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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 Davydov2-2/+8
* 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
2017-12-18spack install: make restaging the default (#6465)Massimiliano Culpo2-3/+9
Fixes #5940 This PR changes the option '--restage' of 'spack install' to '--dont-restage', inverting its meaning and the default behavior of the command.
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
2017-12-16build lapacke with tmg (#6654)fpruvost1-1/+4
2017-12-16bwa: added version 0.7.16a and checksum (#6658)David Orman1-0/+2
2017-12-16Hadoop: Replace broken url (#6671)Jack Morrison1-2/+2
2017-12-16Caliper update, add version 1.6.0 (#6680)David Böhme1-4/+17
2017-12-16py-bx-python: Create new package (#6672)Eric1-0/+39
2017-12-16py-tetoolkit: Create new package (#6673)Eric1-0/+42
2017-12-16py-pandas: add versions 0.19.2 and 0.21.1 (#6687)Eric1-0/+2
2017-12-16Add petsc version 3.8.3 (#6688)Paschalis Korosoglou1-0/+1
2017-12-16Add clanguage variant for petsc (#6689)Paschalis Korosoglou1-0/+8
2017-12-16bedtools2: Add version 2.27.1 (#6693)Eric1-0/+1
2017-12-16MetaSV: adding new package (#6691)peetsv1-0/+39
2017-12-16PANDAseq: Create new package (#6694)Eric1-0/+48
2017-12-16DeNovoGear: Create new package (#6699)Eric1-0/+43
2017-12-16mefit: Create new package. (#6700)lingnanyuan1-0/+47
2017-12-16moltemplate: add new package (#6702)Denis Davydov1-0/+38
2017-12-15new package: gatk (#6674)David Orman2-0/+91
2017-12-14new package: Percept (#6636)Jon Rood4-0/+151
This also adds the 'exception' boost library to the set of default libraries built by boost.
2017-12-14Skip collection of compilers which report an empty version (#6684)scheibelp2-19/+39
Fixes #6200 For compilers that successfully run a version detection script but don't actually return a version, Spack was keeping track of the empty version and then failing when attempting to construct a compiler spec. This skips any attempt to add a compiler entry when no version is reported (but logs when a compiler fails to report a version).
2017-12-14added breakdancer (#6319)Douglas Duckworth1-0/+47
2017-12-14fftw: added version 3.3.7 (#6678)Massimiliano Culpo1-0/+1
2017-12-14misc fixes, changed to EnvironmentModifications (issue #6501) (#6541)Mark Olesen1-11/+52
* Support pruning of vars with Env from_sourcing_file (issue #6501) - Blacklist string literals or regular expressions of environment variables that are to be removed from consideration as being affect by the sourcing of the file. Conversely, whitelist modifications that should not ignored. Whitelisted variables have priority over blacklisting. Eg, EnvironmentModifications.from_sourcing_file ( bashrc blacklist=['JUNK_ENV', 'OPTIONAL_.*'], whitelist=['OPTIONAL_REQUIRED.*'] ) This modification can be used to eliminate environment variables that are not generalized for modules (eg, user-specific variables). * BUG: module prepend-path in wrong order (fixes #6501) * STYLE: module variables in sorted order (issue #6501) - looks nicer and also helps when comparing the contents of different module files. * ENH: remove duplicates from env paths when creating modules (issue #6501) - this makes for a cleaner module environment and helps avoid some unnecessary changes to the environment that are only provoked by redundancies in the PATH. eg, before PATH=/usr/bin after PATH=/usr/bin:/usr/bin:/my/application/bin should only result in /my/application/bin being added to the PATH and not /usr/bin:/my/application/bin Activate via the 'clean' flag (default: False): EnvironmentModifications.from_sourcing_file(bashrc, clean=True,..
2017-12-14Add TIOGA package and optional dependency of Nalu on TIOGA (#6638)Jon Rood2-0/+64
2017-12-14libharu: Make dependencies on zlib and libpng explicit (#6682)Scott Wittenburg1-0/+13
2017-12-13relion: add version and cuda arch variant (#6317)Douglas Duckworth1-1/+20
Add preferred version 2.0.3. Added beta version. Added conflict with gcc versions >= 5 when building with cuda@8 (which is currently the only supported cuda version). Added cuda architecture variant. Added comment about current lack of cuda@9 support.
2017-12-13tasmanian: add new package (#6659)Denis Davydov1-0/+36
2017-12-13CUDA: 9.1 (#6663)Axel Huebl1-1/+4
Add the latest CUDA release, 9.1
2017-12-13py-pysam: adding old version 0.7.7 (#6675)peetsv1-0/+1
2017-12-13SPAdes: add version 3.11.1 (#6668)Eric1-0/+1