)

* remove uncommented line

* get rid of unnecessary import

* convert to MakefilePackage class

* get rid of make() in install phase, remove spaces

* make flake8 happy!
 2018-04-08 08:21:02 -05:00
Axel Huebl
2b0252ccb3 Add Package: nlohmann_json (#7690) 
Adds a spack package for the JSON C++ library
  https://github.com/nlohmann/json
 2018-04-07 11:00:00 -05:00
Axel Huebl
5c98b8bde5 Catch2: make install (#7668) 
Add a proper install variant for Catch(2).

This allows to use Catch2 downstram with `pkg-config` and
CMake's `find_package` commands via standard environment hints.
 2018-04-07 10:36:10 +02:00
peetsv
3bf863bb06 py-pyfaidx: adding new package (#7684) 
* py-pyfaidx: adding new package

* updating the url
 2018-04-06 20:07:35 -05:00
carns
e1856f3129 Darshan 3.1.6 (#7686) 
* update darshan-util to 3.1.6, add bzip2 option

* add darshan-runtime 3.1.6
 2018-04-06 16:49:07 -05:00
Eric Müller
58a57bf391 Fix build of xerces-c (#7611) 
The build requires libiconv (but it doesn't find it when not providing
LDFLAGS).
 2018-04-06 15:46:47 -05:00
Sergey Kosukhin
c328c667c0 Package 'serf': link to the spack provided zlib installation. (#7667) 2018-04-06 15:44:39 -05:00
lingnanyuan
fa3edd4af0 hapdip: Create new package and its dependency k8. (#7685) 
* k8: Create new package.

* hapdip: Create new package.

* Change description.
 2018-04-06 15:40:58 -05:00
lingnanyuan
27b1069e0c readfq: Create new package. (#7673) 
* readfq: Create new package.

* fix flake8 error
 2018-04-05 17:23:25 -05:00
Adam J. Stewart
bde69177be Don't prepend Tcl/Python to PATH if in system directory (#7677) 2018-04-05 14:39:05 -07:00
healther
a63450bc45 add package py-discover (#7671) 
Change-Id: I67b9e4eb4dfd3a962b7fe8840f5eb012fcd009cc
 2018-04-05 09:18:07 -05:00
peetsv
ceab7e5f54 rsync: adding version 3.1.3 (#7669) 2018-04-04 18:13:50 -05:00
Denis Davydov
3f14212ded octopus: add 7.3 (#7666) 2018-04-04 16:35:03 +02:00
Massimiliano Culpo
79251dde40
mvapich2: added version 2.3rc1 + variant to use alloca if available (#7595) 
* mvapich2: added version 2.3rc1 + variant to use alloca if available

* mvapich2: removed version 1.9 + cleaned recipe
 2018-04-04 09:41:37 +02:00
lingnanyuan
b1a5764956 soapdenovo-trans: Create new package. (#7649) 
* soapdenovo-trans: Create new package.

* change header

* soapdenovo-trans: change package type to makefile.

* soapdenovo-trans: fix flake8 error.
 2018-04-03 17:46:25 -05:00
Denis Davydov
338fa8d7d6 fix dealii dependencies for Clang 9.1.0 C++17 (#7644) 
* fix boost and muparser for Clang 9.1.0 with C++17

* muparser: add C++11 flags

* dealii: temporary disable python by default

* dealii: make CMake find right python
 2018-04-03 10:15:09 -05:00
Matthias Diener
17ace14751 lsof: create new package (#7660) 2018-04-02 21:29:19 -05:00
Howard Pritchard
32c8237256 Open MPI: add 3.0.1 (#7661) 
Open MPI 3.0.1 bug fix release is out the door!

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
 2018-04-02 19:22:59 -05:00
Robert Pavel
a759fcf33e Current versions of kokkos conflict with hwloc 2.x (#7654) 
* Current versions of kokkos conflict with hwloc 2.x

Current versions of kokkos cannot build with hwloc v2.x due to changes
in the associated structs. Requiring v1.11.9 for the time being
until it becomes clear what the kokkos model will be

* Explicitly commenting fix for posterity

Explicitly commented version number of hwloc dependency for kokkos for
posterity purposes and to pass code coverage for speedy merging

* Generalized Kokkos's Hwloc Dependency

Generalized dependency to v1.x of hwloc

* Fixed Flake8 issue

Fixed comment to conform to flake8

* Fixed ordering for Version Requirements

Fixed ordering to indicate <= 1.11.9, not >1

* Generalized kokkos dependency
 2018-04-02 19:22:46 -05:00
Yifan Zhu
d9e057842a r-flexclust: new package (#7656) 2018-04-02 16:29:59 -05:00
Yifan Zhu
9d8ab78b32 r-gss: new package (#7655) 2018-04-02 16:29:20 -05:00
David Orman
5106efe495 Features/pindel (#7619) 
* added htslib 1.7 and checksum

* pindel:  added new package pindel

* pindel: added package pindel

* removed py-pybind11 edit

* made flake8 happy

* fixed additional flake8 errors

* added comments about Makefile2 and removed FIXME template section

* spelling
 2018-03-31 10:24:47 -05:00
David Orman
c032b2d9db Features/py breakseq2 (#7642) 
* added htslib 1.7 and checksum

* py-breakseq2: new package!!!!

* py-breakseq2: fixed whitespace

* py-breakseq2: added additional dependencies

* py-breakseq2: fixed build/run  depends

* py-breakseq2: added additonal dependencies
 2018-03-31 10:24:16 -05:00
healther
42c14e0fdb Fix build of boost@:1.58.999 +python (and +mpi) (#7630) 
* explicitly specify user-config.jam as it isn't found
  via the environment variable on older boost versions
  (cf. what debian/rules does)
  => fixes +mpi build
* fix "error: Ambiguous key" error on :1.58.999 boost
  (cf. https://github.com/boostorg/boost/blob/boost-1.59.0/bootstrap.sh#L357)
 2018-03-31 07:36:56 -05:00