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Author SHA1 Message Date
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
healther
6a0f9ccf82 make view understand hashes (#7573) 
Fixes #7548

This updates the "spack view" command to use the same parsing logic
as "spack install" on the user-provided specs. For example you can
provide a DAG hash to refer to an exact installed spec instead of
specifying name, compiler, etc.
 2018-04-04 10:40:56 -07:00
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
Adam J. Stewart
c50628ebdf Fix bug in test_find_with_globbing unit test (#7652) 2018-04-03 22:27:17 -07:00
Zack Galbreath
f613437a44 Do not call sys.exit() in except block (#7659) 
When an invalid spec is encountered by `parse_specs()` we now raise a
`SpackError` instead of calling `sys.exit()`
 2018-04-03 22:22:28 -07:00
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
Adam J. Stewart
cdefbd7475 Avoid double 'lib' for packages whose name already starts with lib (#7651) 2018-03-31 17:33:41 +02:00
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