Commit graph

6785 commits

Author SHA1 Message Date
becker33
30f6d2ab90 fix callpath bug (#4659)
* fix callpath bug I found while testing env/cc

* fix hanging indent for flake
2017-07-25 13:51:56 -07:00
Audrey Thoma
6693dc1092 transdecoder: new package (#4895)
* transdecoder: new package

* fixed package structure
2017-07-25 15:51:14 -05:00
Audrey Thoma
402233ecc8 transposome: new package (#4896) 2017-07-25 15:50:42 -05:00
Audrey Thoma
668233a819 trimgalore: new package (#4899) 2017-07-25 15:50:23 -05:00
Gregory Lee
42717bd8e8 fix config.guess patch for ppc64le (#4858)
* fix config.guess patch for ppc64le

* explicit patch for config.guess not required
2017-07-25 13:44:51 -07:00
Audrey Thoma
71991cd9c9 cleaveland4: new package (#4894)
* cleaveland4: new package

* fixing return line in viennarna url_for_version
2017-07-25 13:18:34 -05:00
Audrey Thoma
20ab66a2e9 tabix: new package (#4886)
* tabix: new package

* fixed docs location
2017-07-25 13:02:08 -05:00
Audrey Thoma
5184dda309 sumaclust: new package (#4884)
* sumaclust: new package

* tweaking url and make specs
2017-07-25 08:04:25 -05:00
Jimmy Tang
1d1a0e3d63 Update zstd version (#4873)
* Update zstd version

* Change order of versions

* Use MakefilePackage
2017-07-25 07:55:02 -05:00
Jimmy Tang
2b792f943f Rename the gpu variant to cuda, this is to be consistent with other (#4890)
packages.
2017-07-25 07:53:33 -05:00
Denis Davydov
b0b86e5ffe fix GobjectIntrospection on Darwin (#4872)
* fix GobjectIntrospection on Darwin

* minor
2017-07-24 19:51:17 -05:00
Audrey Thoma
4237e5fffd stacks: new package (#4875) 2017-07-24 19:50:40 -05:00
Stas Sergienko
07e60bc26b added new version of jdk 8u141-b15 (#4876) 2017-07-24 19:50:16 -05:00
Audrey Thoma
d2f08c95d9 swarm: new package (#4885) 2017-07-24 19:49:59 -05:00
Audrey Thoma
8038945145 structure: new package (#4879)
* structure: new pacakge

* fixing package structure (not a pun)
2017-07-24 18:02:20 -05:00
Audrey Thoma
0c96c330ec subread: new package (#4882) 2017-07-24 18:01:56 -05:00
Stas Sergienko
9aa3749787 added new version of cdo (#4877) 2017-07-24 15:50:44 -05:00
Audrey Thoma
bd0699b026 stringtie: new package (#4878) 2017-07-24 15:50:32 -05:00
Adam J. Stewart
250ee413e9 Change Version formatting properties and functions to return Version objects (#4834)
* Change version.up_to() to return Version() object
* Add unit tests for Version.up_to()
* Fix packages that expected up_to() to return a string
* Ensure that up_to() preserves separator characters
* Use version indexing instead of up_to
* Make all Version formatting properties return Version objects
* Update docs
* Tests need to test string representation
2017-07-24 13:02:13 -07:00
Jimmy Tang
df2fc25ddf Add a py-theano version from git repo (#4871) 2017-07-24 08:56:54 -05:00
健美猫
8a06e3d867 Add cuda variant for mvapich2. (#4800)
* Add cuda variant for mvapich2.

* Disable cuda for mvapich2 by default.
2017-07-23 12:18:05 -05:00
Stephen McDowell
1cdb3c61ca fix sphinx dependencies, add v1.6.3 (#4870) 2017-07-23 09:44:12 -05:00
Milton Woods
4044e9f918 Perl - allow package activation without PERL5LIB variable (#4540)
* perl: prepend default perl @INC path to support package activation

* perl: remove stray comma from list of configure arguments

* perl: final comma in configure arguments makes adding arguments safer

This reverts commit fdc10cd611f525ebc31ca1953e048095b1c75350.

* perl: add comment about modified @INC (thanks to George Hartzell)

* perl: use self.prefix.lib and self.prefix.bin for clarity

* perl: convert tabs added by editor to spaces for flake8

* perl: use new path syntax: prefix.lib.perl5

* perl: avoid line break before binary operator

* perl: use compact spack syntax for perl executable
2017-07-23 09:41:45 -05:00
Axel Huebl
62b4087c09 gBenchmark: Development Package (#4847)
* gBenchmark: Development Package

Add the development version (master branch) of `gBenchmark`

* gBenchmark: Remove Duplicate

Remove duplicate `gbenchmark` library
and keep its patch to remove the shipped
-Werror
2017-07-23 09:35:16 -05:00
Todd Gamblin
f159246d1d Make testing spack commands simpler (#4868)
Adds SpackCommand class allowing Spack commands to be easily in Python

Example usage:

    from spack.main import SpackCommand
    info = SpackCommand('info')
    out, err = info('mpich')
    print(info.returncode)

This allows easier testing of Spack commands.

Also:
* Simplify command tests
* Simplify mocking in command tests.
* Simplify module command test
* Simplify python command test
* Simplify uninstall command test
* Simplify url command test
* SpackCommand uses more compatible output redirection
2017-07-22 21:27:54 -07:00
Kshitij Mehta
c07d93a3e5 Savanna (#4856)
Installing the stable version 0.5 through the checksummed tar.gz does not fetch the git submodule in the package.
The submodule appears as an empty directory.

Thus, clone the commit tagged as v0.5 using git to get around this issue

* savanna: modified adios dependency spec
* Replaced adios+staging with adios+flexpath+dataspaces
* savanna: Enabling fortran support in adios by default
* savanna: reverting to variant 'staging' for enabling all staging transports
2017-07-21 23:47:13 -07:00
Audrey Thoma
aa96e1671b sparta: new package (#4867)
* sparta: new package

* fixing homepage
2017-07-21 21:40:31 -05:00
jiseung
e191ead9ac new package: miniGMG (#4849)
* new package: miniGMG

* changed based on comments

* removed cuda version
2017-07-21 20:52:09 -05:00
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