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2017-03-29add package py-bokeh (#3618)healther1-0/+45
* add package py-bokeh * remove setuptools dependency * add missing dependencies
2017-03-29Allow py-py2cairo to be built with cairo~X (#3620)healther1-1/+1
2017-03-29add package py-pympler (#3621)healther1-0/+42
* add package py-pympler * add python@2.5: dependency
2017-03-29Add package py-pynn (#3622)healther1-0/+50
* add package py-pynn * fix docstring * fix dependency mess * add python dependency
2017-03-29Add py-pymongo dependencies (#3624)healther1-0/+4
* add package py-mongo * add dependencies
2017-03-29htslib depends_on version must match samtools (#3625)George Hartzell1-1/+3
2017-03-29Add abipy package and dependencies (#3352)Adam J. Stewart13-15/+459
* Add abipy package and dependencies * Add first official release of py-abipy * Ignore files from dependencies during activation
2017-03-29add package py-mongo (#3619)healther1-0/+34
2017-03-29add package py-brian2 (#3617)healther1-0/+50
2017-03-29Add version 3.5.9 to package gnutls (#3616)healther1-2/+14
2017-03-28Add Blast+ package. (#3562)George Hartzell2-0/+229
* Add Blast+ package. Adds support for NCBI's blast+@2.6.0. I'll be adding a few historical versions in the near future. It's a fairly direct transliteration of the [Homebrew Science recipe][hbs]. I skipped the mysql support. There is a problem with HDF5 support. Blast's configure script test program defines a macro 'HOST' to a string value and one of the HDF5 bits has an variable named 'HOST'. Fun things happen. I've disabled support for now. I've run very very basic tests. I'll get this out to my users and ensure that it works and fine tune the options and etc.... [hbs]: https://github.com/Homebrew/homebrew-science/blob/master/blast.rb * Flake8 fixes * Update w.t.r. mamelara's PR and cleanup Add paths to things in the --with-* config args Add add'l config flags from #3394. Update patch to no-op and add comment. Add add'l dependencies after studying `configure --help`. * Flake8 cleanup * Add support for blast+@2.2.30 Need to work around a configure bug. See https://github.com/Homebrew/homebrew-science/issues/2337#issuecomment-170011511. * Re-wrap comment, line length not a problem. I'd broken a comment across to line in a fit of flake8 induced fear. Adam pointed out that it's ok. * Remove explicit prefix config Remove explicit prefix config, the autotools package does it for us.
2017-03-28Add info for version 2.16 (#3601)George Hartzell1-0/+1
2017-03-28Add support for v1.9.9 (#3602)George Hartzell1-0/+1
2017-03-28Add packages for jq and ongiruma (#3607)George Hartzell2-0/+70
jq is a commandline JSON processor. Oniguruma is a regexp library on which jq depends.
2017-03-28Add package for direnv (#3608)George Hartzell1-0/+39
2017-03-28Add package for BATS (#3611)George Hartzell1-0/+38
Add package for the BASH Automated Testing System.
2017-03-28bowtie2: add support for version 2.3.1 (#3599)George Hartzell3-4/+28
* Add support for 2.3.1 Updated digest and added a dependency on tbb. * Cleanup patch name and add description
2017-03-28Update/samtools (#3595)George Hartzell3-0/+5
* Update samtools family to 1.4 * simple cleanup * Make bzip depends_on for future versions too
2017-03-28New package: ncftp client (#3603)George Hartzell1-0/+37
* Add package for ncftp * Flake8 cleanups
2017-03-28New package: staden-io-lib (#3604)George Hartzell1-0/+37
* Add package for staden-io-lib * Flake8 cleanups
2017-03-28New package: mummer (#3606)George Hartzell1-0/+55
* Add package for mummer Blocked on https://github.com/LLNL/spack/pull/3555. * Make "check" step optional and flake8 cleanups
2017-03-28new package: pigz (#3612)George Hartzell1-0/+46
* Add package for pigz * Whitespace * Remove leftover instructions (oops...) * Flake8 cleanup * Convert to MakefilePackage
2017-03-28new package: blat (#3610)George Hartzell1-0/+44
* Add package for blat * Whitespace cleanup * Flake8 cleanup
2017-03-28Add packages for miniconda[23] (#3613)George Hartzell2-0/+86
2017-03-28Add support for version 20170322 (#3598)George Hartzell1-0/+1
2017-03-28Add version info for 7.4.1 (#3600)George Hartzell1-0/+1
2017-03-28Add support for v8.0.0503 (#3596)George Hartzell1-0/+1
2017-03-28Nextflow versions 0.24.1 and 0.23.3 (#3597)George Hartzell1-1/+8
Add support for nextflow versions 0.24.1 and 0.23.3.
2017-03-28fix for #3588 (#3589)sknigh1-0/+2
* fix for #3588 * set 'build_directory' variable instead
2017-03-28Add a package: cub. (#3584)健美猫1-0/+39
2017-03-28add package double-conversion (#3585)healther1-0/+47
2017-03-28Add new version to glog (#3586)healther1-1/+2
2017-03-28Add SST/macro and Dumpi trace packages (#3025)sknigh2-0/+116
* Added packages for Structural Simulation Toolkit and Dumpi trace * sst-dumpi deps Remove extraneous dependency from sst-dumpi * Removed redundant function and fake-url from sst-dumpi package * Fixed URL, Added git branches, requested changes sst-dumpi version listed as 6.1, made an upstream change to 6.1.0 sst-macro and sst-dumpi can be installed as v6.1.0 and master branch * Added bootstrap. Tweaked URLs and description
2017-03-28Restore newlines to easy-install.pth files. (#3583)Todd Gamblin1-2/+6
Previous syntax fix in 8a873bb was not quite right.
2017-03-28Fix bug in `spack find` for installations with unknown namespaces. (#3573)Todd Gamblin1-1/+7
- Spack find would fail with "unknown namespace" for some queries when a package from an unknown namespace was installed. - Solve by being conservative: assume unknown packages are NOT providers of virtual dependencies.
2017-03-28Bugfix: allow deactivating installs that don't have packages anymore. (#3572)Todd Gamblin1-5/+4
- deactivate -a wouldn't work if the installation's package was no longer available. - Fix installed_extensions_for so that it doesn't need to look at the package.py file.
2017-03-28Add package kaldi. (#3503)健美猫4-0/+189
2017-03-28googletest: Convert to CMakePackage (#3571)Erik Schnetter1-14/+22
* googletest: New version 1.8.0 * googletest: Simplify
2017-03-28openblas: raise an error when using unsupported Apple clang (#3577)Denis Davydov1-0/+6
2017-03-28CONFIG: update versions for paraview (#3537)Mark Olesen4-68/+126
- drop old TCL support from paraview build. - add +plugins variant to have include directories installed. This is enabled by default since the additional diskspace for includes is really minimal and since this also allows re-use of the VTK libraries from ParaView without necessarily requiring a separate VTK installation. - +opengl2 is now the default. As per all newer VTK and paraview versions. BUG: broken install for paraview-5.0.1 with includes and without python - incorrect conditional for ui_pqExportStateWizard.h when python is disabled and includes are to be installed. gcc compiler detection patch. These have both been fixed in paraview 5.3.0 ENH: refactor as a CMakePackage. - Note that "spack install paraview" works as expected, but "spack build paraview" fails in weird unrelated ways.
2017-03-27this builds cvs CentOS Linux release 7.2.1511 (#3574)Peter Doak1-0/+36
2017-03-27Merge pull request #3570 from LLNL/packages/elfutils-preferred-versionGregory Lee1-1/+1
Make 0.163 the preferred version of elfutils.
2017-03-27Fix easy-install.pth syntax (#3569)Gregory Lee1-11/+2
2017-03-27Make 0.163 the preferred version of elfutils.Todd Gamblin1-1/+1
- later versions do not seem to work well with libdwarf.
2017-03-27Update to version 0.4.8-1 (#3568)George Hartzell1-0/+1
2017-03-27Bugfix/gnutls (#3565)George Hartzell1-1/+5
* Fix nettle dependency GnuTLS requires a nettle from the 2.7 series, won't work with 3.x (so sayeth configure when it crashes...). * Fix configure symlinking GNUmakefile to itself I'm confused about how this ever worked, but.... As configure runs, it does something like this: ``` config.status: linking /home/hartzelg/tmp/spack/var/spack/stage/gnutls-3.3.9-uq2u4ecucncv2l3akran765aystyvkys/gnutls-3.3.9/GNUmakefile to GNUmakefile ``` and since that is the cwd the build crashes with: ``` ==> 'make' '-j28' make: GNUmakefile: Too many levels of symbolic links make: stat: GNUmakefile: Too many levels of symbolic links make: *** No rule to make target `GNUmakefile'. Stop. ``` Since the comment in the configure script points out that the GNUmakefile is "only for the maintainer" I've just commented out the bit that leads to the symlinking. Builds for me on CentOS 7. (I do have a recent-ish set of auto-* things in my patch via linuxbrew) * Wordsmith * Fix symbolic link problem properly Autotools magic. See #3565 for the details. * Flake8 cleanup * Add some headroom on the version number constraint We really want < 3.0 but there's not a good way to express it. We'd like to avoid having to update the file if they release 2.7.2. This seems like a good compromise.
2017-03-27CONFIG: update qt package to build qt-5.7.1 (#3535)Mark Olesen1-9/+25
- adjusted formatting to reduce some flake8 complaints
2017-03-27fftw: Add 3.3.6-pl2, remove 3.3.6-pl1. (#3566)健美猫1-1/+1
2017-03-27ENH: add int64 variant to scotch (as per metis +int64) (#3536)Mark Olesen2-2/+22
BUG: provide patch for scotch 6.0.4 if building non-threaded - corresponds to issue #20179 from the scotch issue trackter
2017-03-26Update texlive digest/md5 (sigh...) (#3564)George Hartzell1-1/+1
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