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5918 commits

Author SHA1 Message Date
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