Commit graph

8752 commits

Author SHA1 Message Date
junkudo
d69d692203 CoinHSL : Prevent CoinHSL from building in parallel (#6715)
CoinHSL does not seem to be able to be built in parallel. This commit forces serial compilation.
2017-12-19 08:30:39 +01:00
Denis Davydov
548c225d45 dealii: add GMSH, add CMAKE_FIND_APPBUNDLE to CMakePackage (#6723)
* dealii: add GMSH dependency

* CMakePackage: add CMAKE_FIND_APPBUNDLE to prevent picking up binaries from /Applications
2017-12-19 08:28:55 +01:00
peetsv
e8de22ce46 lftp: adding version 4.6.4 (#6721) 2017-12-19 08:19:33 +01:00
Mark Olesen
b3e9192d18 openfoam-org: new version (#6686)
Add new version with a patch.
2017-12-18 19:47:49 -08:00
peetsv
f7a5a27138 IGV: new package (#6710) 2017-12-18 19:37:09 -08:00
Massimiliano Culpo
0192455885 spack install: make restaging the default (#6465)
Fixes #5940

This PR changes the option '--restage' of 'spack install' to
'--dont-restage', inverting its meaning and the default behavior
of the command.
2017-12-18 18:50:02 -08:00
Benedikt Riedel
36fa574779 globus-toolkit: add version and openssl dependency (#6617) 2017-12-18 15:23:56 -08:00
Douglas Duckworth
d3519af7de relion - added new stable version 2.1 (#6706) 2017-12-18 10:38:20 -08:00
healther
0cff0fba73 fix post install method for py3 in mercurial (#6497)
* 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
2017-12-17 12:00:58 -06:00
Sergey Kosukhin
576ef5e2b3 Package 'cdo': get rid of unnecessary dependency on MPI C++ library. (#6632) 2017-12-16 19:48:56 -07:00
nshtg
2a639097b0 Add new package signify (#6645)
OpenBSD tool to sign and verify signatures on files.

See https://github.com/aperezdc/signify
2017-12-16 19:47:59 -07:00
Eric
7d800a0fc2 breseq: Create new package (#6648) 2017-12-16 19:47:11 -07:00
fpruvost
6c81cf1a78 build lapacke with tmg (#6654) 2017-12-16 19:43:46 -07:00
David Orman
7b8d889d31 bwa: added version 0.7.16a and checksum (#6658) 2017-12-16 19:43:02 -07:00
Jack Morrison
d4cc1ac86b Hadoop: Replace broken url (#6671) 2017-12-16 19:42:03 -07:00
David Böhme
3467c207c8 Caliper update, add version 1.6.0 (#6680) 2017-12-16 19:39:52 -07:00
Eric
dac09dd5fb py-bx-python: Create new package (#6672) 2017-12-16 19:38:59 -07:00
Eric
d08dc0c019 py-tetoolkit: Create new package (#6673) 2017-12-16 19:38:36 -07:00
Eric
d3545ed1b3 py-pandas: add versions 0.19.2 and 0.21.1 (#6687) 2017-12-16 19:38:02 -07:00
Paschalis Korosoglou
a69cfd5f78 Add petsc version 3.8.3 (#6688) 2017-12-16 19:37:35 -07:00
Paschalis Korosoglou
61dbd3182d Add clanguage variant for petsc (#6689) 2017-12-16 19:37:20 -07:00
Eric
87420dccee bedtools2: Add version 2.27.1 (#6693) 2017-12-16 19:36:35 -07:00
peetsv
5d0e7abcc5 MetaSV: adding new package (#6691) 2017-12-16 19:36:11 -07:00
Eric
5539c94e67 PANDAseq: Create new package (#6694) 2017-12-16 19:35:48 -07:00
Eric
554d4045fa DeNovoGear: Create new package (#6699) 2017-12-16 19:34:53 -07:00
lingnanyuan
34cf796b54 mefit: Create new package. (#6700) 2017-12-16 19:34:30 -07:00
Denis Davydov
f78418d8bb moltemplate: add new package (#6702) 2017-12-16 19:33:28 -07:00
David Orman
176b518d4b new package: gatk (#6674) 2017-12-15 11:00:55 -08:00
Jon Rood
7369ba21bf new package: Percept (#6636)
This also adds the 'exception' boost library to the set of default
libraries built by boost.
2017-12-14 18:11:47 -08:00
scheibelp
020ce7735d
Skip collection of compilers which report an empty version (#6684)
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).
2017-12-14 17:54:57 -08:00
Douglas Duckworth
1aed3f7c01 added breakdancer (#6319) 2017-12-14 14:43:32 -07:00
Massimiliano Culpo
6c1fa37e3d
fftw: added version 3.3.7 (#6678) 2017-12-14 21:38:33 +01:00
Mark Olesen
5727054c4a misc fixes, changed to EnvironmentModifications (issue #6501) (#6541)
* 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,..
2017-12-14 21:24:06 +01:00
Jon Rood
b447c2ba51 Add TIOGA package and optional dependency of Nalu on TIOGA (#6638) 2017-12-14 11:46:25 -08:00
Scott Wittenburg
ce832fca59 libharu: Make dependencies on zlib and libpng explicit (#6682) 2017-12-14 08:58:42 +01:00
Douglas Duckworth
5a66065dfa relion: add version and cuda arch variant (#6317)
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.
2017-12-13 10:30:38 -08:00
Denis Davydov
c0aa12111b tasmanian: add new package (#6659) 2017-12-13 16:01:51 +01:00
Axel Huebl
836bf65250 CUDA: 9.1 (#6663)
Add the latest CUDA release, 9.1
2017-12-13 14:43:40 +01:00
peetsv
2e4c9e47a8 py-pysam: adding old version 0.7.7 (#6675) 2017-12-13 09:01:45 +01:00
Eric
5fa9e61321 SPAdes: add version 3.11.1 (#6668) 2017-12-13 08:57:29 +01:00
David Orman
c5cb8ae159 picard: added version 2.13.2 (#6669) 2017-12-13 08:57:06 +01:00
Scott Wittenburg
6628b6ca01 Ignore log files that appear in root dir with "spack -d install ..." (#6670) 2017-12-13 08:35:39 +01:00
Audrey Thoma
45784af7f2 new packages: biopieces and dependencies (#6478)
This also adds the tcl, tk, and libx11 dependencies to ruby. All other
changes are new packages.
2017-12-12 18:35:13 -08:00
Christoph Junghans
27be66420a
laghos: inject CXX (#6664) 2017-12-12 17:26:02 -07:00
Christoph Junghans
e80a27d713
swfft: inject CC/CXX (#6666) 2017-12-12 17:25:48 -07:00
Satish Balay
80284617a5 xsdk: update xsdk@develop to use sundials, plasma, magma (#6649)
Also update xsdk@0.3.0 to use a fixed version of magma
2017-12-12 09:31:08 -08:00
nshtg
e831ecbf3a Add new package minisign (#6644)
A dead simple tool to sign files and verify signatures.

See https://jedisct1.github.io/minisign
2017-12-11 17:27:40 -07:00
nshtg
45e8e4b4fb libsodium: Update to 1.0.15 (#6643) 2017-12-11 17:27:09 -07:00
nshtg
25aa21a7a7 git: Update to 2.15.1 (#6642) 2017-12-11 17:26:53 -07:00
nshtg
74938f58d2 openssl: Update to 1.0.2n (#6641)
From 07.12.2017, fixes CVE-2017-3737
2017-12-11 17:26:37 -07:00