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2018-01-04py-umi-tools: Create new package (#6823)Eric1-0/+45
* py-umi-tools: Create new package * py-umi-tools: fix dependencies
2018-01-03Update grackle (#6822)Loikki1-2/+3
2018-01-03package openfoam-com: add version 1712 and update patches (#6820)Mark Olesen12-906/+956
* combine all patches for 1612 into a single file, with additional comments to explain the rational. * Add kahip decomposition variant. * Add support for ARM64 architecture. * filter instead of patching etc/config.*/settings. This eliminates patch files for 1706, perhaps for the future as well. * URLs at or before version 1612 have a different structure, so provide a url_for_version implementation to handle this
2018-01-03package/r-rjags: create new package (#6804)Sinan1-0/+46
* package/r-rjags: create new package * fix typo fix typo * package/r-rjags small fix to pass flake8 tests * package/r-rjags: more fixes to satisfy flake8 tests
2018-01-03fltk depends on libx11. (#6816)健美猫1-0/+2
2018-01-03Add a new version and runtime dependency for MotionCor2. (#6817)健美猫1-0/+3
* Update motioncor2 to 1.0.4 and add libtiff dependency. * Add comments for libtiff dependency in MotionCor2.
2018-01-03Add libtiff@3. (#6818)健美猫1-0/+1
2018-01-03suite-sparse: support 64bit BLAS (#6767)Denis Davydov1-0/+6
* suite-sparse: support 64bit BLAS * use double quotes instead of escaped quotes
2018-01-03Flex v2.6.4 conflicts with gcc@7.2.0 (#6819)stefanosoffia1-0/+4
2018-01-02singularity - added master branch (#6631)Douglas Duckworth1-0/+1
* singularity - added master branch as this has latest fixes - 2.4 does not compile on centos 6 without use of this branch * renamed to develop * added master branch properly
2018-01-02New Package: py-adios (#5686)Axel Huebl1-0/+78
The ADIOS1 numpy bindings depend on an installed, fully loaded ADIOS C library + its config tools to build properly.
2018-01-02Intel mkl dnn (#6268)Brian Van Essen1-0/+39
* Added a package for the MDAnalysis toolkit. * Added a package for the Intel MKL-DNN project. * Fixed flake8 errors. * Fixed Flake8
2018-01-02rsem: update version 1.3.0 md5sum (#6650)Eric1-1/+1
2018-01-02atom-dft: new package plus dependencies (#6653)Michael Kuron3-0/+156
* atom-dft: new package plus dependencies * Indentation fix * Use the compiler wrappers * Pass variables instead of using FileFilter
2018-01-02Install all the cli tools from all the sub-directories (#6705)Jimmy Tang1-1/+6
* Install all the cli tools from all the sub-directories * Satisfy pep8
2018-01-02py-lrudict: a LRU-based cache dictionary (#6734)Feiyi Wang1-0/+38
* add py-lrudict * style fix * style fix: add blank lines
2018-01-02py-scandir: a better directory iterator, backport to 2.7 (#6739)Feiyi Wang1-0/+37
2018-01-02gatk: boilerplate cleanup (#6744)Levi Baber1-15/+0
2018-01-02add OctavePackage (#6746)Denis Davydov5-40/+3
* add OctavePackage 1. remove import CudaPackage which is not needed anymore 2. mention CudaPackage and OctavePackage in packaging guide 3. adjust OctavePackageTemplate 4. add clue file for Octave build 5. sanity check on self.prefix * use setup_environment
2018-01-02py-xattr: a python interface to access extended file attribute (#6747)Feiyi Wang1-0/+38
* py-xattr: a python interface to access extended file attribute * py-xattr: style fix
2018-01-02Lbann update (#6751)Brian Van Essen1-2/+59
* Added a package for the MDAnalysis toolkit. * Updated the LBANN recipe to use the revised cmake environment being rolled out. * Flake8 errors
2018-01-02likwid: add stable 4.3.0 (#6761)Denis Davydov1-3/+2
2018-01-02mesa: disable binutils on macOS (#6763)Denis Davydov1-2/+2
2018-01-02jags: lapack fix (#6764)Levi Baber1-2/+4
* jags: fixing openblas thows a lapack error when compiling. atlas works. other lapack providers may work. also adding tags * changing blas/lapack reference * removing openblas conflict * jags: whitespace cleanup for flake8
2018-01-02Esmf fixes for Cray, OSX and mpich (#6768)Milton Woods2-3/+31
* esmf: put .mod files in the spack compiler search path * esmf: allow building with Cray mpi * esmf: create run-path dependent libraries on osx * esmf: link fortran interface libraries when building with mpich
2018-01-02Adding option to build Nalu with Hypre support. (#6782)Jon Rood1-1/+10
2018-01-02perl-xml-libxml: adding perl module (#6783)peetsv1-0/+35
* perl-xml-libxml: adding perl module * line length change
2018-01-02create perl-file-which package (#6800)Sinan1-0/+34
* create perl-file-which package * trivial edits for package.py so trivial edits for package.py so that flake8 will not complain
2018-01-02Updated 'nginx' from v1.12.0 to v1.13.8. (#6810)stefanosoffia1-0/+1
This fixes build issues with most recent gcc versions. See issue #6252.
2018-01-02py-pyani: Create new package (#6811)Eric1-0/+55
2018-01-02MinCED: Create new package (#6815)Eric1-0/+44
2018-01-02adding specific version url for augustus 3.3 due to old folder structure (#6813)Levi Baber1-1/+2
2018-01-02Tioga package: Explicitly list MPI compilers for Cmake (#6741)Jon Rood1-1/+4
2018-01-02paraview package: Explicitly specify MPI compilers in Cmake (#6738)Jon Rood1-1/+4
2018-01-02new package: Pfunit: unit testing framework for Fortran (#6795)Milton Woods1-0/+97
2018-01-02new package: DIAMOND (#6793)Eric1-0/+35
2018-01-02new package: tantan (#6792)Eric1-0/+38
2018-01-02Cython only needed for develop version of mpi4py (#6780)Adam J. Stewart1-1/+1
2018-01-02new package: py-rseqc (#6773)Eric1-0/+42
2018-01-02package py-biopython: remove py-mx dependency (#6772)Eric1-1/+0
2018-01-02package r-rcurl: boilerplate cleanup (#6771)Eric1-15/+0
2018-01-02bamtools: Add version 2.5.1 (#6770)Eric1-0/+1
2017-12-30Add: lines-are-beautiful (#6784)Axel Huebl1-0/+49
Adds the C++ File API library "lines-are-beautiful" for the reMarkable e-ink tablet.
2017-12-22QMCPACK package: update blas/lapack detection (#6753)Nichols A. Romero2-37/+125
* Fix detection of blas and lapack: provide libraries/includes as arguments to CMake rather than using CMake's auto-detection. This includes a patch to QMCPACK's CMake files to refer to Spack-built blas/lapack implementations. This also includes special-case logic for the intel-mkl implementation of blas/lapack * Break up unit tests and short tests. Only hard failure if the unit tests fail, if short tests fail issue a warning only. * Add QMCPACK 3.3.0, get rid of 3.0.0
2017-12-22dealii: support 64bit BLAS (#6758)Denis Davydov1-1/+9
2017-12-22clang,flang: update CC, CXX environment in installation module (#6737)Andrey Prokopenko2-0/+9
2017-12-22gmap-gsnap: adding version 2014_12_28 (#6720)peetsv1-0/+1
2017-12-20Feature/fasttree (#6227)Levi Baber1-0/+50
* fasttree: new package * fasttree: better version handling * fixing line length for flake8
2017-12-20ENH: better handling of mpich for openfoam packagesMark Olesen3-69/+74
- define MPICH_SKIP_MPICXX, link libmpich instead of libmpi (as per disussion in PR #4990) ENH: more flexible editing/patching of openfoam env files CONFIG: comment out requirement for openmpi+thread_multiple - was originally slated for the 1712 release and beyond, but there are reportedly unstable version/network combinations. Leave as comment for future reference, since it may be arise again. STYLE: renamed openfoam-site.patch as 1706-site.patch (and reformatted) - to preserve against impending changes in the layout of config.{csh,sh}/settings
2017-12-20ENH: improved openfoam module creation (issue #4942)Mark Olesen3-19/+146
- post-install module settings for openfoam-com and foam-extend.
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