Commit graph

5888 commits

Author SHA1 Message Date
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