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Author SHA1 Message Date
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
e17862c421 Add package for fastx toolkit 
Tools for working with FASTA/FASTQ files.
 2016-08-04 14:18:02 -04:00
George Hartzell
d5bb2955b1 Add package for libgtextutils 
Gordon's Text utils Library, in support of fastx toolkit.
 2016-08-04 14:18:02 -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
George Hartzell
1b9becc541 Add the std spack header to perl/package.py 
Stole the example header from antlr/package.py, included it at the top
of perl/package.py.
 2016-08-02 11:16:46 -04:00
George Hartzell
08ff7b65af Make running perl's tests conditional 
Make running perl's tests conditional, one must now specify the
`--run-tests` flag to the `spack install` command in order to run the
tests.

On one system (8 core, 16GB Digital Ocean Droplet), installing without
tests takes 3 minutes, with tests takes 16 minutes.
 2016-08-02 11:16:46 -04:00
George Hartzell
4d72e0fb9d Make the cpanm version a variant 
Rather than hard-coding the verison of `cpanm` that's [optionally]
installed into the core, make it a variant with a default value of
'1.7042'.

Also discovered that `prefix + 'bin'` is the same as `prefix.bin`, so
embetter that bit of code.
 2016-08-02 11:16:46 -04:00
George Hartzell
a5a4525bed Add perl package 
Add perl package, based on [work by
justintoo](https://github.com/LLNL/spack/pull/105).  He had too many
things pulled into that pull request, this just adds a perl package.

Support the current releases on the past three minor branches.

Run perl's tests before installing.

Install cpanm into the core (makes building on top of this perl *much*
simpler).  Controlled by a variant.
 2016-08-02 11:16:46 -04:00
George Hartzell
949621eb7f Add package for texlive 2016-08-02 11:15:42 -04:00
George Hartzell
857a03c127 Ack should depends_on('perl') 
Add a depends_on('perl') and rewrite the script's `#!` line to refer to
that Perl's `perl` executable.
 2016-08-02 11:11:05 -04:00
George Hartzell
114da813a3 Remove unnecessary imports. 
Now that it's sporting a cleaner install method, these imports are
unnecessary.
 2016-08-02 11:11:05 -04:00
George Hartzell
bf467c5df3 Remove override of unpack(self) 
I cargo culted that from my *nextflow* package.  I [thought I] needed it
to work around Spack trying to use tar to unpack something that was
neither a tar ball nor unpackable.

This package works fine without it.  In retrospect, the error that I was
seeing in the *nextflow* package was probably this problem #1308.
 2016-08-02 11:11:05 -04:00
George Hartzell
6c3623422f Use cleaner mech to install script 
Use @adamjstewart's nicer bit of python code in the
install method.
 2016-08-02 11:11:05 -04:00
George Hartzell
63121a0c49 Add package for ack 
Add a package for [ack](http://beyondgrep.com/install/).  Simply install
the fatpacked script.

It uses '#!/usr/bin/env perl' and it very much not choosy about what
perl it needs.  For now just trust that there's one available, perhaps
someday we can/should uncomment the depends_on('perl').

Follows the methodolgy I used in nextflow.  Has the same
uninstall/install problem that nextflow has, there is an issue in
progress for that: https://github.com/LLNL/spack/issues/1308.

Tested on CentOS7.
 2016-08-02 11:11:05 -04:00
George Hartzell
12d1263980 Update several R packages (r-shiny prereqs) 
r-jsonlite 0.0.21 -> 1.0
r-mime     0.4    -> 0.5
rcpp       0.12.5 -> 0.12.6

CRAN is funny.  The older versions of these packages are still available
in package specific directories but the current version is not there, so
I don't see any way to make the older versions work.
 2016-08-02 11:10:41 -04:00
George Hartzell
6f332c7e4c Fix whitespace, make flake8 happ{y,ier}. 2016-08-02 11:10:12 -04:00
George Hartzell
bfcec69630 Add standard header, use spack helpers 
Added the standard header (stolen from R).

Touched up the install to use set_executable rather than doing it
myself.
 2016-08-02 11:10:12 -04:00
George Hartzell
4373a2b629 First cut package for nextflow, has issues 
This is my first cut at a package to support nextflow.  It's also my
first package.  It works, but has issues.  I'm going to submit a pull
request and get some coaching on how to deal with it.

One issue particular: if I install, then uninstall, then try to install
again (which uses the cached copy of the "distribution file"), it
explodes.
 2016-08-02 11:10:12 -04:00
Glenn Johnson
a57d94af03 Fix flake8 issues. 2016-08-02 09:53:57 -05:00
Denis Davydov
a1703bf70d kdiff3: add license block 2016-08-02 16:37:14 +02:00
Gilles Fourestey
dea7bbb4a0 added plumed 
* plumed : first version
* plumed : added dependencies and docs
 2016-08-02 15:06:46 +02:00
Denis Davydov
565bd5f51e atlas: revert to lapack 3.5.0 2016-08-02 13:52:32 +02:00
Denis Davydov
bef7e2645a atlas: flake8 fixes 2016-08-02 13:52:32 +02:00
Denis Davydov
f6a4a6b00f atlas: add install_test 2016-08-02 13:52:32 +02:00
Denis Davydov
0c0b37800d atlas: set (blas|lapack)_shared_lib 2016-08-02 13:52:32 +02:00
Denis Davydov
4ecf481337 atlas: fix shared libs; set compilers 2016-08-02 13:52:32 +02:00
Denis Davydov
6f7e12d49b atlas: fix urls and use lapack 3.6.0 2016-08-02 13:52:32 +02:00
Denis Davydov
0aa513ad70 libxau: mark pkg-config as build-type dependency 2016-08-02 13:50:46 +02:00
Denis Davydov
450c750214 kdiff3: initial version of the package 2016-08-02 13:49:40 +02:00
Denis Davydov
a4e59c2758 libxau: add missing dependency 2016-08-02 13:49:40 +02:00
Kelly (KT) Thompson
9433e84776 Formatting changes for flake8. 2016-08-01 22:54:51 -06:00
Kelly (KT) Thompson
17f0eb5148 Provide correct download urls and additional dependencies. 2016-08-01 22:10:54 -06:00
ba11f19efc Merge remote-tracking branch 'upstream/develop' into gktplus3-deps 2016-08-01 20:50:28 -06:00
becker33
b892cebe8a Merge pull request #1343 from glennpj/r_unfilter 
R extension dependencies with compiler wrapper
 2016-08-01 13:51:13 -07:00
becker33
e861e35acf Merge pull request #1234 from mwilliammyers/package-opencv 
Update opencv package
 2016-08-01 13:44:31 -07:00
becker33
1847aa035d Merge pull request #1348 from glennpj/rcurl 
r-curl update and changed remote archive
 2016-08-01 13:38:38 -07:00
becker33
94238eebfa Merge pull request #1381 from davydden/pkg/mkl_linux 
MKL linux fixes
 2016-08-01 13:36:10 -07:00
becker33
dc9fcea989 Merge pull request #1365 from hartzell/feature/add-package-for-tree 
Add package for tree
 2016-08-01 13:21:09 -07:00
becker33
15514792d5 Merge pull request #1374 from hartzell/bug/fix-jdk-import-of-distutils 
Bug: fix jdk package's use of distutils
 2016-08-01 13:20:44 -07:00
becker33
851bc506e4 Merge pull request #1367 from adamjstewart/features/pgi 
Add latest version of PGI
 2016-08-01 13:07:35 -07:00
becker33
932300256c Merge pull request #1413 from mdevlin1/fixes/libxsmm 
Fixed libxsmm package
 2016-08-01 13:06:05 -07:00
becker33
6361f5c2d4 Merge pull request #1359 from sknigh/libhio 
added libhio package
 2016-08-01 13:05:29 -07:00
Mitchell Devlin
2d51ea5da4 fixed libxsmm makefile filter 2016-08-01 14:38:16 -05:00
Adam J. Stewart
fed7ba1dab Add latest version of PGI 2016-08-01 13:42:00 -05:00
Adam J. Stewart
ab885a5397 Allow git to depend on gettext now that it works 2016-08-01 13:35:22 -05:00
Adam J. Stewart
4014a29d2b Use proper deptype so that spack activate works 2016-08-01 13:35:22 -05:00
Adam J. Stewart
f5aed63b0b pkg-config should be a build dependency only 2016-08-01 13:35:22 -05:00
Adam J. Stewart
5cac0a528c Fix undefined symbols by building shared libraries 2016-08-01 13:35:22 -05:00
Adam J. Stewart
bdb64c2e39 Tell MEEP where to find libctl 2016-08-01 13:35:22 -05:00
Adam J. Stewart
0903ae0599 Final fixes to get libctl working 2016-08-01 13:35:22 -05:00
Adam J. Stewart
1e3a5d4e26 Final fixes to get guile to build 2016-08-01 13:35:21 -05:00
Adam J. Stewart
6db99a4fe7 Rename gc => bdw-gc, fix libunistring bug 2016-08-01 13:35:21 -05:00
Adam J. Stewart
5b1a882fc2 Update meep's url_for_version 2016-08-01 13:35:21 -05:00
Adam J. Stewart
a2578c21e4 Supply flags to bdist 2016-08-01 13:35:21 -05:00
Adam J. Stewart
8d0758fc4c Allow py-meep to link properly 2016-08-01 13:35:21 -05:00
Adam J. Stewart
880cbb2217 Better testing for MEEP 2016-08-01 13:35:21 -05:00
Adam J. Stewart
3b4820f290 Patch pkg-config and update installs for various packages 2016-08-01 13:35:21 -05:00