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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.
2017-12-20picard: Add version 2.17.0 (#6729)Eric1-0/+1
2017-12-20octave: add optim and struct packages (#6733)Denis Davydov2-0/+98
2017-12-19sqlite package: apply B0 patch to additional versions (#6728)Gregory Lee1-1/+1
2017-12-19slepc: add 3.8.2 (#6724)Denis Davydov1-0/+1
2017-12-19intel-tbb: add 2018.2 (#6725)Denis Davydov1-0/+2
2017-12-19hypre: add 2.13.0 (#6726)Denis Davydov1-0/+1
2017-12-19suite-sparse: add 5.1.0 (#6727)Denis Davydov1-0/+1
2017-12-19Added GDB verison 8.0 (#6704)Jack Morrison1-0/+1
2017-12-19nextflow: adding version 0.21.0 (#6722)peetsv1-0/+2
2017-12-19Emacs: added gnutls variant (tested on Centos 7) (#6711)Peter Doak2-0/+12
2017-12-19gmsh: add 3.0.6 (#6718)Denis Davydov1-0/+1
2017-12-19CoinHSL : Prevent CoinHSL from building in parallel (#6715)junkudo1-0/+3
CoinHSL does not seem to be able to be built in parallel. This commit forces serial compilation.
2017-12-19dealii: add GMSH, add CMAKE_FIND_APPBUNDLE to CMakePackage (#6723)Denis Davydov1-1/+4
* dealii: add GMSH dependency * CMakePackage: add CMAKE_FIND_APPBUNDLE to prevent picking up binaries from /Applications
2017-12-19lftp: adding version 4.6.4 (#6721)peetsv1-0/+1
2017-12-18openfoam-org: new version (#6686)Mark Olesen2-2/+29
Add new version with a patch.
2017-12-18IGV: new package (#6710)peetsv1-0/+54
2017-12-18globus-toolkit: add version and openssl dependency (#6617)Benedikt Riedel1-0/+3
2017-12-18relion - added new stable version 2.1 (#6706)Douglas Duckworth1-5/+2
2017-12-17fix post install method for py3 in mercurial (#6497)healther1-3/+5
* fix post install method for py3 in mercurial * Update package.py * Update package.py * use print_str instead of manual print detection * Update package.py * use only depends_on * Update package.py * Update package.py State py3 compatibility for @4.3: according to setup.py from the 4.3.tar.gz from pypi
2017-12-16Package 'cdo': get rid of unnecessary dependency on MPI C++ library. (#6632)Sergey Kosukhin1-2/+9
2017-12-16Add new package signify (#6645)nshtg1-0/+39
OpenBSD tool to sign and verify signatures on files. See https://github.com/aperezdc/signify
2017-12-16breseq: Create new package (#6648)Eric1-0/+44