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2193 commits

Author SHA1 Message Date
becker33
18d155e713 Merge pull request #1452 from hartzell/feature/add-package-for-samtools 
Add package for samtools
 2016-08-05 15:09:41 -07:00
George Hartzell
769408130a Samtools depends on htslib from 1.3.1 onward 
Samtools used to (before 1.3.1) include it's own copy of htslib.  Going
forward, it needs to use the standalone htslib.
 2016-08-05 17:47:11 -04:00
becker33
8e20a14945 Merge pull request #1453 from hartzell/feature/add-package-for-seqtk 
Add package for seqtk
 2016-08-05 10:25:19 -07:00
becker33
f403f256ca Merge pull request #1450 from hartzell/feature/add-package-for-bwa 
Add package for bwa
 2016-08-05 10:21:10 -07:00
becker33
594a6710ed Merge pull request #1442 from suraia/update-scorep-2.0 
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.
 2016-08-05 08:57:25 -07:00
George Hartzell
d6dedee6ff Flake8 cleanup 2016-08-04 15:23:04 -04:00
Bruno Turcksin
0c02ee86a7 Add Trilinos 12.6.4 (#1447) 2016-08-04 11:29:10 -07:00
George Hartzell
e12d7aadda Add package for seqtk 
Seqtk is a tool for working with fast[aq] files.
 2016-08-04 14:18:03 -04:00
George Hartzell
fd11db92e1 Add package for bcftools 2016-08-04 14:18:03 -04:00
George Hartzell
ba0577dc96 Update samtools to support v1.3.1 
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.
 2016-08-04 14:18:03 -04:00
George Hartzell
ef1369c365 Add package for htslib 
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.
 2016-08-04 14:18:03 -04:00
George Hartzell
d4274b32f2 Make flake8 happy (long lines) 2016-08-04 14:18:01 -04:00
Michael Kuhn
d7665a63e3 flake8 fixes 2016-08-04 19:04:48 +02:00
becker33
1ac1cc3d2c Merge pull request #1437 from jgalarowicz/update-xercesc 
Update the version of xerces-c, where the developers remove the old v…
 2016-08-04 09:00:36 -07:00
becker33
3c6f6fc811 Merge pull request #1438 from jgalarowicz/update-libmonitor 
Update libmonitor to use its new github location, it does not exist w…
 2016-08-04 08:59:35 -07:00
becker33
cabcdf0ec9 Merge pull request #1443 from davydden/pkg/dealii_python 
dealii: add optional python bindings
 2016-08-04 08:43:36 -07:00
becker33
fcc8b1d3e4 Merge pull request #1431 from hartzell/feature/add-package-for-unison 
Add package for unison (and ocaml)
 2016-08-04 08:41:45 -07:00
Denis Davydov
af8741c23c dealii: add optional python bindings 2016-08-04 16:11:14 +02:00
Michael Kuhn
584e5506f2 Update Score-P to 2.0 2016-08-04 14:24:25 +02:00
Todd Gamblin
b7fa2c4e21 Fix #1429: Remove git dep from gettext; break circular dependency. 
- 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.
 2016-08-03 21:53:53 -07:00
Jim Galarowicz
2e1dbd0697 Fix flake8 errors for: Update libmonitor to use its new github location, it does not exist where the package file now points to. 2016-08-03 21:32:15 -05:00
Jim Galarowicz
e69423a154 Fix flake8 errors for Update the version of xerces-c, where the developers remove the old version, so there is no fallback. 2016-08-03 21:28:56 -05:00
Jim Galarowicz
e68b7d8c63 Update libmonitor to use its new github location, it does not exist where the package file now points to. 2016-08-03 21:08:48 -05:00
Jim Galarowicz
638f779841 Update the version of xerces-c, where the developers remove the old version, so there is no fallback. 2016-08-03 21:04:17 -05:00
George Hartzell
43371c31a2 Flake8 cleanup 2016-08-03 16:51:53 -04:00
Todd Gamblin
dce105d16f Merge pull request #1382 from KineticTheory/gktplus3-deps 
GTK+3: Provide updates to package dependencies.
 2016-08-03 13:45:18 -07:00
George Hartzell
4acf6d76bf Add package for unison 
Add package for unison (the file synchronizer).

Needs the ocaml compiler to build.
 2016-08-03 16:41:31 -04:00
George Hartzell
a7bfaa3797 Add package for ocaml compiler 
Installs the ocaml compiler.
 2016-08-03 16:41:31 -04:00
Kelly (KT) Thompson
7c46a4c0e4 Provide minor updates after code review 
+ 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.
 2016-08-03 13:26:02 -06:00
becker33
3e6ebd577f Merge pull request #1378 from LLNL/bugfix/gh-1324-intel-parallel-studio 
Bugfix/gh 1324 intel parallel studio
 2016-08-03 10:46:40 -07:00
becker33
353726f08f Merge pull request #1156 from adamjstewart/features/py-meep 
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
 2016-08-03 10:07:05 -07:00
becker33
b9195b415a Merge pull request #1420 from epfl-scitas/packages/plumed 
plumed : added package
 2016-08-03 08:36:31 -07:00
alalazo
2f1c000f62 qa : flake8 issues 2016-08-03 08:26:58 +02:00
Kelly (KT) Thompson
d7d12aa2dc One more formatting change to make flake8 happy. 2016-08-02 19:05:48 -06:00
becker33
48997cffa1 Merge pull request #1233 from hartzell/add-nextflow 
First cut package for nextflow, has issues
 2016-08-02 11:52:19 -07:00
Denis Davydov
f90692cf81 arpack-ng: fix blas/lapack libraries 2016-08-02 20:27:34 +02:00
becker33
b5a117c923 Merge pull request #1366 from hartzell/feature/add-package-for-ack 
Add package for ack
 2016-08-02 10:11:11 -07:00
becker33
1534a115bd Merge pull request #1421 from hartzell/feature/add-package-for-texlive 
Add package for texlive
 2016-08-02 10:10:43 -07:00
becker33
a03a35565e Merge pull request #1339 from hartzell/features/add-perl 
Add perl package
 2016-08-02 10:10:04 -07:00
George Hartzell
fa70a837d4 Remove accidentally committed cabal-install bits 2016-08-02 13:00:47 -04:00
becker33
91004158c6 Merge pull request #1243 from davydden/pkg/atlas_urls 
atlas: fix urls and shared libs
 2016-08-02 09:59:05 -07:00
becker33
3f26bbc8b3 Merge pull request #864 from davydden/kdiff3 
kdiff3: initial version of the package
 2016-08-02 09:35:00 -07:00
becker33
a3322fab0a Merge pull request #1360 from glennpj/pysetuptoolsdep 
Add py-setuptools dependencies to packages
 2016-08-02 09:33:40 -07:00
becker33
21158195fb Merge pull request #1354 from paulhopkins/bugfix/preferred_variants_do_not_recognise_-variant 
Bugfix/preferred variants do not recognise  -variant
 2016-08-02 09:15:06 -07:00
George Hartzell
74a181febc Remove local copy of cpanm installer 
This is handled as a resource in the package now.
 2016-08-02 12:13:24 -04:00
George Hartzell
4c8672ed1f Add previous versions back into package 
Following the advice of @glennpj, added the old versions back into the
packages.

I can install the current packages and the previous packages.
 2016-08-02 11:45:16 -04:00
George Hartzell
c77425bb22 Remove useless def unpack 
Before I learned that I was stumbling over a real but (#1308), I thought
I needed to arrange for the fetcher to skip the unpack step.

This commit removes the useful `def unpack`.
 2016-08-02 11:32:19 -04:00
George Hartzell
a6605d842b Flake8 cleanup. 2016-08-02 11:25:03 -04:00
George Hartzell
f2f5f6c279 Touch up variant comment 2016-08-02 11:18:50 -04:00
George Hartzell
c994565c62 Use "resource" machinery to manage cpanm tarball 
Use the resource machinery to fetch/cache/unpack/... the App::cpanminus
tarball.

- this hardcodes the version, I can't figure out how to use a variant to
  hold/set the value and access it in the resource().
- change up the install to use the `with working_dir()` meme.
 2016-08-02 11:16:46 -04:00