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2017-07-18new package to be added: NuT (#4760)jiseung1-0/+62
* 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
2017-07-18price: new package (#4810)Audrey Thoma1-0/+40
2017-07-18New package busco (#4678)Audrey Thoma1-0/+59
* busco: new package * busco: fixing fussy paths * removing paths, probably was a problem with our module setup * fixed dep type
2017-07-18Adding a bit more Mellanox MXM capability to OpenMPI. (#4762)Jon Rood1-0/+23
2017-07-18raxml: new package (#4777)Audrey Thoma1-0/+107
* raxml: new package * changed compiler variable * removing if statement regarding intel compiler
2017-07-18Package/minimd (#4788)homerdin1-0/+74
* New Package: miniMD * Minor Changes * Corrected Dependency * Renamed Executable * Change to use build directory directly
2017-07-18New Package: OpenMC (#4790)pkondamudi1-0/+89
* New Package: OpenMC * comments addressed. * comments addressed. * changed 'os.makedirs' to 'mkdirp' * flake 8 fix.
2017-07-18Open ended variants (#4746)becker331-1/+7
* Change directives to allow open-ended variants more easily * make None default to open-ended
2017-07-18Change path to CMakeLists.txt to be relative to root, not pwd (#4420)Adam J. Stewart9-23/+20
* 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
2017-07-18package: removed default no-op patch (#4103)Massimiliano Culpo1-4/+5
* package: removed default no-op patch fixes #4085 * do_patch: handles NoSuchMethodError nicely
2017-07-18Repalce ftp:// with http:// for gdbm, mesa-glu and udunits2. (#4798)健美猫3-3/+3
2017-07-18somatic-sniper depends_in('curses') (#4796)George Hartzell1-0/+2
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.
2017-07-18Add version 3.4.1 for r. (#4799)健美猫1-0/+1
2017-07-18pcma: new package (#4793)Audrey Thoma1-0/+43
2017-07-18New Package: tig (#4794)Adam Fidel1-0/+36
2017-07-17Package/minixyce (#4789)homerdin1-0/+78
* New Package: miniXyce * Removed Tag
2017-07-17partitionfidner: new package (#4791)Audrey Thoma1-0/+52
2017-07-17qhull: fix to work around a known issue of the library with intel compiler ↵Massimiliano Culpo2-0/+20
(#4648)
2017-07-17bsseeker2: new package (#4770)Audrey Thoma1-0/+49
2017-07-17codar-cheetah: Experimentation harness from the ECP CODAR project (#4658)Kshitij Mehta1-0/+45
* codar-cheetah: Experimentation harness from the ECP CODAR project * codar-cheetah: conforming to flake8
2017-07-17mrbayes: new package (#4757)Audrey Thoma2-0/+119
* mrbayes: new package * fixing beagle version * fixing typos * fixing libbeagle dependency types
2017-07-17New Package: miniSMAC2D (#4767)homerdin1-0/+78
2017-07-17Package/minighost (#4773)homerdin1-0/+94
* New Package: miniGhost * Fixed empty string formatting
2017-07-17ZeroMQ: 4.2.2 & develop (#4785)Axel Huebl1-0/+14
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
2017-07-17pkg-config: aclocal env (#4736)Axel Huebl1-4/+7
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`.
2017-07-15orfm: new package (#4769)Audrey Thoma1-0/+37
2017-07-15Add package for the Python regex library (#4771)George Hartzell1-0/+36
Lightly tested on CentOS 7 with `python@2.7.13` and `python@3.6.0`.
2017-07-15Add package for r-ada, update r-rpart version (#4772)George Hartzell2-0/+39
* 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)
2017-07-15Add package for MuSE (#4779)George Hartzell1-0/+38
2017-07-15Add package for Somatic Sniper (#4778)George Hartzell1-0/+36
Lightly tested on CentOS 7.
2017-07-14New Package: miniFE (#4712)homerdin1-0/+80
* New Package: miniFE * Removed extra property, using variant value directly
2017-07-14Savanna (#4713)Kshitij Mehta1-0/+50
* 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
2017-07-14New Package: Pathfinder (#4714)homerdin1-0/+55
* New Package: Pathfinder * Added index for String format * Changed to make Makefile edit more specific * Make Flake8 Happy * Removed unneeded conversion
2017-07-14Add package for freebayes (#4718)George Hartzell1-0/+51
* Add package for freebayes * Don't include url, must use git info. * Fix flake8 complaints
2017-07-14Add package for Sniffles (#4719)George Hartzell1-0/+42
* 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...
2017-07-14hybpiper: new package (#4720)Audrey Thoma2-0/+104
* hybpiper: new package and spades dependency * hybpiper: making flkae8 happy * hybpiper: fixing dependency errors * fixing python dep type * removing cmake from spade dependencies
2017-07-14Package/cloverleaf (#4759)homerdin1-0/+108
* New Package: CloverLeaf * Removed Tag and Added Documentation * Corrected Dependencies and Variant Values
2017-07-14New Package: Nekbone. (#4748)pkondamudi1-0/+52
2017-07-14New Package: EBMS (#4749)pkondamudi1-0/+46
2017-07-14libwebsockets: new versions (#4764)Axel Huebl2-1/+3
* 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.
2017-07-14slepc: fix download url (#4763)Denis Davydov1-1/+1
2017-07-13New Package:XSBench (#4751)pkondamudi1-0/+59
* New Package:XSBench * minor changes * replaced extend() with append() * addressed comment. * removed tags as per PR# 4749
2017-07-13Add two python packages for editing mach-O headers. (#4725)Patrick Gartung2-0/+73
* Add two python packages for editing mach-O headers. Much faster than calling otool and install_name_tool directly * remove non-overriding function * autopep8
2017-07-13py-deeptools: new package and dependencies (#4717)Audrey Thoma5-0/+159
* py-deeptools: new package and dependencies * py-deeptools: fixing python things * missed a fix
2017-07-13New Package: CloverLeaf3D (#4705)homerdin1-0/+93
* New Package: CloverLeaf3D * Fixed Flake8 Mistake * Removed unnecessary check
2017-07-13graphmap: new package (#4707)Audrey Thoma1-0/+43
2017-07-13Adding OpenMP variant to Trilinos. Also building NetCDF with PNetCDF ↵Jon Rood1-19/+25
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.
2017-07-13idba: new package (#4722)Audrey Thoma1-0/+48
2017-07-13infernal: new package (#4724)Audrey Thoma1-0/+49
2017-07-13last: new package (#4729)Audrey Thoma1-0/+39
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