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Author SHA1 Message Date
George Hartzell
88cb8b493b Add package for freebayes (#4718) 
* Add package for freebayes

* Don't include url, must use git info.

* Fix flake8 complaints
 2017-07-14 15:49:46 -05:00
George Hartzell
ea8c05b263 Add package for Sniffles (#4719) 
* Add package for Sniffles

* Wire up a manual install step

The cmake infra doesn't install anything, so do it by hand.

The binaries land in a location that embeds the version...
 2017-07-14 15:49:02 -05:00
Audrey Thoma
1e205c09d8 hybpiper: new package (#4720) 
* hybpiper: new package and spades dependency

* hybpiper: making flkae8 happy

* hybpiper: fixing dependency errors

* fixing python dep type

* removing cmake from spade dependencies
 2017-07-14 15:48:30 -05:00
homerdin
c78ee4a733 Package/cloverleaf (#4759) 
* New Package: CloverLeaf

* Removed Tag and Added Documentation

* Corrected Dependencies and Variant Values
 2017-07-14 15:46:20 -05:00
pkondamudi
76d95b1798 New Package: Nekbone. (#4748) 2017-07-14 19:40:18 +02:00
pkondamudi
b3692d14fd New Package: EBMS (#4749) 2017-07-14 19:37:52 +02:00
Axel Huebl
0d8b126d66 libwebsockets: new versions (#4764) 
* libwebsockets: new versions

both new versions fix a nasty bug leading to a hanging
connection on connect.

* ISAAC Server: Fix libwebsockets

ISAAC server did hang in docker containers due to a bug
in libwebsockets.
 2017-07-14 10:28:15 -05:00
Denis Davydov
d929ea8102 slepc: fix download url (#4763) 2017-07-14 08:00:28 -05:00
pkondamudi
dfd56da358 New Package:XSBench (#4751) 
* New Package:XSBench

* minor changes

* replaced extend() with append()

* addressed comment.

* removed tags as per PR# 4749
 2017-07-13 22:21:30 -05:00
Patrick Gartung
f63cdc7b61 Add two python packages for editing mach-O headers. (#4725) 
* Add two python packages for editing mach-O headers. Much faster than calling otool and install_name_tool directly

* remove non-overriding function

* autopep8
 2017-07-13 22:07:22 -05:00
Audrey Thoma
3eedbd7c4e py-deeptools: new package and dependencies (#4717) 
* py-deeptools: new package and dependencies

* py-deeptools: fixing python things

* missed a fix
 2017-07-13 22:02:08 -05:00
Alen Kansakar
29fd896179 jags: Adding atlas as it depends on atlas 2017-07-13 09:48:30 -05:00
homerdin
34aea1328a New Package: CloverLeaf3D (#4705) 
* New Package: CloverLeaf3D

* Fixed Flake8 Mistake

* Removed unnecessary check
 2017-07-13 09:22:45 -05:00
Audrey Thoma
d68aa03868 graphmap: new package (#4707) 2017-07-13 09:21:37 -05:00
Jon Rood
47fe9e7aad Adding OpenMP variant to Trilinos. Also building NetCDF with PNetCDF directly, for Trilinos. (#4687) 
* Adding OpenMP variant to Trilinos. Also building NetCDF with PNetCDF in Trilinos when necessary.

* Adding runtime error for PNetCDF variant in Trilinos when necessary. Omitting unnecessary openmp variant for Trilinos in Nalu.

* Changing variant checks to conflicts statements.

* Adding comments to Trilinos package.
 2017-07-13 09:14:15 -05:00
Audrey Thoma
bde58a319b idba: new package (#4722) 2017-07-13 08:35:22 -05:00
Audrey Thoma
c104fa233a infernal: new package (#4724) 2017-07-13 08:32:55 -05:00
Audrey Thoma
4cbe1b338f last: new package (#4729) 2017-07-13 08:26:17 -05:00
Audrey Thoma
e257ea59c2 maverick: new package (#4731) 2017-07-13 08:09:23 -05:00
George Hartzell
adcaa82b88 Add package for daligner (#4734) 2017-07-13 08:08:36 -05:00
Audrey Thoma
c7af89d8fc mcl: new package (#4732) 2017-07-13 08:03:26 -05:00
Denis Davydov
92e6616a8a dealii: workaround for concretization bug (#4735) 
* dealii: workaround for concretization bug

* trilinos: add Anasazi which got disabled recently
 2017-07-13 07:51:45 -05:00
Audrey Thoma
1ecb389dcb mitofates: new package and dependency libsvm (#4741) 2017-07-13 07:44:44 -05:00
Akhil Reddy Patlolla
5ac2020c98 Added ASPA Proxy App (#4743) 2017-07-13 07:30:01 -05:00
Alen Kansakar
6ce33d7773 Jags: Changing depends on to only include lapack 2017-07-12 14:52:54 -05:00
Alen Kansakar
d930c8d01a Jags: Fixing problems found by flack8 2017-07-12 11:39:08 -05:00
kansakar
8873fc3a20 Jags: Adding jags defination 2017-07-12 11:39:07 -05:00
Christoph Junghans
a95f40f18e hpx: added new package (#4709) 2017-07-12 07:54:27 +02:00
George Hartzell
ff906faf9a Typo: submdoules -> submodules (#4716) 2017-07-12 07:48:31 +02:00
Audrey Thoma
3566966d47 genometools: new package (#4706) 
* genometools: new package

* genometools: fixing perl dependency type
 2017-07-11 07:49:00 -05:00
Audrey Thoma
143d50ab67 fseq: new package (#4702) 
* fseq: new package

* fseq: fixed dependency type
 2017-07-10 18:30:24 -05:00
homerdin
5bad9dfeac New Package: MiniAMR (#4701) 
* New Package: MiniAMR

* Removed empty braces string formatting
 2017-07-10 18:30:08 -05:00
homerdin
45e731d574 New Package: HPCCG (#4693) 
* New Package: HPCCG

* Moved Run Script Install Location
 2017-07-10 12:31:41 -05:00
homerdin
c908ccecdc New Package: MiniAero (#4694) 2017-07-10 12:31:23 -05:00
Audrey Thoma
02258056fd exabayes: new pacakge (#4695) 
* exabayes: new pacakge

* exabayes: added configure arg

* exabayes: adding comments regarding compilers
 2017-07-10 12:29:59 -05:00
Audrey Thoma
1f9d6927b7 csdp: new pacakge (#4700) 2017-07-10 12:28:51 -05:00
Audrey Thoma
c80bca00ff ea-utils: new package (#4690) 
* ea-utils: new package

* ea-utils: simplifying self.spec.prefix

* ea-utils: added comment about perl

* ea-utils: fixing flake8 error
 2017-07-10 12:26:03 -05:00
EmreAtes
1abf31d3fa New package: CoMD (#4697) 
* New package: comd

* Avoid re-defining build
 2017-07-09 09:05:11 -05:00
Mike DePaulo
72aa99cb24 GCC: Add strip variant to reduce installation size (#4670) 
* gcc: Add strip variant

* gcc: Fix strip variant description being too long
 2017-07-07 22:17:52 -05:00
George Hartzell
efecefd4dd Add a package for tophat (#4698) 
Lightly tested on CentOS 7.
 2017-07-07 22:15:38 -05:00
Audrey Thoma
56b959501a fastx-toolkit: solving gcc conflict (#4696) 2017-07-07 16:53:15 -05:00
Christoph Junghans
1886b0b370 New package: quinoa (#4686) 2017-07-07 11:11:53 +02:00
homerdin
60a8b68a7e Added TeaLeaf Package (#4683) 2017-07-07 10:54:34 +02:00
Axel Huebl
46e3c2b274 Isaac Server 1.3.1: New version (#4689) 
adds a new release of isaac-server.
 2017-07-07 10:51:09 +02:00
Audrey Thoma
d64405a30f emboss: new package (#4691) 2017-07-07 10:47:26 +02:00
Axel Huebl
396e76eb7c New Packages: gearshifft, clFFT (#4560) 
Adds the `gearshifft` package, a benchmark suite for heterogeneous implementations of FFTs.
Adds clFFT, a software library containing FFT functions written in OpenCL.

see: https://github.com/clMathLibraries/clFFT
 2017-07-07 10:46:35 +02:00
Gregory Lee
28cb1e4379 patch config.guess after autoreconf step (#4604) 2017-07-06 23:07:54 -05:00
Audrey Thoma
e003e2f78b cap3: new package (#4680) 
* cap3: new package

* cap3: removing boilerplate

* cap3: fixed version and added doc
 2017-07-06 13:34:40 -05:00
George Hartzell
8fe51b3ffc Make vcftools actually install its libraries (#4682) 
The vcftools package was installing its Perl libraries into a
directory in the staging directory named 'lib', instead of installing
them into `prefix.lib` where they should have been because the value
passed to the configure script was wrong.

The result was that any attempt to run one of the scripts in the
package failed with something like:

> Can't locate VcfStats.pm in @INC (you may need to install the
> VcfStats module) [...]

This fix provides the correct information in `configure_args`.

Tested lightly on CentOS 7.
 2017-07-06 13:33:57 -05:00
Axel Huebl
b749986dcc Isaac 1.3.1: New version (#4685) 
adds a new release of isaac.
(1.3.0 forgot to bump the internal version number
in include macros)
 2017-07-06 13:23:11 -05:00