Commit graph

8761 commits

Author SHA1 Message Date
Audrey Thoma
cd9742a30b revbayes: trying this again (#4861) 2017-07-21 20:51:39 -05:00
Audrey Thoma
b56add1517 sortmerna: new package (#4866) 2017-07-21 20:51:03 -05:00
Gregory Lee
644f5b3229 added new pruners-ninja version (#4859) 2017-07-21 17:57:12 -05:00
Michael Kuhn
37d6907382 lmdb: Update to 0.9.21 (#4830)
Convert to MakefilePackage and add pkg-config file.
2017-07-21 17:12:17 -05:00
Audrey Thoma
aa98e35e58 singularity: new package (#4852) 2017-07-21 15:36:03 -05:00
Audrey Thoma
4164c5d5e6 smalt: new package (#4853) 2017-07-21 15:35:47 -05:00
Audrey Thoma
469e77068f seqprep: new package (#4850) 2017-07-21 14:25:18 -05:00
Audrey Thoma
cf88490059 sickle: new package (#4851) 2017-07-21 14:25:02 -05:00
Axel Huebl
e864e3bb51 New Package: C-Ares (#4840)
Adds the c-ares library, a C library for asynchronous DNS requests.

Required for the google gRPC library.
2017-07-21 09:36:14 -05:00
Audrey Thoma
51ad3a622e salmon: new package (#4833) 2017-07-21 09:17:55 +02:00
Audrey Thoma
7afce8d8cc satsuma2: new package (#4838) 2017-07-21 08:58:20 +02:00
Milton Woods
7876262826 py-cdat-lite: ensure that RPATH includes netcdf (#4521) 2017-07-20 14:13:36 -05:00
Mark Olesen
0ea2c7904a add mesa +swrender variants (gallium software/off-screen rendering) (#4602)
- +swrender variant lets you compile an off-screen only version for
  software rendering on clusters.

- +swrender+llvm for using llvm for the software pipe

- added newer versions (17.1 and 13.0) and corrected the url location
  to use the canonical location.
2017-07-20 14:12:05 -05:00
Kshitij Mehta
31425974b4 GTKorvo (#4657)
* gtkorvo-atl: atl library from gtkorvo

* gtkorvo-dill: dill library from gtkorvo

* gtkorvo-cercs-env: cercs_env library from gtkorvo

* gtkorvo-enet: Enet networking library from gtkorvo

* libffs: FFS middleware communication library from GTKorvo

* libevpath: EVPath high performance communication library from GTKorvo

* gtkorvo-cercs-env: Added homepage and removed function configure_args

* gtkorvo-cercs-env: Re-add of accidental removal of cmake_args function in previous commit

* gtkorvo-enet: Removed configure_args since unused
2017-07-20 14:07:52 -05:00
pkondamudi
b39e6c6fd0 New Package: SNbone. (#4754)
* removed the tags as per comment in PR# 4749

* addressed above comments

* changed fortran compiler.

* added proxy application tags.

* added tags by removing them from description.

* addressed comments

* used join_path instead of path concat.

* addressed comments

* removed string formatting for LDFLAGS.
2017-07-20 13:26:31 -05:00
Jim Galarowicz
5173a8bef9 Spack updates to three Krell packages (#4765)
* Update the krell institute products to use the latest features of spack for building on cluster platforms.

* Address travis error messages and resubmit the pull request.

* Update the contents of openspeedshop package.py so it passes the flake8 tests.

* Fix flake8 error-whitespack issue in mrnet package.py file.

* Add updates based on spack reviewer feedback.

* More fixes based on comments from reviewers.  Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.

* More review related changes.  Update MPIOption.append lines and take out xercesc references.

* Create a base options function for common openspeedshop base cmake options to reduce redundencies.

* Add libxml2+python depends on to get around issues with the libxml2 package file.

* Using boost over 1.60.0 causes compile errors.  This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.

* Fix bad syntax in specifying the boost version range.

* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.

* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.

* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.

* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.

* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.

* Trim comments to fit more concisely.

* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.

* Fix issues with the cbtf-argonavis build, update to use dyninst-9.3.2, fixes to openspeedshop package build.

* Fix issues with the cbtf-argonavis package.py files related to comments.

* Add changes for changing the krell packages from Package to CMakePackage.

* Add better changes for changing the krell packages from Package to CMakePackage.

* Add more modifications for changing the krell packages from Package to CMakePackage.

* Add additional modifications for changing the krell packages from Package to CMakePackage and fixing Travis erros

* Fix new travis errors.

* Fix new travis errors.

* Add more changes for PR 4765.

* Add more refinements to the conversion from Package to CMakePackage.

* Fix new travis errors.

* Add dependencies for MPI to be passed to cbtf-krell, so it can build the MPI collectors requested by the builder of openspeedshop.

* Remove extra unnecessary routine to adjust build arguments. Fix if-else clause issue.

* Fix more flake issues caused by last changes.
2017-07-20 13:25:57 -05:00
Audrey Thoma
5f0e1514ac kentutils: new pacakge (#4831) 2017-07-20 13:16:32 -05:00
jiseung
16fbd0fc41 new package:SNAP (#4826) 2017-07-20 13:15:43 -05:00
becker33
f962aba6ce Allow packages to control handling of compiler flags (#4421)
* Initial work on flag trapping using functions called <flag>_handler and default_flag_handler

* Update packages so they do not obliterate flags

* Added append to EnvironmentModifications class

* changed EnvironmentModifications to have append_flags method

* changed flag_val to be a tuple

* Increased test coverage

* added documentation of flag handling
2017-07-19 20:12:00 -07:00
George Hartzell
acca75b368 Add info for zsh@5.3.1 (#4827) 2017-07-19 21:49:15 -05:00
pkondamudi
9df9a809a8 Add MPI support and tags to embs package (#4824) 2017-07-19 19:04:48 -05:00
pkondamudi
bdcd63ed70 Add tags to nekbone package (#4825) 2017-07-19 19:03:53 -05:00
jiseung
9ae36849af new package: cns-nospec (#4806)
* new package: cns-nospec

* made changes as suggested and added proxy-app tag

* updated edit()

* adjusted logic for '+debug'
2017-07-19 17:05:19 -05:00
jiseung
301b457de3 new package: amr-exp-parabolic (#4821)
* new package: amr-exp-parabolic

* removed boilerplate and added tag
2017-07-19 17:04:53 -05:00
pkondamudi
1b0d2888bb Package/xsbench (#4822)
* removed the tags as per comment in PR# 4749

* addressed above comments

* changed fortran compiler.

* added proxy application tags.

* added tags by removing them from description.

* addressed comments

* used join_path instead of path concat.

* added tags and other minor changes.

* removed tags from description.
2017-07-19 17:04:17 -05:00
jiseung
60cffbb9d0 new package PENNANT added (#4708)
* new package PENNANT

* made adjustments based on comments

* edited logic for mpi variant

* replaced with 'else'

* prefix.bin instead of 'bin'
2017-07-19 08:50:53 -05:00
Akhil Reddy Patlolla
a6cac6ac99 Added Proxy App CoSP2 (#4726)
*  Added Proxy App CoSP2

*  Updated the PATH

* Updated MPI Fix

*  Fixed Issues

*  Fixed Issues with compiler and Flake8

*  Enhanced block of code.

*  Intended
2017-07-19 08:49:29 -05:00
Akhil Reddy Patlolla
7165129598 Added Proxy App CoHMM (#4727)
*  Added Proxy App CoSP2

*  Added Proxy App CoHMM

*  Updated PATH cohmm

*  Chages Fixing Minor issues

* Minor Fix  git add cohmm/package.py

*  Updated

* Resolved TAG Conflict

*  Updated based on the codecov failure
2017-07-19 08:48:41 -05:00
jiseung
e3e8893ed9 new package: CLAMR (#4728)
* new package: CLAMR

* changed from bool variants to single value variants and corresponding logic in build_type and cmake_args

* lowercase variant values

* updated conditionals for variants

* adjusted url and docstring
2017-07-19 08:48:03 -05:00
pkondamudi
45a7e8bb12 New Package: SimpleMOC (#4742)
* New Package SimpleMOC

* addressed comments

* removed tags as per PR# 4749

* flake8 fix.

* travis fix.

* added proxy app tags to description.

* added mpi and openmpi depedency.

* removed openmpi depdedency.

* addressed comments.

* adding openmp flag conditionally.

* flake 8 fix for tabs.
2017-07-19 08:46:42 -05:00
Kshitij Mehta
6e2eb83943 codar-cheetah: URL fix (#4815) 2017-07-18 22:49:51 -05:00
Adam J. Stewart
5fc0243d35 Improve version detection of release versions (#4816) 2017-07-18 22:48:39 -05:00
jiseung
d1c199e15d new package: SMC (#4817)
* new package: SMC

* removed template and added proxy-app tag

* added comp variant in edit()

* edited comp variant in edit()
2017-07-18 22:48:21 -05:00
Gregory Lee
b411849200 Misc python updates (#4807)
* updated py-pylint version

* setuptools required at runtime for pkg_resources

* fixed url for updated pylint
2017-07-18 19:37:40 -05:00
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