hlrs-software-stack/spack
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2240 commits

Author SHA1 Message Date
Andrew Williams
87d15212eb Cleaned branch to only include plumed package 2016-08-22 12:30:17 +01:00
Andrew Williams
226d4f04f3 Spelling tweaks and consistent quoting 2016-08-22 12:09:50 +01:00
Andrew Williams
5661afa315 Passed flake8 tests 2016-08-22 12:03:47 +01:00
Andrew Williams
0c8462723b Found upstream plumed package and modified this one to match 2016-08-22 11:24:03 +01:00
Andrew Williams
90e5ccd98c Cleaned up commented out code in intelmpi package 2016-08-19 15:01:46 +01:00
Andrew Williams
13f636ec68 Added required arguments to get plumed to build with intelmpi 2016-08-19 15:00:21 +01:00
Andrew Williams
6641f42417 Not compiling due to mpi error. Also getting this error from the command line so could be separate issue. Otherwise package definition first draft complete. 2016-08-18 13:19:36 +01:00
Andrew Williams
b99e945e6d Added variants and dependencies to plumed but I'm getting an error when trying to resolve mpi to a valid virtual package 2016-08-17 15:43:59 +01:00
Andrew Williams
27793d97dc temp commit in current state 2016-08-15 16:16:00 +01:00
Andrew Williams
3edfa390f7 Basic package file for plumed and boilerplate for external intel mpi 2016-08-15 11:19:40 +01:00
Todd Gamblin
e6a122417a Merge pull request #1491 from eschnett/eschnett/curl 
Update curl to 7.50.1
 2016-08-11 03:04:07 -07:00
Todd Gamblin
84e331c586 Remove unneeded noqa comments. 2016-08-10 16:33:39 -07:00
Todd Gamblin
240f1fd223 Spack packages now PEP8 compliant. 2016-08-10 16:33:39 -07:00
Erik Schnetter
158deae625 Update curl to 7.50.1 2016-08-10 13:51:57 -04:00
Matt Belhorn
2be065418b Openssl package should not require openssl (https) to obtain source. 2016-08-09 15:57:07 -04:00
alalazo
38dcd6bce9 qa : flake8 issues 2016-08-09 09:54:24 +02:00
alalazo
5362864cc9 plumed : fixed name clash on attribute 2016-08-09 09:24:36 +02:00
Massimiliano Culpo
15d9fb1879 plumed : adding dependents 
* cp2k : added plumed
* gromacs : patched pme load balancing
* gromacs : added plumed
 2016-08-09 09:23:53 +02:00
becker33
3ea1325620 Merge pull request #1345 from hartzell/feature/add-perl-dependency-to-git 
Add depends_on('perl'), depends_on('pcre') to git package
 2016-08-08 09:44:50 -07:00
Todd Gamblin
dd30066feb Merge pull request #1449 from hartzell/feature/add-package-for-prank 
Add package for prank and supporting tools
 2016-08-07 23:43:40 -07:00
Todd Gamblin
e65a8b6a9a Merge pull request #1463 from davydden/pkg/opium 
opium: add new package
 2016-08-07 15:56:27 -07:00
Todd Gamblin
8121ac2c27 Merge pull request #1464 from hartzell/feature/update-lmod 
No need to patch Lmod after 6.4.4
 2016-08-07 15:55:16 -07:00
Todd Gamblin
93f5a750cb Merge pull request #1465 from glennpj/pango_url 
Add list_url to pango package
 2016-08-07 15:55:04 -07:00
Todd Gamblin
281f6f18e1 Merge pull request #1466 from pramodk/develop 
PDT should download full installer package
 2016-08-07 15:54:50 -07:00
Denis Davydov
db87a9d3ce tar: fix 1.28 on macOS; add 1.29 (#1462) 2016-08-07 15:54:01 -07:00
Adam J. Stewart
d7329d7bc2 Fix erroneously stripped trailing whitespace in patch (#1467) 2016-08-07 15:53:25 -07:00
Pramod Kumbhar
e9edfec0ec PDT should download full installer package pdtoolkit-X.tar.gz (default pdt-X.tar.gz is only for x86 and cray) 2016-08-07 01:14:26 +02:00
Glenn Johnson
2ad21e7070 Add list_url to pango package 
Added a `list_url` so the updated pango tar file can be retrieved.
 2016-08-06 18:12:47 -05:00
George Hartzell
09d96bef9f No need to patch Lmod after 6.4.4 
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...
 2016-08-06 17:39:05 -04:00
George Hartzell
9ebbde0e01 Make configure use our gettext library 
The configure script needs extra encouragement to link against our
gettext/libintl library.
 2016-08-06 16:28:47 -04:00
George Hartzell
1de5817b58 Clean up rebase problems 
My rebase duplicated the depends_on('zlib') and dropped the --with-curl
from the configure.

This fixes those.
 2016-08-06 16:28:47 -04:00
George Hartzell
f699d7c08e [Whitespace] Gather the depends_on's together. 2016-08-06 16:28:47 -04:00
George Hartzell
152fa33a55 Call configure --with-libpcre=... to use our pcre 
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.
 2016-08-06 16:28:47 -04:00
George Hartzell
3cf2fd40a8 Enable depends_on('pcre') also 
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).
 2016-08-06 16:28:47 -04:00
George Hartzell
653905e3a2 Add depends_on('perl') to git package 
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.
 2016-08-06 16:28:47 -04:00
George Hartzell
f800708ef3 Switch to using *std_cmake_args 2016-08-06 16:27:40 -04:00
George Hartzell
6a62a6b693 Flake8 whitespace cleanup 2016-08-06 16:27:40 -04:00
George Hartzell
a07a0ef54b Add Bio++ tool suite and supporting libs 
Add the Bio++ suite and its supporting libraries.
 2016-08-06 16:27:40 -04:00
George Hartzell
3c81bb44ba Add package for mafft 2016-08-06 16:27:40 -04:00
George Hartzell
e0db1f0268 Add package for exonerate 2016-08-06 16:27:40 -04:00
George Hartzell
9e16902397 Fix name of bpp-suite (missing -...) 2016-08-06 16:27:40 -04:00
George Hartzell
63592096c5 Add package for prank 2016-08-06 16:27:40 -04:00
Denis Davydov
4983ebcf7c opium: add new package 2016-08-06 21:35:52 +02:00
becker33
d3f115933e Merge pull request #1451 from hartzell/feature/add-package-for-fastx_toolkit 
Add package for fastx toolkit
 2016-08-05 15:09:46 -07:00
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
a6afaeb974 Remove lingering FIXME commentary 2016-08-05 17:51:24 -04:00
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