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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...
2016-08-06opium: 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
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
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