Commit graph

13421 commits

Author SHA1 Message Date
Toyohisa Kameyama
b89fa3e01a fastqvalidator: add zlib dependency and Removes erroneous deletes in Chromosome (#13030) 2019-10-03 22:19:58 -05:00
Toyohisa Kameyama
4046e10b95 hapcut2: add zlib dependency. (#13032) 2019-10-03 22:19:43 -05:00
Toyohisa Kameyama
2233a7b493 liblbxutil: Add zlib dependency. (#13033) 2019-10-03 22:19:22 -05:00
Toyohisa Kameyama
bb1d0ff6fb metabat: Add zlib and ncurses dependency. (#13034) 2019-10-03 22:18:55 -05:00
Toyohisa Kameyama
58a64f69e7 muse: add zlib dependency. (#13040) 2019-10-03 22:18:27 -05:00
Toyohisa Kameyama
c97be22ff5 ngmlr: add zlib dependency. (#13041) 2019-10-03 22:18:12 -05:00
Andreas Baumbach
4e7ea627c8 fix ipykernel dependency, newer versions are python3-only (#13019)
* fix ipykernel dependency, newer versions are python3-only

* Update var/spack/repos/builtin/packages/py-ipykernel/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-ipykernel/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-03 22:17:16 -05:00
George Hartzell
882843974b Update cctools to v7.0.18 (#13037)
- add version/checksum info for v7.0.18
- update checksum for v6.1.1 to use sha256, while I have the editor
  open...
2019-10-03 18:57:20 -05:00
Owen Solberg
bef702d0f3 updated manta checksum (#13038) 2019-10-03 18:23:47 -05:00
Adam J. Stewart
69acb024a5
Add py-flye 2.6 (#13025) 2019-10-03 10:32:00 -05:00
Adam J. Stewart
24f8d1042b
Update compilers.yaml location in Getting Started docs (#13029) 2019-10-03 10:31:32 -05:00
Adam J. Stewart
dac34147c0 Add EasyBuild 4.0.0 (#13024)
* Add EasyBuild 4.0.0

* Update homepage, remove no longer required deps

* Replace version ranges with fixed versions
2019-10-03 16:48:42 +02:00
Chuck Atkins
b973f038fd
Update ECP Data & Vis SDK packages (#13027)
* ecp-io-sdk: Add faodel and sort variants

* ecp-viz-sdk: Re-enable catalyst, sort variants, turn on by default

* ecp-io-sdk and ecp-viz-sdk: Fix dependency variants
2019-10-03 10:05:02 -04:00
Massimiliano Culpo
78577c0a90
Generic x86_64 code compiled with GCC uses non deprecated mtune flags (#13022)
fixes #12928
2019-10-03 10:31:03 +02:00
Massimiliano Culpo
76b9c56110 Remove support for generating dotkit files (#11986)
Dotkit is being used only at a few sites and has been deprecated on new
machines. This commit removes all the code that provide support for the
generation of dotkit module files.

A new validator named "deprecatedProperties" has been added to the
jsonschema validators. It permits to prompt a warning message or exit
with an error if a property that has been marked as deprecated is
encountered.

* Removed references to dotkit in the docs
* Removed references to dotkit in setup-env-test.sh
* Added a unit test for the 'deprecatedProperties' schema validator
2019-10-02 22:15:01 -07:00
Miroslav Stoyanov
b11984767b added tasmanian version 7.0 to spack (#13003) 2019-10-02 18:35:49 -05:00
Sinan
b084d095bc New package: mapnik (#12708) 2019-10-02 13:50:57 -07:00
Tiziano Müller
d99b92febd libint + cp2k: 2-stage build with 'tune' and 'fortran' variants (#12475)
* libint: switch to 2-stage build for 2.6.0+

* libint: add tune and fortran variants

* cp2k: add support for libint >= 2.0

* cp2k: use pkg-config for linking libxc
2019-10-02 21:31:19 +02:00
Toyohisa Kameyama
da18ac3a0f cdhit: add zlib dependency. (#13015)
* cdhit: add zlib dependency.

* Add zlib variant.
2019-10-02 12:55:05 -05:00
Toyohisa Kameyama
b85ff04681 denovogear: Add missing zlib depenbdency and fix open handling error. (#13017) 2019-10-02 12:54:50 -05:00
Toyohisa Kameyama
58c01792ef cnpy: add zlib dependency. (#13016) 2019-10-02 12:54:31 -05:00
Dan Lipsa
210dd594a1 Add cuda to paraview build. (#12996) 2019-10-02 12:00:03 -05:00
George Hartzell
21e95e4141 Singularity 3.4.1 still needs the makefile patch (#13008)
* Singularity 3.4.1 still needs the makefile patch

* Constrain build patch to 3.4.0:3.4.1
2019-10-02 11:59:11 -05:00
Sinan
afca223b3d new package: openldap (#12748)
* new package: openldap

* fix mistake

* remove template text

* fix build error involving perl

* flake8

* improvements

* introduce multi valued variant for tls support

* improve tls variant

* overwrite build phase as opposed install

* improve style
2019-10-02 11:58:46 -05:00
Toyohisa Kameyama
1550d5cae6 ants: missing zlib dependency and fix working directory in install. (#13010) 2019-10-02 11:58:25 -05:00
Toyohisa Kameyama
7d9514d3fa breakdancer: missing ncurses dependency. (#13011) 2019-10-02 11:57:05 -05:00
Toyohisa Kameyama
d238b9d394 breseq: fix dependency and limit compiler version. (#13013) 2019-10-02 11:56:37 -05:00
t-karatsu
a3a0e1cd2e fujitsu compiler: Add 'required_libs'. (#13014) 2019-10-02 11:55:08 -05:00
Andreas Baumbach
64ff27626e update py-jupyter-notebook to use the real releases (#13020)
* github releases are not released versions, but from-source
  releases
* they lack the mimification of the JS/CSS components and as
  such require node-js and npm, this conflicts with python@3:
* this commit
  * drops the from-source dependencies on node-js and npm and
  * updates the checksums to the correct sha256 hashes of the
    pypi releases. The pypi-tarballs are different
2019-10-02 11:39:55 -05:00
Patrick Gartung
2a739ed03e
Replace expensive store.reindex() call with db.add() call. (#13021) 2019-10-02 11:30:28 -05:00
Axel Huebl
bec2830802
ZFP: CMake Package (#12999)
* ZFP: CMake Package

ZFP is primarily build via CMake, which will have all install logic
and configuration files generated.
The 0.5.0 release did not support this yet, so we toss it.

* Patch ADIOS1: ZFP 0.5.1+ support

* ZFP: Expose all CMake variants
2019-10-01 23:28:36 -07:00
Patrick Gartung
9dfec4a57c
'spack buildcache list' should show all buildaches available. (#13002)
* binary cache: show all packages for compatible differing targets

* Don't restrict spack buildcache list to arch or os

* Fix from merge conflict
2019-10-01 22:54:22 -05:00
George Hartzell
22e75b77e3 direnv: add info for version 2.20.0 (#13007) 2019-10-01 22:34:14 -05:00
Massimiliano Culpo
1b18ec90ab Add all compatible system types directory to module paths
fixes #12915
closes #12916

Since Spack has support for specific targets it might happen that
software is built for targets that are not exactly the host because
it was either an explicit user request or the compiler being used is
too old to support the host.

Modules for different targets are written into different directories
and by default Spack was adding to MODULEPATH only the directory
corresponding to the current host. This PR modifies this behavior to
add all the directories that are **compatible** with the current host.
2019-10-01 19:18:27 -07:00
Sinan
d20e3517c2 new package: py-python-ldap (#12599)
* new package: py-python-ldap

* fix dependency types

* improvements

* Update var/spack/repos/builtin/packages/py-python-ldap/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-python-ldap/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* add openldap dependency
2019-10-01 20:59:53 -05:00
Sinan
91488ed8f5 New package: py-python-mapnik (#12786) 2019-10-01 18:37:34 -07:00
codeandkey
5c2b01ebcf picard: add 2.20.8 2019-10-01 18:19:37 -07:00
Daryl W. Grunau
248bc17bb0 go-md2man: disable module-mode (#12985)
* go-md2man: disable module-mode

* Update var/spack/repos/builtin/packages/go-md2man/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-01 19:17:10 -05:00
Eduardo Arango
c1ecd037d7 add singularity 3.4.1 (#12995)
* add singularity 3.4.1

Signed-off-by: ArangoGutierrez <eduardo@sylabs.io>

* revert some changes

Signed-off-by: ArangoGutierrez <eduardo@sylabs.io>

* add maintainers list to pkg singularity

Add @alalazo and me to the Singularity maintainers list

* Update var/spack/repos/builtin/packages/singularity/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/singularity/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/singularity/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-01 19:16:20 -05:00
Greg Becker
b92977492d binary cache: show all packages for compatible differing targets (#12943) 2019-10-01 17:03:28 -05:00
Axel Huebl
436afdd2a8
Dataspaces: Fix Fetch URL, Savanna Spec (#13001) 2019-10-01 14:52:44 -07:00
Peter Scheibel
3575f9b382
GCC package: don't set CC etc. based on bin dir if it doesn't exist (#13000)
7bcb306 updated setup_environment in the GCC package to examine the
bin/ directory to find alternatively-named instances of CC, but this
failed to account for when GCC was being installed and failed when
it attempted to list the not-yet-existing installation prefix. This
commit updates the logic to skip this search if the bin/ directory
doesn't exist.
2019-10-01 14:29:01 -07:00
Massimiliano Culpo
245c1bb208 libaio: fixed a condition that checks whether we are running on OS X (#12976)
* libaio: fixed a condition that checks whether we are running on OS X

* libaio: simplified package by adding an explicit conflict for darwin

* libaio: added information to the docstring

* fio: added version 3.16, added conflict when using libaio, docstring

* lvm2: conflict due to libaio dep, improved docstring, simpler install

* mariadb: conflict due to libaio dep, improved docstring, version 10.4.7

* mariadb: the dependency on libaio is now conditional, removed conflict

* mariadb: fixed a typo in previous commit

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* libaio: turned into a MakefilePackage
2019-10-01 15:35:50 -05:00
Jeffrey Salmond
76178f31ca When removing a file from a view, don't fail if it doesn't exist (#12960)
Sometimes when remove_file is called on a link, that link is missing
(perhaps ctrl-C happened halfway through a previous action). As
removing a non-existent file is no problem, this patch changes the
behavior so Spack continues rather than stopping with an error.

Currently you would see

  ValueError: /path/to/dir is not a link tree!

and now it continues with a warning.
2019-10-01 10:29:10 -07:00
Jimmy Tang
a7e64e5396 Kaldi package: add version 7637de7 and egs (#12911) 2019-10-01 10:24:03 -07:00
Jeffrey Salmond
5868e0f5f2 add new mercurial versions (#12997) 2019-10-01 12:08:28 -05:00
Christopher Edsall
82a3ee0868 Update chapel to current (1.19 -> 1.20) (#12991) 2019-10-01 11:47:57 -05:00
Axel Huebl
10e4d611a5 ADIOS2: 2.5.0 (#12987)
Add the latest ADIOS2 release, v2.5.0 .
2019-10-01 10:49:52 -05:00
Satish Balay
b9a860820a hypre: add version 2.18.0 (#12992) 2019-10-01 10:48:40 -05:00
Mark Olesen
f939697863 add adios2 dependency and configuration for newest OpenFOAM (#12993) 2019-10-01 10:48:14 -05:00