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7717 Commits

Author SHA1 Message Date
wspear
76feb0205d New package: py-jupyterhub (#10461) 
This package depends on both python 3.5+ and node-js which depends on
python 2.7/2.8 to build. Currently it can only be installed if the
node-js package's python dependency is manually removed, so node-js
will build with python found on the system rather than provided by
spack. Upcoming commits may allow spack to reconcile this
automatically.
 2019-02-07 16:47:46 -06:00
Justin Stanley
ef89ae03bc mirdeep2 package: make sure bins are executable (#10515) 2019-02-07 13:05:19 -06:00
mathsen
570af0c313 Trilinos package: update superlu-dist dependency (#10511) 
Trilinos master branch gets the latest superlu-dist (currently 6.1.0)
 2019-02-07 12:58:45 -06:00
Satish Balay
b8684b318c petsc: petscvariables is used from user makefiles - so it should not have spack compilers listed (#10365) 2019-02-07 09:09:23 -06:00
Satish Balay
1d71a5ea57 petsc4py and libensemble: add @develop dependencies (#10539) 
* py-petsc4py: add @develop

* py-libensemble: add @develop dependency on py-petsc4py@develop
 2019-02-07 09:06:31 -06:00
Satish Balay
0ad1b2a2c8 petsc@xsdk-0.2.0: fix sowing dependency (#10535) 2019-02-07 09:05:43 -06:00
Satish Balay
753fec39ae xsdk@develop fixes (#10521) 
* xsdk@develop: switch trilinos from @master to @develop

* xsdk@develop: dtk - fix trilinos dependency on dtk.
 - dkt-3.0 should be used with trilinos-12.4*
 - dtk/master should be used with trilinos@develop
 2019-02-07 09:05:14 -06:00
Justin Stanley
09a884322f orthofiller: new package at 1.1.4 (#10373) 2019-02-07 10:22:36 +01:00
Gregory Lee
f0cb4580d1 fixed checksum (#10393) 2019-02-07 10:20:45 +01:00
Levi Baber
af7f1bb3ca new package: perl logger simple (#10509) 2019-02-07 10:19:07 +01:00
Levi Baber
07b5a6a512 perl-file-homedir: new package (#10533) 2019-02-07 10:09:20 +01:00
Levi Baber
4679c11098 py-biopython: new version (#10532) 2019-02-07 10:08:45 +01:00
Matthias Diener
d4d402586c cmake: add version 3.13.4 (#10538) 2019-02-07 09:15:32 +01:00
Justin Stanley
401d305f4e phrap-crossmatch-swat: new package at 1.090518 (#10529) 2019-02-06 19:13:44 -06:00
Owen Solberg
cdbaf8dfc5 mafft package: add version 7.407 (#10488) 2019-02-06 13:55:16 -06:00
Matthias Diener
6dbc1afe45 jdk package: add version 1.8.0_202 (#10536) 2019-02-06 13:54:02 -06:00
Levi Baber
0cf0fd47c8 New package: perl-object-insideout (#10508) 2019-02-06 13:53:33 -06:00
Matthias Wolf
5281403fb2 fmt package: fix cmake arguments (#10500) 2019-02-06 13:52:49 -06:00
Stephen Herbein
b028e99cac py-black: add new package 2019-02-06 13:50:04 -06:00
Stephen Herbein
4e92974ed1 py-toml: add latest version and update checksums to sha256 
A version >= 0.9.4 required for py-black.  Added latest, which is
0.10.0.  Manually verified that the .tar.gz for v0.9.3 used to generate
the sha256 matched the previous md5.
 2019-02-06 13:50:04 -06:00
Matthias Diener
bdabdb85ed curl package: add version 7.63.0 (#10516) 2019-02-06 13:48:36 -06:00
Douglas Duckworth
d053eac538 py-multiqc: add version 1.7 (#10520) 
Added sha256 for py-multiqc as well as require py-matplotlib < v 3.0
 2019-02-06 13:47:59 -06:00
Levi Baber
1a34bebe79 genemark et package: add version 4.38 (#10519) 
Also add heu_dir to bin/
 2019-02-06 13:46:35 -06:00
Jon Rood
11c52c3bf7 Paraview package: update PYTHONPATH for dependents (#10501) 
Add vtkmodules directory to PYTHONPATH in Paraview for Trilinos
 2019-02-06 12:45:14 -06:00
Daniel Topa
d9d75635c7 Add Python 3.7.2 updated (#10531) 
Also add versions 3.7.1, 3.6.8, 3.6.7, 3.6.6. Does NOT alter preferred version (2.7.15).

Supplants PR 10491 "Add Python 3.7.2" (https://github.com/spack/spack/pull/10491).

Verification builds on LANL Darwin:

**Intel Xeon**
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.7.2-d3p7vg6w2r563cpmwsmbgjbsiqc4j4fq
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.7.1-ibom6qj2z64egyaqz5htkwp5tr362il6
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.8-rkifc3c7mjgdglw27upiap767ut4wpkz
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.7-meuesn43twttt756exyzqgdhohjgipjq
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/general/opt/spack/linux-centos7-x86_64/gcc-4.8.5/python-3.6.6-qwnwme7otyuoqqudcglfmfy75t5npywl

**Arm**
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.7.2-qj27kzs4ttdqudm3hsi3pt57kv7lshco
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.7.1-io5eneirgvpegy3tosvp6wq5ndf7yjis
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.8-ej3vnvta2hbtrh7p5hokfqkuewxeqgsa
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.7-l3qnue72ewppn2wxza3w6l62l7ijlque
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/arm/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/python-3.6.6-b55pdoqsr5bie4k5djd4vokm3nywhm45

**Power9**
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.7.2-cicayvl7ki4tswoqlljsmcetwqcnoh3x
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.7.1-7vej3zvnvyj2jvz5lnxhnts3ok2fcxbp
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.8-xijljmdanyrybcx2rv65qshycmbrfv6c
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.7-vqdhzg7c3xxxregqmzxsqqfzxt2hajvq
[+] /scratch/users/dantopa/new-spack/pr.new.python-3.7.2/power9/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/python-3.6.6-jf4bnsdwk3qjhtmvjjhblnrcz5dztfdq

2019-02-05
Signed-off-by: Daniel Topa <dantopa@lanl.gov>

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
 2019-02-06 12:03:25 -06:00
Valentin Clement (バレンタイン クレメン)
548e6736c4 Update CLAW package with version 1.2.1 (#10528) 2019-02-06 15:51:52 +01:00
Levi Baber
881ce3a5c2 perl-yaml: new package (#10514) 2019-02-06 15:47:54 +01:00
simo-tuomisto
1be258a587 wordnet: new package (#10526) 2019-02-06 15:38:48 +01:00
Denis Davydov
871e7f525c xsdk: enable slepc in deal.ii (used to be a concretization error) (#10218) 2019-02-06 07:59:36 -06:00
Phil Carns
0b4a7dd04a New package: PMDK (#10453) 2019-02-05 16:53:16 -06:00
Justin Stanley
003ebf8bab r-wgcna: new package at 1.64-1 (#10392) 2019-02-05 09:00:25 -06:00
Axel Huebl
293e5c0781 MPark: Variant v1.4.0 (#10512) 
Add the latest release of Michael Park's C++ Variant lib.
 2019-02-05 15:18:19 +01:00
Phil Carns
de91d0badc mercury package: add 'udreg' variant (#10415) 
Faster and/or more robust in some cases on Cray platforms
 2019-02-04 19:51:04 -06:00
Levi Baber
c7ecb66a2f New package: perl-hash-merge (#10506) 2019-02-04 18:05:36 -06:00
Levi Baber
736a317e0c New package: perl-clone-choose (#10507) 2019-02-04 18:04:55 -06:00
Christoph Junghans
514cf0c1f4 votca*: add v1.5 (#10495) 
* votca-tools: add v1.5

* votca-csg: add v1.5

* votca-xtp: add v1.5

* votca-ctp: add v1.5
 2019-02-04 12:57:19 -07:00
Justin Stanley
478c3f5e8b augustus: fix bam2wig auxprog build (#10362) 
* augustus: fix bam2wig auxprog build

* augustus: few more changes to make new versions work
 2019-02-04 10:36:10 -06:00
Matthias Diener
bca72036a8 tar: add version 1.31 (#10485) 2019-02-04 11:02:13 +01:00
Axel Huebl
17cc4f208f Catch2: v2.6.0 (#10490) 
Add the latest Catch2 release.
 2019-02-04 10:52:47 +01:00
wspear
43fae5b807 New package: py-alembic (#10436) 2019-02-01 16:24:44 -06:00
wspear
ec7c7332c0 New package: py-prometheus-client (#10440) 2019-02-01 16:23:59 -06:00
Nicholas Labello
8c87a937e1 plumed package: add versions 2.4.4 and 2.5.0 (#10496) 2019-02-01 16:21:55 -06:00
Mark W. Krentel
a1969d9eec dyninst: add patch to work with new boost (#10454) 
Add tribool.patch to add explicit casts from tribool to bool in two
places.  Boost, starting with version 1.69, turned on explicit
conversions for tribool, which breaks the build for dyninst.

This is merged into the current dyninst develop and is expected to be
part of the next release, so the version range uses the current
release as an upper bound.
 2019-02-01 16:18:16 -06:00
wspear
c2b06c27ac New package: py-async-generator (#10439) 2019-02-01 12:40:19 -06:00
zschulte
a701c412bc gatk package: new versions, updated helper script (#10459) 
Closes #10168

* Add versions 4.1.0.0 and 4.0.12.0
* Replace md5 checksums with sha256
* Logic to generate a helper script for versions earlier than 4 was
  not running. This corrects the branch which controls whether this
  script is generated.
* Constrain Java dependency to version 8 (GATK does not work with
  Java 11)
* Avoid adding scripts that have dependencies not handled by Spack
  such as gcloud and google-chrome. These scripts are good candidates
  for later extensions.
 2019-01-31 16:10:06 -06:00
Ricardo Silva
cf754245fd py-pybigwig: fix build with python3, add numpy variant (#10444) 
* added patch to correctly pick up non-system curl when building
  with Python 3
* added numpy variant
* add version 0.3.12
* update checksums to sha256
 2019-01-31 14:50:10 -06:00
snehring
21afd258a4 New package: openjdk (#9861) 
Closes #2622

This retrieves and installs the binary of Oracle's OpenJDK (an
open-source JDK implementation). The logic is largely based on the
Spack JDK package (Oracle's closed-source JDK implementation).

For now this is only supports Linux. If the download could be
customized based on OS (for the same version), binaries are also
available for MacOS and Windows.
 2019-01-31 12:54:28 -06:00
Matthias Diener
ec78d362d2 git-lfs: add version 2.6.1, update build system (#10405) 
Build system was changed to use a Makefile. Therefore older versions
(which don't support this) are removed. The new build system also
supports testing by default.
 2019-01-30 21:21:08 -06:00
Tom Payerle
c42528fac2 fftw: fix include error for 2.x versions (#10039) 
Fixes #7372

Added patch method which renames config.h in the fftw subdir of the
source tree. fftw 2.1.5 appears to ship with a copy of this file
with all defines commented out. This gets read by the #include
directives instead of the version in the build directory with the
correct defines. As a result, many C preprocessor macros left
undefined, including F77_FUNC_ which causes the bulk of fttwf77.c
to be skipped due to an #ifdef, so fftw_reverse_int_array et al
not included in library. Fixes #7372

Also fixed some inconsistencies with the handling of quad and
long_double in specs between the configure method and the build,
check, and install methods.
 2019-01-30 21:18:10 -06:00
Axel Huebl
2aad75d98f HDF5: Add develop Version (#10382) 2019-01-30 21:04:24 -06:00