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2017-08-23pgdspider: new package (#5186)Audrey Thoma2-0/+60
* pgdspider: new package * couple of fixes
2017-08-23Boost: develop (#5184)Axel Huebl1-0/+5
Adds a development version of boost, based on their github master repo. Git clones the submodules forever, but installs! :) Useful for testing since boost tends to break complex software dependencies quite often. This helps testing it before releases.
2017-08-22tcoffee: new package (#5185)Audrey Thoma4-0/+142
2017-08-22Boost: 1.65.0 (#5182)Axel Huebl1-0/+3
Adds the latest boost release. Downloads seem to be pointing to bintray from the official homepage.
2017-08-22Package 'libaec': no need to specify per version urls. (#5176)Sergey Kosukhin1-6/+6
2017-08-22Updates for package 'cdo'. (#5179)Sergey Kosukhin1-39/+39
* Package 'cdo': removed obsolete version 1.6.9. * Package 'cdo': updated urls. * Package 'cdo': added version 1.9.0. * Package 'cdo': no need to specify per version urls. * Package 'cdo': switched from Package to AutotoolsPackage. * Package 'cdo': added new variant 'openmp'. * Package 'cdo': variants 'curl' and 'magics' by default.
2017-08-21py-pyrad: new package (#5181)Audrey Thoma1-0/+41
2017-08-21Added custom messages for conflicts directive. fixes #4965 (#5083)Massimiliano Culpo1-2/+11
Users can now add an optional custom message to the conflicts directive. Layout on screen has been changed to improve readability and the long spec is shown in tree format. Two conflicts in `espresso` have been modified to showcase the feature.
2017-08-21Protobuf: 3.4 (#5177)Axel Huebl1-0/+1
2017-08-20Unbuffer so that output from packages appears when redirectingTodd Gamblin1-0/+45
- Python I/O would not properly interleave (or appear) with output from subcommands. - Add a flusing wrapper around sys.stdout and sys.stderr when redirecting, so that Python output is synchronous with that of subcommands.
2017-08-19Group Travis CI jobs in stages (#5104)Massimiliano Culpo1-0/+2
- This should speed-up Travis CI tests and refers to #5049 - Travis uses build-stages to group tests together - The idea is to let fast tests fail first, then move to longer ones. - Added external perl to avoid download failure from CPAN and reduce build time - Disabling perl-dbi: continues to fail with (504 Gateway Time-out) on Travis - We now cover all the build systems in tests: - Add back `openblas` to Travis as a separate package. - Switched `openblas` for `astyle` to build a simpler MakefilePackage. - Added 'tut' (WafPackage) - Added 'py-setuptools' (PythonPackage) - Added 'perl-dbi' (PerlPackage) - Added 'build_systems' directory to the ones for which we get a summary - Added 'openjpeg' (CMakePackage) - Added 'r-rcpp' (RPackage) - Added comments to build tests to show the covered build system
2017-08-19Add version 1.7.1 for cub. (#5164)健美猫1-0/+1
2017-08-19lbann: add depends_on hwloc (#5165)Adam Moody1-0/+1
2017-08-18cufflinks: new package (#5158)Audrey Thoma1-0/+46
2017-08-18muscle: fix (#5160)Audrey Thoma1-0/+5
2017-08-18For Tk, also provide a symlink for wishX.X. (#5161)Kelly (KT) Thompson1-0/+5
+ gitk (and possibly other tools) expect to find the Tk executable `wish`, so add a symlink with this name that points to the the versioned filename. + Example: `wish --> wish8.6`
2017-08-18build boost with graph library even when +mpihealther1-1/+0
Previously, when +graph and +mpi were enabled, the graph library was replaced with the graph_parallel library. This alters the logic for +graph+mpi to build both libraries.
2017-08-18corset: new package (#5157)Audrey Thoma1-0/+44
2017-08-18parsimonator: new package (#5143)Audrey Thoma1-0/+65
* parsimonator: new package * adding variant conflict
2017-08-18vegas2: new package (#5150)Audrey Thoma4-1/+126
* vegas2: new package * small version things
2017-08-18Add info for nextflow@v0.25.6 (#5148)George Hartzell1-0/+2
2017-08-18add man-db package and friends (#4844)Stephen McDowell5-0/+212
* add man-db package and friends * fix groff, libpipeline, and man-db dependencies * remove parallel groff altogether, build-only deps
2017-08-17Add a new package for gaussian (#5149)zenln1-0/+71
* Gaussian: Gaussian install * Adding Patch to spack installed files * Adding extra environment variables for gaussian at run time * Adding provides linda * Adding linda as a provided package * Shortning vars and fixing flake8 indentation and spacings
2017-08-17pagit: new package (#5140)Audrey Thoma1-0/+68
* pagit: new package * removed unneeded env var
2017-08-17new package libfabric (#5146)Audrey Thoma1-0/+35
* pbmpi: new package * forgot about libfabric
2017-08-17pbmpi: new package (#5144)Audrey Thoma1-0/+48
2017-08-17paml: new package (#5142)Audrey Thoma1-0/+52
2017-08-17microbiomeutil: new package (#5134)Audrey Thoma1-0/+53
* microbiomeutil: new package * got rid of unnecessary self * oops
2017-08-17Add new package for rhash, a cmake dependency (#5120)Adam J. Stewart2-40/+120
* Add new package for rhash, a cmake dependency * Add missing libuv dependency to cmake
2017-08-17py-faststructure: new package (#5131)Audrey Thoma1-0/+39
2017-08-17add libiconv dependency to libxslt (#5138)healther1-0/+1
this is a fix to an installation that failed due to configure for some reason not finding the libiconv shipped with glibc, but still trying to link against it see http://xmlsoft.org/FAQ.html
2017-08-16add missing dependencies to elfutils (#5135)sknigh1-2/+10
2017-08-16tppred: new package (#5091)Audrey Thoma2-1/+55
* tppred: new package * fixed url_for_version * fixed version spec on dependency * removing unneeded dependency
2017-08-16dialign-tx: new package (#5126)Audrey Thoma1-0/+50
* dialign-tx: new package * utilizing build_directory variable * forgot one
2017-08-16discovar: new package (#5129)Audrey Thoma1-0/+36
2017-08-16gapcloser: new package (#5130)Audrey Thoma1-0/+39
2017-08-16py-misopy: new package (#5119)Audrey Thoma1-0/+46
* py-misopy: new package * waiting for link to be fixed * got correct url and checksum * specifying dependency version requirements
2017-08-16Add package rtags (#5111)healther2-0/+116
* Add package rtags * fixed license * transform to cmakepackage and add dependencies * add dependencies and patch for rtags * flake8 fix * clean up dependencies
2017-08-16Adding Thrift versions 0.10.0 and 0.9.3 (#5117)Cesare Cugnasco1-0/+2
* Adding Thrift version 0.10.0 and 0.9.3 Hi, I've added the versions 0.10.0 and 0.9.3 * fixed flake8 errors
2017-08-16phylip: new package (#5121)Audrey Thoma1-0/+45
2017-08-16preseq: new package (#5122)Audrey Thoma1-0/+44
2017-08-16Add better generator support to CMakePackage (#4988)Adam J. Stewart2-23/+6
* Add better generator support to CMakePackage * List valid CMake generators on error
2017-08-16Refactor IntelInstaller into IntelPackage base class (#4300)Adam J. Stewart7-499/+584
* Refactor IntelInstaller into IntelPackage base class * Move license attributes from __init__ to class-level * Flake8 fixes: remove unused imports * Fix logic that writes the silent.cfg file * More specific version numbers for Intel MPI * Rework logic that selects components to install * Final changes necessary to get intel package working * Various updates to intel-parallel-studio * Add latest version of every Intel package * Add environment variables for Intel packages * Update env vars for intel package * Finalize components for intel-parallel-studio package Adds a +tbb variant to intel-parallel-studio. The tbb package was renamed to intel-tbb. Now both intel-tbb and intel-parallel-studio+tbb provide tbb. * Overhaul environment variables set by intel-parallel-studio * Point dependent packages to the correct MPI wrappers * Never default to intel-parallel-studio * Gather env vars by sourcing setup scripts * Use mpiicc instead of mpicc when using Intel compiler * Undo change to ARCH * Add changes from intel-mpi to intel-parallel-studio * Add comment explaining mpicc vs mpiicc * Prepend env vars containing 'PATH' or separators * Flake8 fix * Fix bugs in from_sourcing_file * Indentation fix * Prepend, not set if contains separator * Fix license symlinking broken by changes to intel-parallel-studio * Use comments instead of docstrings to document attributes * Flake8 fixes * Use a set instead of a list to prevent duplicate components * Fix MKL and MPI library linking directories * Remove +all variant from intel-parallel-studio * It is not possible to build with MKL, GCC, and OpenMP at this time * Found a workaround for locating GCC libraries * Typos and variable names * Fix initialization of empty LibraryList
2017-08-16mpiblast: new package (#5106)Audrey Thoma2-0/+233
2017-08-16scorep: Fix build with GCC 7 (#5107)Michael Kuhn2-0/+44
2017-08-16otf2: Add 2.1 (#5108)Michael Kuhn1-0/+1
2017-08-16Fix future import in hdf5-blosc (#5010)Adam J. Stewart1-1/+0
2017-08-16Add package rr (#5105)healther1-0/+66
* Add package rr * Flake8 fixes * fix flake8 no2 * add future dependency stub, add hw dependency and clean up * add missing self
2017-08-16Add package PyPytestXdist and dependencies (#5095)healther3-0/+114
* Add py-pytest-xdist * fixed licenses * attempt to fix flake8 * added missing build dependency
2017-08-16Add package py-pybind11 (#5096)healther1-0/+51
* py-pybind11 package was missing * fixed license file * attempt to fix flake8 * use python3 compatible python detection
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