Commit graph

6623 commits

Author SHA1 Message Date
Adam J. Stewart
2bd8d7a36a Always install xproto in serial (#4809) 2017-07-18 19:37:12 -05:00
Audrey Thoma
e2485efb94 poamsa: new package (#4808)
* poamsa: new package

* fixed version specs
2017-07-18 19:36:48 -05:00
jiseung
78c11320d6 new package to be added: NuT (#4760)
* new package to be added: NuT

* removed cmake_args() and made other changes as suggested

* Added setup_environment()

* PEP8 compliant

* edited version name, build_targets, and files/directories to install

* corrected executable directory

* compiler dependencies based on version
2017-07-18 16:37:47 -05:00
Audrey Thoma
748221840a price: new package (#4810) 2017-07-18 16:35:33 -05:00
Audrey Thoma
3e72263d79 New package busco (#4678)
* busco: new package

* busco: fixing fussy paths

* removing paths, probably was a problem with our module setup

* fixed dep type
2017-07-18 13:49:18 -05:00
Jon Rood
904f6f0572 Adding a bit more Mellanox MXM capability to OpenMPI. (#4762) 2017-07-18 13:45:43 -05:00
Audrey Thoma
0e28afef1e raxml: new package (#4777)
* raxml: new package

* changed compiler variable

* removing if statement regarding intel compiler
2017-07-18 13:43:42 -05:00
homerdin
68a8f63569 Package/minimd (#4788)
* New Package: miniMD

* Minor Changes

* Corrected Dependency

* Renamed Executable

* Change to use build directory directly
2017-07-18 13:42:57 -05:00
pkondamudi
e291f59ea3 New Package: OpenMC (#4790)
* New Package: OpenMC

* comments addressed.

* comments addressed.

* changed 'os.makedirs' to 'mkdirp'

* flake 8 fix.
2017-07-18 13:42:11 -05:00
becker33
d2a63d55fa Open ended variants (#4746)
* Change directives to allow open-ended variants more easily

* make None default to open-ended
2017-07-18 10:03:15 -07:00
Adam J. Stewart
1215c3b20c Change path to CMakeLists.txt to be relative to root, not pwd (#4420)
* Change path to CMakeLists.txt to be relative to root, not pwd

* Changes requested during code review

* Revert back to old naming of root_cmakelists_dir
* Make relative directory more clear in docs

* Revert change causing build_type AttributeError

* Fix forgotten abs_path var

* Update CLHEP with new relative path

* Update more packages with new root_cmakelists_dir syntax
2017-07-18 09:58:19 -07:00
Massimiliano Culpo
5a1ee22575 package: removed default no-op patch (#4103)
* package: removed default no-op patch fixes #4085

* do_patch: handles NoSuchMethodError nicely
2017-07-18 09:53:35 -07:00
健美猫
6b2d75a0a6 Repalce ftp:// with http:// for gdbm, mesa-glu and udunits2. (#4798) 2017-07-18 11:22:14 -05:00
George Hartzell
c597bdb284 somatic-sniper depends_in('curses') (#4796)
somatic-sniper installs its own copy of samtools, which needs curses.
I'm not sure why I didn't stumble on this in my dev environment, but I
just stumbled over it in a standalone build.
2017-07-18 09:40:41 -05:00
健美猫
870062076f Add version 3.4.1 for r. (#4799) 2017-07-18 13:04:49 +02:00
Audrey Thoma
07d82422b8 pcma: new package (#4793) 2017-07-18 11:13:17 +02:00
Adam Fidel
da61455cc3 New Package: tig (#4794) 2017-07-18 11:10:39 +02:00
homerdin
7c1ce6e206 Package/minixyce (#4789)
* New Package: miniXyce

* Removed Tag
2017-07-17 15:50:31 -05:00
Audrey Thoma
9872fe980b partitionfidner: new package (#4791) 2017-07-17 15:49:26 -05:00
Massimiliano Culpo
6dcbc30a2c qhull: fix to work around a known issue of the library with intel compiler (#4648) 2017-07-17 14:39:09 -05:00
Audrey Thoma
2bf140601b bsseeker2: new package (#4770) 2017-07-17 19:02:17 +02:00
Kshitij Mehta
9c9f0c9612 codar-cheetah: Experimentation harness from the ECP CODAR project (#4658)
* codar-cheetah: Experimentation harness from the ECP CODAR project

* codar-cheetah: conforming to flake8
2017-07-17 09:33:57 -05:00
Audrey Thoma
990d60d340 mrbayes: new package (#4757)
* mrbayes: new package

* fixing beagle version

* fixing typos

* fixing libbeagle dependency types
2017-07-17 09:20:49 -05:00
homerdin
62f5eafc55 New Package: miniSMAC2D (#4767) 2017-07-17 09:15:15 -05:00
homerdin
f43e4890db Package/minighost (#4773)
* New Package: miniGhost

* Fixed empty string formatting
2017-07-17 09:13:46 -05:00
Axel Huebl
c110d03f95 ZeroMQ: 4.2.2 & develop (#4785)
The 4.X branches are now on the homepage, so we take the GitHub release
artifact (careful: take their upload, not the automatic tarball).

Adds a development version of ZeroMQ.
Requires a autogen run, as for all their unreleased versions,
and the pkg-config fix in #4736
2017-07-17 08:40:48 -05:00
Axel Huebl
febf41e0e2 pkg-config: aclocal env (#4736)
Always sets the `pkg-config` environment hint for
autotools.

Required dependency for `autoreconf` of ZeroMQ when
build from source (e.g. v4.2.2) via autotools in `autogen.sh`
step for `autoreconf`.
2017-07-17 08:40:22 -05:00
Audrey Thoma
7e32756fce orfm: new package (#4769) 2017-07-15 19:03:55 +02:00
George Hartzell
89ef576ba4 Add package for the Python regex library (#4771)
Lightly tested on CentOS 7 with `python@2.7.13` and `python@3.6.0`.
2017-07-15 18:11:54 +02:00
George Hartzell
ad2a22fa01 Add package for r-ada, update r-rpart version (#4772)
* Add package for r-ada, update r-rpart version

Adds a package for r-ada.

Update the version for r-rpart because the previous version is
no longer at that URL.  The previous version *is* in the Archive,
but list_url does not seem to be able to find it.

* Clean up FIXMEs (blush)
2017-07-15 18:08:36 +02:00
George Hartzell
8e6d7f117a Add package for MuSE (#4779) 2017-07-15 18:06:43 +02:00
George Hartzell
8bd22c3294 Add package for Somatic Sniper (#4778)
Lightly tested on CentOS 7.
2017-07-15 18:05:51 +02:00
homerdin
246c07f864 New Package: miniFE (#4712)
* New Package: miniFE

* Removed extra property, using variant value directly
2017-07-14 15:55:51 -05:00
Kshitij Mehta
31503cb058 Savanna (#4713)
* savanna: Runtime framework for online workflow management from the ECP CODAR project

* savanna: added version 0.5

* savanna: Copying the package contents to prefix as part of installation

* savanna: Doing submodules=true for git checkout of develop version

* savanna: removed dependency on adios@develop. depends on adios

* Savanna: Converted package to MakefilePackage
2017-07-14 15:54:57 -05:00
homerdin
f5f37845d6 New Package: Pathfinder (#4714)
* New Package: Pathfinder

* Added index for String format

* Changed to make Makefile edit more specific

* Make Flake8 Happy

* Removed unneeded conversion
2017-07-14 15:54:31 -05:00
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
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