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2016-08-10Spack packages now PEP8 compliant.Todd Gamblin381-1644/+2484
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.
2016-08-04Flake8 cleanupGeorge Hartzell1-4/+5
2016-08-04Add Trilinos 12.6.4 (#1447)Bruno Turcksin1-0/+1
2016-08-04Add package for seqtkGeorge Hartzell1-0/+43
Seqtk is a tool for working with fast[aq] files.
2016-08-04Add package for bcftoolsGeorge Hartzell1-0/+43
2016-08-04Update samtools to support v1.3.1George Hartzell2-29/+16
Update the samtools package to support v1.3.1, which - now uses configure script; and - now depends on external htslib package. The dependency on mpc seems to have been bogus, it's never linked in, nor is it mentioned in the source tree. I *do* have a version in /usr/lib64, but ldd does not sure it being linked in either.... By depending on 'ncurses' I can do away with the need for the patch.
2016-08-04Add package for htslibGeorge Hartzell1-0/+41
Htslib was pulled out of samtools and made into a standalone thing. This commit adds a packag for it, in support of the samtools package.
2016-08-04Add package for fastx toolkitGeorge Hartzell1-0/+43
Tools for working with FASTA/FASTQ files.
2016-08-04Add package for libgtextutilsGeorge Hartzell1-0/+43
Gordon's Text utils Library, in support of fastx toolkit.
2016-08-04Make flake8 happy (long lines)George Hartzell1-0/+52
2016-08-04flake8 fixesMichael Kuhn3-20/+27
2016-08-04Merge pull request #1437 from jgalarowicz/update-xercescbecker331-4/+5
Update the version of xerces-c, where the developers remove the old v…
2016-08-04Merge pull request #1438 from jgalarowicz/update-libmonitorbecker331-5/+3
Update libmonitor to use its new github location, it does not exist w…
2016-08-04Merge pull request #1443 from davydden/pkg/dealii_pythonbecker331-2/+15
dealii: add optional python bindings
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