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Author SHA1 Message Date
Eric
0dddb98869 metabat: Create new package (#7991) 
* metabat: Create new package

* fix Perl script shebangs and BOOST_ROOT environment

* add perl script fix function

* add perl dependency and fix positional argument for Python 2.6
 2018-05-06 10:56:03 -05:00
healther
17ce5fd912 Add package wireshark and dependencies (#8024) 
* add wireshark

Change-Id: I1ef674ff286db2e06baaf9fca65982d1145cfa79

* fix qt4 build

Change-Id: Ieb9989b9fec1a0e02388197f971ee66b591d45c5

* remove commented lines

Change-Id: Ia67bfaf1beba06dd710cee56aec06bc36b293d34

* flake8 fix

Change-Id: Ica1b2cce2be2faca82a4177c3cdc3a0bb005c031

* remove clutter

Change-Id: I6061fe56a88f8c7b7e03fdce5e3eae04036ad2d8

* fix dependencies

Change-Id: I8160c70c9333c9f5e82ed5fc73633455df568972

* use dot syntax instead of join_path

Change-Id: Id1f737299b603fa4093b58571d46a64b0dd84895
 2018-05-06 09:32:06 -05:00
Adam J. Stewart
b83be5f2d4
macOS-specific patch no longer applies to GCC 8 (#8029) 2018-05-06 09:28:33 -05:00
Elizabeth Fischer
f3c9b98bbd py-udunits: New package (#7998) 
* py-udunits: update

* Use standard py-netcdf4

* Remove unnecssary import?

* Suggested simplifications

* flake8
 2018-05-05 17:33:44 -05:00
健美猫
e499a4d071 A new library: libshm. (#8028) 2018-05-05 17:16:48 -05:00
健美猫
dfe0752807 Bump pysam to 0.14.1. (#7988) 
* py-pysam requires curl.

* py-pysam conflicts with htslib@1.7.

* Bump py-pysam versions.

* Add more dependencies.
 2018-05-04 22:11:26 -05:00
sknigh
4fe6d9acee Added GCC 8.1.0 (#8026) 
Built once on Centos 7 w/ external GCC 4.8.5 compiler
 2018-05-04 18:52:03 -05:00
Jungwon Kim
cd80c7cf18 a new package: papyrus. (#8023) 
* a new package: papyrus.

* removed the empty cmake_args

* changed md5 checksum for v1.0.0

* make a long line short

* one long line url
 2018-05-04 18:51:37 -05:00
健美猫
c53541e448 Bump samtools, hstlib and bcftools to version 1.8. (#8020) 
* Bump samtools and hstlib to version 1.8.

* rm .bak.

* Bump bcftools to 1.8.

* bcftools@1.8 depends on libzip.
 2018-05-04 16:27:54 -05:00
Elizabeth Fischer
490cde87dd py-more-itertools: new package (#8004) 
* py-more-itertools: new package

* code review
 2018-05-04 16:27:14 -05:00
健美猫
51c2dbb707 Hic-Pro: fix a typo and replace hard-coded version. (#8022) 
* Fix a typo and replace hard-coded version.

* version -> self.version.
 2018-05-04 10:56:04 -05:00
Massimiliano Culpo
0570b075d4
openmpi: don't build static libraries if slurm is activated (#8021) 
According to this comment:

    https://github.com/open-mpi/ompi/issues/4338#issuecomment-383982008

on an OpenMPI issue, using `--enable-static` silently disable slurm
support.
 2018-05-04 16:27:54 +02:00
Elizabeth Fischer
593ad23a9f gdal: update (#8008) 
* gdal: update

* Remove unneeded depends(python)
 2018-05-03 22:55:31 -05:00
健美猫
0812fd1635 Bump r-rcpp versions. (#8016) 2018-05-03 22:54:45 -05:00
Elizabeth Fischer
ea4829880f pism: new package (#8010) 
* pism: new package

* Implement code review

* Remove pointless docstring5

* Fixed missing trailing quote
 2018-05-03 22:54:00 -05:00
Elizabeth Fischer
d52eb8b34d py-numpy: update (#8003) 
* py-numpy: update

* Better constrain when can / cannot parallel build.

* Update SciPy parallel logic to be specific to Python 3.5+, same as in Numpy.
 2018-05-03 22:53:41 -05:00
Elizabeth Fischer
60c1e41e4c py-bsddb3: update (#8006) 
* py-bsddb3: update

* Change py-setuptools to build dependency
 2018-05-03 19:20:14 -05:00
Elizabeth Fischer
ffcf3ef2c8 pfunit: update (#7994) 2018-05-03 17:02:20 -05:00
Elizabeth Fischer
28adaa4e55 Everytrace: update (#7995) 2018-05-03 17:00:21 -05:00
Elizabeth Fischer
7542fbfefd py-yamlreader: new package (#7997) 2018-05-03 16:58:40 -05:00
Elizabeth Fischer
5656529974 gmp: update (#7999) 2018-05-03 16:53:19 -05:00
Elizabeth Fischer
bf896c5a43 py-scipy: update (#8000) 2018-05-03 16:52:46 -05:00
Elizabeth Fischer
e93c880a79 py-pyside: update (#8002) 2018-05-03 16:50:55 -05:00
Elizabeth Fischer
ebca867496 py-cython: update (#8005) 2018-05-03 16:46:15 -05:00
Eric
2aea56da07 genomefinisher: Create new package (#7989) 2018-05-03 13:11:00 -05:00
Eric
a128fa88c5 py-crispresso: Create new package (#7990) 
* py-crispresso: Create new package

* py-crispresso: Create new package
 2018-05-03 13:09:59 -05:00
Kelly (KT) Thompson
7846dfa817 New Package: ruby-svn2git (#7979) 
* New Package: svn2git

https://github.com/nirvdrum/svn2git

svn2git is a tiny utility for migrating projects from Subversion to Git while
keeping the trunk, branches and tags where they should be. It uses git-svn to
clone an svn repository and does some clean-up to make sure branches and tags
are imported in a meaningful way, and that the code checked into master ends up
being what's currently in your svn trunk rather than whichever svn branch your
last commit was in.

* Actually requires +perl variant of subversion.

* fix style issue.
 2018-05-03 10:12:57 -05:00
健美猫
c8157e31e1 A new package: nanopb. (#7981) 
* A new package: nanopb.

* flake8.

* Remove py-pytorch.
 2018-05-03 10:12:37 -05:00
健美猫
78d8bd7d40 Bump pgi to 18.4. (#7980) 
* Bump pgi to 18.4.

* Remove the empty line.

* Update.
 2018-05-03 10:12:17 -05:00
健美猫
05f51c46dd Bump gatk version to 4.0.4.0. (#7985) 
* Bump gatk version to 4.0.4.0.

* Update.

* Fixed.

* Fixed.
 2018-05-03 10:08:48 -05:00
健美猫
fb9898230e A new package: py-openslide-python. (#7907) 
* A new package: py-openslide-python.

* Update.

* Remove py-pytorch package.

* Remove nektar package.

* Remove install_time_test_callbacks
 2018-05-03 08:37:52 -05:00
Michael Kuhn
937ab7d5cc go: Update to 1.10.2 (#7982) 2018-05-03 12:14:52 +02:00
Elizabeth Fischer
cbd77e3a8d make symlinking python3->python optional (#7960) 
* Make symlinking python3->python optional
* Added reference to PEP 394
 2018-05-02 12:26:30 -07:00
Adam Moody
7909e15d83 mvapich2: add 2.3rc2 (#7976) 2018-05-02 14:23:32 -05:00
Elizabeth Fischer
f054fa2f43 sphinx: Updated to v1.7.4 (#7977) 
* sphinx: Updated to v1.7.4

* Update package.py
 2018-05-02 14:23:02 -05:00
Tim Law
73ded1a60c Added BookLeaf_Cpp and Typhon packages. (#7969) 2018-05-02 10:45:30 -05:00
Michael F. Herbst
f1ce2e3351 Add libcint version 3.0.12 (#7972) 2018-05-02 10:44:58 -05:00
Eric
fdc6ea0645 bedops: Create new package (#7956) 
* bedops: Create new package

* fix install method
 2018-05-02 08:14:00 -05:00
David Wootton
c23387e89b Fix Spectrum MPI package spec file for PGI compilers (#7964) 
* Added magma package

* Incorporated Serban's change

* Remove deleted files

* argparse.py

* Sync forked Spack repo in github

* Use reported version of IBM XL Fortran compiler for compiler versions
>= 16.0.

Starting with the April 2018 release, the IBM XL C and Fortran
compilers report the same version, 16.0.  Consequently, there is
no need to downgrade the Fortran compiler version to match that
of the C compiler.

* Eliminate blank lines.

* Update the Spectrum MPI package.py file to specify the correct compilation
scripts for the PGI compilers.
 2018-05-02 08:12:08 -05:00
Christoph Junghans
9d1456393f
openmc is not a proxy (#7968) 
https://github.com/spack/spack/issues/7965#issuecomment-385953224
 2018-05-02 06:48:16 -06:00
Adam Moody
29b47e0e01 mvapich2: add registration cache and file systems variants (#7948) 
* mvapich2: add registration cache and file systems variants, avoid empty --with-pm= if no process manager is specified, add missing leading dash in --disable-silent-rules
 2018-04-30 18:12:13 -07:00
Adam Moody
2db4beac12 mpifileutils: roll back to dtcmp v1.0.3, add option to build master branch (#7949) 
* mpifileutils: roll back to dtcmp v1.0.3 due to API change, add option to build master branch

* add comment to explain why certain dtcmp is required, rename version for git branch

* dtcmp v1.0.2 is missing github tarball
 2018-04-30 18:46:17 -05:00
Eric
7088e547a3 vt: Create new package (#7947) 2018-04-30 12:11:06 -05:00
健美猫
094eb5f9a8 Build shared libs for tinyxml. (#7914) 2018-04-30 10:03:24 -05:00
Kelly (KT) Thompson
d02b5b96d3 Patch eospac package to allow compilation with %clang. (#7928) 
When building eospac with %clang, spack's Fortran compiler wrapper is called
'flang', which is rejected by the eospac build system..Allow compilation with
%clang by patching the eospac build system.

My testing only covers %clang where flang is actually gfortran.  However, this
patch only registers 'flang' as a known Fortran compiler and does not set any
flags or options that are compiler specific.
.
 2018-04-29 18:40:27 -06:00
Christoph Junghans
810fe884d0 mfem: fix concretization (#7923) 
* mfem: fix concretization

* Fix hypre deps again

* Update package.py
 2018-04-28 07:16:43 -05:00
Chris Green
dec7a10249 Update with recent versions through 4.8.3 and add variants. (#7933) 
Add configurable HTTP, Python and readline support.

Add previously missing dependencies.

Minor patch to improve Python support (see https://github.com/xrootd/xrootd/pull/695).
 2018-04-27 10:11:33 -05:00
Levi Baber
dfc4a2aef1 bcftools: new version (#7930) 2018-04-26 22:48:01 -05:00
Sinan
581a240c86 add versions 3.4.3. and 3.5.0 (#7929) 2018-04-26 21:12:17 -05:00
Levi Baber
310addea91 samtools: new version (#7921) 2018-04-26 17:17:00 -05:00
Sergey Kosukhin
0f35f00b6e Use GitLab's API endpoint for fetching a git snapshot. (#7881) 
* Use GitLab's API endpoint for fetching a git snapshot.

* More GitLab packages use the API.

* find_list_url for GitLab's API URLs.

* Flake8

* Url for 'hacckernels'.

* Check GitLab API regexps before the non-API ones.
 2018-04-26 16:40:11 -05:00
healther
8afdaa5805 add patch to get aspell to build on OSX (#7919) 2018-04-26 15:19:52 -05:00
Simon Flood
6a99ca362f Add Trinity package (#7828) 
* Add Trinity package

New package to install Trinity - another odd installer (assumes installation to /usr/local/bin and doesn't copy dot files hence deleting them)

* Update package.py

added dependencies from https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity

* Update package.py

Copy tree to prefix.bin so that PATH can correctly be set for the Trinity command - can't split it off as it seems everything needs to stay together.

* Update package.py

Fixed over-length lines and space before comma
 2018-04-26 09:11:58 -05:00
Sergey Kosukhin
fd85c1f0c0 Package 'gdbm': do not set CC. (#7912) 2018-04-26 08:44:17 -05:00
Geoffrey Oxberry
d54ceb6ce7 mfem: add valid range of hypre version numbers (#7903) 
This commit fixes #7900.

In short: in the absence of constraints to the contrary, spack will
download the preferred version of a package, which is usually the most
recent non-develop version. On a clean spack installation without
hypre installed, `spack install mfem` will download hypre 2.14.0,
which is API-incompatible with mfem 3.3.2 (and earlier versions of
mfem), so spack will throw compiler errors re: the API mismatch.

This commit fixes that error by restricting mfem release versions
3.3.2 and earlier to hypre version 2.10.b to 2.13.999 (only 2.13.0
currently exists, but if it has a non-2.14.x maintenance release,
these versions of hypre should also be permitted).
 2018-04-26 08:43:20 -05:00
Denis Davydov
2ec701d1dd adol-c: add boost optional dependency (#7905) 2018-04-26 08:42:03 -05:00
健美猫
3b82124d96 A new package: loki. (#7908) 
* A new package: loki.

* Flake8.
 2018-04-26 08:37:03 -05:00
Massimiliano Culpo
50122a585a
Added the latest versions of a few packages (#7910) 
* automake: added version 1.16.1

* lmod: added version 7.7.29

* git: added version 2.17.0

* tmux: added version 2.7

* scala: added version 2.12.5, fixed typo in version 2.10.6

* Added spark@2.3.0, hadoop@3.1.0, jdk@8u172-b11

* picard: added version 2.18.3

* tar: added version 1.30
 2018-04-26 14:46:45 +02:00
健美猫
e2092896b9 A new package: openslide. (#7906) 2018-04-26 07:17:15 +02:00
Bruno Turcksin
de9894a063 Add boost 1.67.0 (#7889) 
* Add boost 1.67.0

* Remove boost 1.67.0 release candidate and the associated patch
 2018-04-25 21:00:22 -05:00
mcneish1
94afb2430c Additional r packages (#7892) 
* Add r-bbmisc

* Add r-dicekriging

* Add r-lhs

* Add r-mco

* Add r-misc3d

* Add r-mlr

* Remove boilerplate from r-mlr package

* Add r-mlrMBO

* Add r-parallelmap

* Add r-paramhelpers

* Add r-plot3d

* Add r-rgenoud

* Add r-smoof

* Add r-rinside 0.2.14

* Fix flake8 issues

* Add specific required versions

* Add more up-to-date versions of r-{mco, mlr, mlrMBO, smoof}
 2018-04-25 20:59:46 -05:00
Robert Pavel
28901c8104 Added OpenMP Variant for Kokkos (#7902) 
Added OpenMP variant for kokkos that can be disabled to build and test
on platforms where OpenMP is not available or desired. Also updated
version list
 2018-04-25 10:50:58 -05:00
Levi Baber
a4e786a415 openmpi: libfabric support, ucx cleanup (#7842) 
* openmpi: libfabric support, ucx cleanup

* openmpi: remove unnecessary parentheses
 2018-04-25 10:37:48 -05:00
Levi Baber
7120e59c6a Libfabric: updating fabrics & adding deps (#7838) 
* libfabric: mxm deprecated, adding mlx aka ucx

* libfabric: adding dependencies that we have in spack
 2018-04-25 10:35:36 -05:00
Levi Baber
14e0307f04 ucx: needs numactl and rdma-core (#7836) 2018-04-25 10:34:55 -05:00
Levi Baber
a7ecb0364a psm: new package (#7834) 
* psm: new package

* psm: setting latest stable to preferred
 2018-04-25 10:34:31 -05:00
Levi Baber
0b284b45db rdma-core: new package (#7835) 
* rdma-core: new package

* rdma-core: change to platform conflict
 2018-04-25 10:33:30 -05:00
Levi Baber
a21571e737 libnl: new package (#7833) 
* libnl: new package

* libnl: change platform constraint to a conflict
 2018-04-25 10:33:01 -05:00
Sajid Ali
24f15a5f4b Added checksums for newer versions of numpy (#7853) 
*  Committer: sajid <sajid@xrmlite.phys.northwestern.edu>

	modified:   var/spack/repos/builtin/packages/py-numpy/package.py

* Corrected typo

* removing whitespace

* remove whitespace

* remove whitespace, if not will do this in vim
 2018-04-25 10:30:25 -05:00
Eric
4fdd24effa py-testinfra: Create new package (#7883) 
* py-testinfra: Create new package

* py-testinfra: flake8 fixes

* py-testinfra: fix pytest version dependency

* py-testinfra: fix py-importlib version dependency
 2018-04-25 10:29:45 -05:00
Levi Baber
0d5dd96762 fabtests: new package (#7837) 
* fabtests: new package

* fabtests: fix hashes for github archive behavior & add libfabric dep

* fabtests: both versions confirmed working

* fabtests: use developer provided archive
 2018-04-25 10:29:29 -05:00
健美猫
48a3cc67fc Add a new package: gloo. (#7894) 
* Add a new package: gloo.

* Remove dependencies.
 2018-04-25 10:05:16 -05:00
健美猫
fca267468e Add a new package: cpuinfo. (#7895) 2018-04-25 10:04:45 -05:00
健美猫
7095d4f414 Add a new package: fp16. (#7896) 2018-04-25 07:30:07 -05:00
Daniel Topa
82ac1571c2 Openmpi update multithread (#7893) 
--enable-mpi-thread-multiple option not viable in Open MPI 3.0+

Signed-off-by: Dan Topa <dantopa@lanl.gov>
 2018-04-25 07:01:17 +02:00
Eric
5f04b0c538 new package: py-weblogo (#7886) 2018-04-24 19:31:37 -07:00
Denis Davydov
f7da156879 petsc and slepc: add 3.9.0; hypre: add 2.14 (needed by petsc) (#7877) 2018-04-24 07:10:46 -05:00
Eric
8e1a7eaafa ARAGORN: Create new package (#7875) 2018-04-23 16:51:42 -05:00
Eric
e3c708fafe prinseq-lite: Create new package (#7873) 
* prinseq-lite: Create new package

* prinseq-lite: set variant description and add dependency type
 2018-04-23 16:11:27 -05:00
Ross Miller
b5d9a44e17 7851 pmix aarch64 (#7852) 
* Fix build issue with PMIx on aarch64

Work around a bug in PMIx that causes build issues on aarch64.  Bug was
fixed in PMIx 2.1.1, so the spack package checks both the architecture
and the PMIx version.  Workaround is to just not build the PMIx test and
example code.

* Minor code cleanups

Minor corrections to make 'spack flake8' happy.

* Add support for version 2.1.1
 2018-04-23 14:09:52 -05:00
Mark Olesen
50fb9352f0 New colm, ragel packages (#7867) 
- Ragel is a parser and finite state machine generator that can be
  used as an alternative means for solving parsing problems without
  Flex.
 2018-04-23 10:50:58 -05:00
健美猫
b33f01c799 Add a new version 5.4.1.7 for mono. (#7866) 2018-04-23 07:31:29 -05:00
Dan Ibanez
130d0c8b2e omega-h: new package (#7861) 
* omega-h: new package

* omega-h: fix multiple package.py issues

* omega-h: use tarball checksum to avoid warning

* omega-h: wrap lines for flake8
 2018-04-22 17:26:52 -05:00
Sinan
af82f5529d new package: racon (bioinformatics) (#7726) 
* new package: racon (bioinformatics)

* add cmake_arg method
 2018-04-22 07:54:48 -05:00
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
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