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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.
2016-08-05Merge 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
2016-08-04Merge pull request #1431 from hartzell/feature/add-package-for-unisonbecker332-0/+94
Add package for unison (and ocaml)
2016-08-04dealii: add optional python bindingsDenis Davydov1-2/+15
2016-08-04Update Score-P to 2.0Michael Kuhn3-1/+12
2016-08-03Fix #1429: Remove git dep from gettext; break circular dependency.Todd Gamblin1-4/+0
- It's not really a circular dependency -- git is a run dependency of gettext - We can revert this change when Spack is smart enough to make git a run dependency and build it.
2016-08-03Fix flake8 errors for: Update libmonitor to use its new github location, it ↵Jim Galarowicz1-2/+1
does not exist where the package file now points to.
2016-08-03Fix flake8 errors for Update the version of xerces-c, where the developers ↵Jim Galarowicz1-2/+3
remove the old version, so there is no fallback.
2016-08-03Update libmonitor to use its new github location, it does not exist where ↵Jim Galarowicz1-3/+2
the package file now points to.
2016-08-03Update the version of xerces-c, where the developers remove the old version, ↵Jim Galarowicz1-2/+2
so there is no fallback.
2016-08-03Flake8 cleanupGeorge Hartzell1-0/+1
2016-08-03Merge pull request #1382 from KineticTheory/gktplus3-depsTodd Gamblin5-9/+64
GTK+3: Provide updates to package dependencies.
2016-08-03Add package for unisonGeorge Hartzell1-0/+50
Add package for unison (the file synchronizer). Needs the ocaml compiler to build.
2016-08-03Add package for ocaml compilerGeorge Hartzell1-0/+43
Installs the ocaml compiler.
2016-08-03Provide minor updates after code reviewKelly (KT) Thompson1-4/+2
+ Always depend on the gettext package. This simplifies the logic and I no longer need to 'import sys' + Only apply the patch for the older version of glib.
2016-08-03Merge pull request #1378 from LLNL/bugfix/gh-1324-intel-parallel-studiobecker331-1/+32
Bugfix/gh 1324 intel parallel studio
2016-08-03Merge pull request #1156 from adamjstewart/features/py-meepbecker3316-47/+685
Add py-meep package and dependencies Merging to add the gettext support, will submit a separate issue for the LD_LIBRARY_PATH issue with MPI and py-meep
2016-08-03Merge pull request #1420 from epfl-scitas/packages/plumedbecker331-0/+84
plumed : added package
2016-08-03qa : flake8 issuesalalazo1-5/+7
2016-08-02One more formatting change to make flake8 happy.Kelly (KT) Thompson1-1/+1
2016-08-02Merge pull request #1233 from hartzell/add-nextflowbecker331-0/+42
First cut package for nextflow, has issues
2016-08-02arpack-ng: fix blas/lapack librariesDenis Davydov1-9/+30
2016-08-02Merge pull request #1366 from hartzell/feature/add-package-for-ackbecker331-0/+51
Add package for ack
2016-08-02Merge pull request #1421 from hartzell/feature/add-package-for-texlivebecker331-0/+57
Add package for texlive
2016-08-02Merge pull request #1339 from hartzell/features/add-perlbecker331-0/+75
Add perl package
2016-08-02Remove accidentally committed cabal-install bitsGeorge Hartzell2-62/+0
2016-08-02Merge pull request #1243 from davydden/pkg/atlas_urlsbecker333-9/+120
atlas: fix urls and shared libs
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