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2016-08-19py-sphinx requires py-setuptools during runtimeAdam J. Stewart1-1/+4
2016-08-19Swap lowercase for uppercase in URLAdam J. Stewart1-1/+1
2016-08-19Fix binary conflicts during sphinx activationAdam J. Stewart1-1/+1
2016-08-19Add all Sphinx dependenciesAdam J. Stewart13-40/+275
2016-08-18py-cffi: set LDSHARED env so that rpath is setStephen Herbein1-0/+10
py-cffi's .so was being built without the rpath being set. distutils looks at the LDSHARED for which compiler to use to build the final .so. Since it was not set, distutils fell back to the system provided compiler. Setting it forces the shared library to be compiled with the spack compiler (meaning that the rpath is set correctly).
2016-08-16Merge pull request #1531 from davydden/pkg/apebecker331-0/+55
ape: add new package
2016-08-16Merge pull request #1530 from davydden/pkg/octopusbecker331-0/+86
octopus: new package
2016-08-16ape: add new packageDenis Davydov1-0/+55
2016-08-16octopus: new packageDenis Davydov1-0/+86
2016-08-12Merge pull request #1342 from adamjstewart/features/cgnsTodd Gamblin1-0/+73
Add CGNS package
2016-08-11Merge pull request #1491 from eschnett/eschnett/curlTodd Gamblin1-0/+1
Update curl to 7.50.1
2016-08-10Remove unneeded noqa comments.Todd Gamblin20-60/+109
2016-08-10Spack packages now PEP8 compliant.Todd Gamblin381-1644/+2484
2016-08-10Update curl to 7.50.1Erik Schnetter1-0/+1
2016-08-09Openssl package should not require openssl (https) to obtain source.Matt Belhorn1-1/+1
2016-08-09qa : flake8 issuesalalazo1-12/+13
2016-08-09plumed : fixed name clash on attributealalazo1-2/+2
2016-08-09plumed : adding dependentsMassimiliano Culpo3-18/+71
* cp2k : added plumed * gromacs : patched pme load balancing * gromacs : added plumed
2016-08-08Merge pull request #1345 from hartzell/feature/add-perl-dependency-to-gitbecker331-6/+6
Add depends_on('perl'), depends_on('pcre') to git package
2016-08-07Merge pull request #1449 from hartzell/feature/add-package-for-prankTodd Gamblin7-0/+304
Add package for prank and supporting tools
2016-08-07Merge pull request #1463 from davydden/pkg/opiumTodd Gamblin1-0/+55
opium: add new package
2016-08-07Merge pull request #1464 from hartzell/feature/update-lmodTodd Gamblin1-3/+5
No need to patch Lmod after 6.4.4
2016-08-07Merge pull request #1465 from glennpj/pango_urlTodd Gamblin1-0/+2
Add list_url to pango package
2016-08-07Merge pull request #1466 from pramodk/developTodd Gamblin1-3/+5
PDT should download full installer package
2016-08-07tar: fix 1.28 on macOS; add 1.29 (#1462)Denis Davydov2-2/+494
2016-08-07Fix erroneously stripped trailing whitespace in patch (#1467)Adam J. Stewart1-4/+5
2016-08-07PDT should download full installer package pdtoolkit-X.tar.gz (default ↵Pramod Kumbhar1-3/+5
pdt-X.tar.gz is only for x86 and cray)
2016-08-06Add list_url to pango packageGlenn Johnson1-0/+2
Added a `list_url` so the updated pango tar file can be retrieved.
2016-08-06No need to patch Lmod after 6.4.4George Hartzell1-3/+5
The Lmod author changed the src so that it uses the tclsh (and shared libraries) discovered at configure time. He did it differently that I did in this patch, but he changes solve our problem too, so...
2016-08-06Make configure use our gettext libraryGeorge Hartzell1-0/+1
The configure script needs extra encouragement to link against our gettext/libintl library.
2016-08-06Clean up rebase problemsGeorge Hartzell1-1/+1
My rebase duplicated the depends_on('zlib') and dropped the --with-curl from the configure. This fixes those.
2016-08-06[Whitespace] Gather the depends_on's together.George Hartzell1-0/+1
2016-08-06Call configure `--with-libpcre=...` to use our pcreGeorge Hartzell1-1/+1
An earlier commit claimed that this package depends_on('pcre') but I didn't fix the call to configure that enabled it. This fixes that.
2016-08-06Enable depends_on('pcre') alsoGeorge Hartzell1-3/+1
While I have the patient on the operating table, @adamjstewart asked me to uncomment and test the depends_on('pcre'). Did it and it Works For Me(tm).
2016-08-06Add depends_on('perl') to git packageGeorge Hartzell1-3/+3
This commit changes the git package to depend_on('perl'). The system perl is not always sufficient to install git (e.g. a CentOS7 system with the development tools group installed has perl but not the ExtUtils::MakeMaker package that git needs) and one can't always update the system's perl. This PR depends_on PR #1339, which adds a perl package to spack.
2016-08-06Switch to using *std_cmake_argsGeorge Hartzell4-7/+4
2016-08-06Flake8 whitespace cleanupGeorge Hartzell4-4/+8
2016-08-06Add Bio++ tool suite and supporting libsGeorge Hartzell4-0/+173
Add the Bio++ suite and its supporting libraries.
2016-08-06Add package for mafftGeorge Hartzell1-0/+42
2016-08-06Add package for exonerateGeorge Hartzell1-0/+44
2016-08-06Fix name of bpp-suite (missing -...)George Hartzell1-1/+1
2016-08-06Add package for prankGeorge Hartzell1-0/+44
2016-08-06opium: add new packageDenis Davydov1-0/+55
2016-08-05Merge pull request #1451 from hartzell/feature/add-package-for-fastx_toolkitbecker332-0/+83
Add package for fastx toolkit
2016-08-05Merge pull request #1452 from hartzell/feature/add-package-for-samtoolsbecker334-29/+101
Add package for samtools
2016-08-05Remove lingering FIXME commentaryGeorge Hartzell1-3/+0
2016-08-05Samtools depends on htslib from 1.3.1 onwardGeorge Hartzell1-2/+2
Samtools used to (before 1.3.1) include it's own copy of htslib. Going forward, it needs to use the standalone htslib.
2016-08-05Merge pull request #1453 from hartzell/feature/add-package-for-seqtkbecker331-0/+43
Add package for seqtk
2016-08-05Merge pull request #1450 from hartzell/feature/add-package-for-bwabecker331-0/+52
Add package for bwa
2016-08-05Merge pull request #1442 from suraia/update-scorep-2.0becker333-21/+39
Update Score-P to 2.0 Most likely this can be generalized to link against older versions of dependencies, but it looks good for now.
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