Commit graph

5970 commits

Author SHA1 Message Date
Eric
d6c6a7016f manta: Create new package (#8043)
* manta: Create new package

* manta: Create new package

* manta: fix dependency types
2018-05-07 17:22:43 -05:00
Eric
fa93df49bd py-pysqlite: Create new package (#8042) 2018-05-07 13:42:24 -05:00
Denis Davydov
3a88227c83 perl: add 5.26.2 (#7984)
* perl: add 5.26.2

* perl: add 5.22.4

* move Misc releases to EOL
2018-05-07 13:40:32 -05:00
Christoph Junghans
b5c6bbb2a2
pkgconf: use alpine linux mirror to avoid ssl error (#8039) 2018-05-07 10:46:58 -06:00
anne-glerum
9557a6881f Add patch (#8034) 2018-05-07 09:51:27 -05:00
Andrey Prokopenko
231664e22c trilinos: minor cleanup (#7987) 2018-05-07 06:45:49 -05:00
Eric
df575382ba py-dlcpar: Add package description (#8032) 2018-05-07 06:44:16 -05:00
Stephen McDowell
506f8e9f3e add opencv 3.4.1 (#8031) 2018-05-06 21:40:27 -05:00
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