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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
健美猫
c451644f12 Support *.TAR.gz extension. (#7973) 2018-05-06 09:34:16 -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
Adam J. Stewart
3a29cc3f5c Fix coloring of URLs containing @ symbol (#7799) 
* Fix coloring of URLs containing @ symbol

* Fix coloring of descriptions containing @ symbol
 2018-05-05 17:27:40 -05:00
Adam J. Stewart
8d681925b2 Change default elf provider on macOS (#7939) 2018-05-05 17:27:13 -05:00
Adam J. Stewart
5af4d4f0ac Set default provider for every virtual package (#7784) 
* Set default provider for every virtual package

* Add unit test to ensure that every virtual package has a default provider explicitly set
 2018-05-05 17:26:47 -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
scheibelp
d17372290d Fix initialization of defaults in yaml schema validation (#7959) 
Fixes #7924

Spack's yaml schema validator was initializing all instances of
unspecified properties with the same object, so that updating the
property for one entry was updating it for others (e.g. updating
versions for one package would update it for other packages).

This updates the schema validator to instantiate defaults with
separate object instances and adds a test to confirm this behavior
(and also confirms #7924 without this change).
 2018-05-01 17:23:27 -07:00
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