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2017-05-23opencoarrays: new version (#4271)Erik Schnetter1-0/+1
2017-05-23Add support for addl versions of bcl2fastq2 (#4328)George Hartzell1-1/+5
Two changes: - It seems that Illumina version numbers are dotted and that the dashed version in the 2.18... filename is an anomaly (based on the names for 2.17.1.14 and 2.19.0). `url_for_version` does the right thing for 2.18. It will need to be fixed when support for 2.19 is added. 2.17 is no longer generally available so it gets a pass. - Add version and hash for 2.17.1.14. 2.17.1.14 is no longer distributed. If you have a copy of the source tarball, you can drop it into a local mirror w/ the name mirror/bcl2fastq2/bcl2fastq2-2.17.1.14.zip and go from there.
2017-05-23Add latest version of libpciaccess (#4325)Adam J. Stewart1-1/+2
2017-05-23Magics with eccodes variant (#4320)Milton Woods2-16/+15
* magics: use filter_file to avoid using system python in all versions * magics: add eccodes variant to switch between eccodes and grib-api
2017-05-23Packages/r ergm (#4314)Tom Merrick10-0/+384
* Add mpi support to R * Add multiple precision math routines to R * Add packages for r-ergm and it's dependents * Fixed depends-on types * Correct flake8 errors
2017-05-23plumed: fixed compilation on rhel6 (#4318)Massimiliano Culpo1-1/+11
* plumed: fixed compilation on rhel6 with mvapich2 and gcc@5.4.0 (#77) * plumed: prevent parallel compilation, as it breaks for the newest version
2017-05-22Add Microsoft's C++ Rest SDK (#4315)Robert D. French1-0/+41
2017-05-22magics: use spack perl instead of system perl (#4310)Milton Woods1-3/+3
2017-05-21qt: patch JavaScriptCore to favour internal pcre headers (#4270)Milton Woods2-0/+36
2017-05-21libdrm depends on pkg-config (#4308)Michael Kuhn1-0/+1
2017-05-21flex: create variant +lex that creates symlinks for lex and libl.{a,so} (#3894)Milton Woods1-0/+17
* flex: create variant +lex that creates symlinks for lex and libl.{a,so} * flex: enable variant +lex by default * flex: use dso_suffix for portability; replace repetitive code with a loop
2017-05-20spark: remove whitespaces from run_env variable (#4210)Massimiliano Culpo1-2/+7
2017-05-20Fix ncview with netcdf+mpi (#4305)Michael Kuhn1-0/+10
ncview has to be compiled using the same compiler as netcdf.
2017-05-20magics fixes for versions > 2.29.x (#4302)Michael Kuhn1-3/+9
2017-05-19julia: New version 0.5.2 (#4259)Erik Schnetter1-1/+2
2017-05-19hwloc: new version (#4272)Erik Schnetter1-0/+1
2017-05-19hpx5: new version (#4273)Erik Schnetter1-0/+1
2017-05-19cmake: new version (#4274)Erik Schnetter1-0/+1
2017-05-19gobject-introspection depends on pkg-build (#4301)Michael Kuhn1-0/+1
2017-05-19Mpifileutils (#4283)Adam Moody1-0/+81
* adding mpifileutils * mpifileutils: add +lustre variant * mpifileutils: add variant for xattr * mpifileutils: update to AutotoolsPackage * mpifileutils: simplify and eliminate redundant make * mpifileutils: drop unnecessary comments
2017-05-19Fix gcc not finding zlib (#4291)Michael Kuhn1-0/+9
2017-05-19added R 3.4.0, again (#4260) (#4294)Douglas Duckworth1-1/+2
2017-05-19Fix boost@:1.56.0%gcc@:5 (#4295)George Hartzell2-0/+59
I need boost@1.54.0 for bcl2fastq2. I tested bcl2fastq2 using the system compiler (gcc@4.8.5). My full build uses a spack-build gcc@5.4.0. boost@1.54.0 won't build. I found the answer [here](https://github.com/hashdist/hashstack/issues/802) with the details in [this upstream/boost ticket](https://svn.boost.org/trac/boost/ticket/10125). I've confirmed that these combo's build: boost version| compiler ------------ | ------------------ boost@1.54.0 | gcc@4.8.5 (system) boost@1.54.0 | gcc@5.4.0 (Spack) boost@1.64.0 | gcc@5.5.0 (system)
2017-05-19Add r-rmpfr and r-gmp to R (#4287)Tom Merrick2-0/+81
* Add mpi support to R * Add multiple precision math routines to R * Updated the URL to match the version * Remove duplicate packages
2017-05-18Add info for libxml2@2.7.8 (#4290)George Hartzell1-0/+1
bcl2fastq2 needs this older version.
2017-05-18added new version 7.900.1 (#4292)kothah1-0/+1
added new md5
2017-05-18add mpi support to meme (#4265)Douglas Duckworth1-0/+11
* added openmpi support to meme * openmpi is a link dependency which leverages r_path * openmpi support now the default - meme does not have configure argument for mpi - if it's found then it's used * added serial option and set mpi to not be default * modified meme
2017-05-18Add old version of ROOT 5 (#4288)Adam J. Stewart1-0/+1
2017-05-18Fix spec['python'].home (#4228)Adam J. Stewart1-0/+2
2017-05-18Add mpi support to R (#4286)Tom Merrick2-0/+93
2017-05-18Add the gnupg package and missing dependencies. Update versions of ex… (#4281)Patrick Gartung6-2/+171
* Add the gnupg package and missing dependencies. Update versions of existing dependencies. * this ended up in the wrong repo * put versions back, remove uneeded function * OK ;) * autopep8 * typo on npth line * whitespace
2017-05-18Add a new package for Open Babel (#4256)Adam J. Stewart3-0/+169
* Add a new package for Open Babel * Add post-installation tests, stolen from the fine folks at Homebrew * Add patch to fix Python 3.6 support * Add a more complete patch to get Python 3.6 support working * Add patch to convert tabs to spaces in test script testpdbformat.py contains mixed tabs and spaces causing the unit tests to fail. With this patch, all tests pass with flying colors.
2017-05-17benchmark: New package for the Google Benchmark library (#4194)Erik Schnetter1-0/+36
* benchmark: New package * benchmark: Remove empty function
2017-05-17Add info for miniconda[23]@4.3.14 (#4263)George Hartzell2-0/+2
2017-05-17Package for bcl2fastq2 (updates libxslt) (#4234)George Hartzell4-2/+131
* Add v1.1.26 and make crypto a variant I need 1.1.26 for bcl2fastq2. I also need to build it without crypto support. * Initial support for bcl2fastq2 * Clean up commentary, messages, names No substantial changes intended, just cleanup. * fix flake8 and extra import * The masked grammarian strikes again... * Be normal (messages don't end in periods) * When +crypto, add --with-crypto Add `--with-crypto` to configure args when user hasn't explicitly set `~crypto`. * self.spec.satisfies is unsatisfying, in is in instead See #4135, self.spec.satisfies has issues. @adamjstewart suggests simply using in.
2017-05-17Add a new package for sphinxcontrib-programoutput (#4267)Adam J. Stewart1-0/+41
2017-05-17Add latest version of matplotlib (#4279)Adam J. Stewart1-1/+2
2017-05-17Add latest version of Sphinx (#4264)Adam J. Stewart15-52/+185
* Add latest version of Sphinx * Flake8 fix
2017-05-16Update checksum for latest version of cudnn (#4254)Adam J. Stewart1-1/+1
2017-05-16added meme package (#4257)Douglas Duckworth1-0/+43
* added albacore package as well as dependency py-ont-fast5-api * added py-cutadapt and dependency py-xopen * made more changes to albacore and cutadapt as well as dependencies * made changes again per @adamjstewart * fixed by python n00b errors i think * fixed? * tw=79 * made changes to py-ont-fast5-api ont-albacore * removed bad characters * albacore requires setuptools as build and run dependency * added vmd * added back albacore * removed vmd package * added meme software * libz is only needed as link depedency for meme * added libxml2 libxslt libgcrypt as link dependencies
2017-05-15albacore requires setuptools as build and run requirement (#4255)Adam J. Stewart1-7/+7
2017-05-15Add missing dependency to glib package (#4253)Adam J. Stewart1-0/+14
2017-05-15Add latest version of util-linux (#4252)Adam J. Stewart1-1/+2
2017-05-15Remove need for autoreconf in glib package (#4240)Adam J. Stewart2-19/+11
2017-05-14mesa-glu: provides libGLU, the OpenGL utility library from SGI (#4244)Milton Woods1-0/+37
2017-05-14harfbuzz: add latest version (1.4.6) (#4245)Milton Woods1-0/+1
2017-05-14ncurses: build "normal" libs, not just "wide-char" libs, for ncurses@6: (#4246)Milton Woods1-1/+2
2017-05-12espressopp: always depends on py-numpy (#4207)Christoph Junghans1-2/+1
Ref espressopp/espressopp#161
2017-05-12albacore and cutadapt again (#4219)Douglas Duckworth4-0/+174
* added albacore package as well as dependency py-ont-fast5-api * added py-cutadapt and dependency py-xopen * made more changes to albacore and cutadapt as well as dependencies * made changes again per @adamjstewart * fixed by python n00b errors i think * fixed? * tw=79 * made changes to py-ont-fast5-api ont-albacore * removed bad characters
2017-05-12LIBXSMM 1.8.1 (#4235)Hans Pabst1-1/+2
* Included LIBXSMM 1.8 into the list of available versions. * LIBXSMM 1.8.1
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