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2018-05-08Py cnvkit: updating dependencies (#8057)peetsv1-1/+3
* py-pyfaidx: adding new package * updating the url * identifying dependencies
2018-05-08intltool requires patching for newer perl versions (#8061)Gregory Lee1-0/+6
2018-05-08added stat version 4.0.0 (#8062)Gregory Lee1-0/+2
2018-05-08added shared-mime-info version 1.9 (#8063)Gregory Lee1-0/+1
2018-05-08Updates to Google Benchmark package: (#8056)Andrew Gaspar1-0/+10
- Adds v1.3.0 and v1.4.0 - List explicit CMake version dependency (from Benchmark CMake files) - Disable the building of tests. Starting in v1.4.0 this introduced a dependency on GoogleTest Tested by building all versions on macOS High Sierra
2018-05-08Fix superlu-dist with PETSc 3.9.0 (#8048)Ce Qin1-2/+2
2018-05-08pybind11: v2.2.3 (#8051)Axel Huebl1-0/+6
* pybind11: 2.2.3 new release for pybind11, v.2.2.3: https://github.com/pybind/pybind11/blob/v2.2.3/docs/changelog.rst#v223-april-29-2018 * pybind11: compiler support mark older versions as conflicts
2018-05-08googletest: add variant to enable/disable threads (#8052)Geoffrey Oxberry1-0/+6
Add Google Test variant to enable/disable building with threads.
2018-05-08openmpi: new version (#8055)Levi Baber1-1/+2
2018-05-07r-genie3: new package (#8044)Yifan Zhu1-0/+38
2018-05-07manta: Create new package (#8043)Eric1-0/+41
* manta: Create new package * manta: Create new package * manta: fix dependency types
2018-05-07py-pysqlite: Create new package (#8042)Eric1-0/+37
2018-05-07perl: add 5.26.2 (#7984)Denis Davydov1-7/+10
* perl: add 5.26.2 * perl: add 5.22.4 * move Misc releases to EOL
2018-05-07pkgconf: use alpine linux mirror to avoid ssl error (#8039)Christoph Junghans1-1/+1
2018-05-07Add patch (#8034)anne-glerum2-0/+35
2018-05-07trilinos: minor cleanup (#7987)Andrey Prokopenko1-96/+115
2018-05-07py-dlcpar: Add package description (#8032)Eric1-1/+2
2018-05-06add opencv 3.4.1 (#8031)Stephen McDowell1-0/+1
2018-05-06metabat: Create new package (#7991)Eric1-0/+54
* metabat: Create new package * fix Perl script shebangs and BOOST_ROOT environment * add perl script fix function * add perl dependency and fix positional argument for Python 2.6
2018-05-06Add package wireshark and dependencies (#8024)healther3-0/+210
* add wireshark Change-Id: I1ef674ff286db2e06baaf9fca65982d1145cfa79 * fix qt4 build Change-Id: Ieb9989b9fec1a0e02388197f971ee66b591d45c5 * remove commented lines Change-Id: Ia67bfaf1beba06dd710cee56aec06bc36b293d34 * flake8 fix Change-Id: Ica1b2cce2be2faca82a4177c3cdc3a0bb005c031 * remove clutter Change-Id: I6061fe56a88f8c7b7e03fdce5e3eae04036ad2d8 * fix dependencies Change-Id: I8160c70c9333c9f5e82ed5fc73633455df568972 * use dot syntax instead of join_path Change-Id: Id1f737299b603fa4093b58571d46a64b0dd84895
2018-05-06macOS-specific patch no longer applies to GCC 8 (#8029)Adam J. Stewart1-1/+1
2018-05-05py-udunits: New package (#7998)Elizabeth Fischer1-0/+69
* py-udunits: update * Use standard py-netcdf4 * Remove unnecssary import? * Suggested simplifications * flake8
2018-05-05A new library: libshm. (#8028)健美猫1-0/+38
2018-05-04Bump pysam to 0.14.1. (#7988)健美猫1-1/+7
* py-pysam requires curl. * py-pysam conflicts with htslib@1.7. * Bump py-pysam versions. * Add more dependencies.
2018-05-04Added GCC 8.1.0 (#8026)sknigh1-0/+1
Built once on Centos 7 w/ external GCC 4.8.5 compiler
2018-05-04a new package: papyrus. (#8023)Jungwon Kim1-0/+38
* a new package: papyrus. * removed the empty cmake_args * changed md5 checksum for v1.0.0 * make a long line short * one long line url
2018-05-04Bump samtools, hstlib and bcftools to version 1.8. (#8020)健美猫3-0/+7
* Bump samtools and hstlib to version 1.8. * rm .bak. * Bump bcftools to 1.8. * bcftools@1.8 depends on libzip.
2018-05-04py-more-itertools: new package (#8004)Elizabeth Fischer1-0/+38
* py-more-itertools: new package * code review
2018-05-04Hic-Pro: fix a typo and replace hard-coded version. (#8022)健美猫1-2/+2
* Fix a typo and replace hard-coded version. * version -> self.version.
2018-05-04openmpi: don't build static libraries if slurm is activated (#8021)Massimiliano Culpo1-1/+9
According to this comment: https://github.com/open-mpi/ompi/issues/4338#issuecomment-383982008 on an OpenMPI issue, using `--enable-static` silently disable slurm support.
2018-05-03gdal: update (#8008)Elizabeth Fischer1-4/+9
* gdal: update * Remove unneeded depends(python)
2018-05-03Bump r-rcpp versions. (#8016)健美猫1-0/+2
2018-05-03pism: new package (#8010)Elizabeth Fischer1-0/+171
* pism: new package * Implement code review * Remove pointless docstring5 * Fixed missing trailing quote
2018-05-03py-numpy: update (#8003)Elizabeth Fischer2-4/+9
* py-numpy: update * Better constrain when can / cannot parallel build. * Update SciPy parallel logic to be specific to Python 3.5+, same as in Numpy.
2018-05-03py-bsddb3: update (#8006)Elizabeth Fischer1-1/+5
* py-bsddb3: update * Change py-setuptools to build dependency
2018-05-03pfunit: update (#7994)Elizabeth Fischer1-12/+15
2018-05-03Everytrace: update (#7995)Elizabeth Fischer1-3/+7
2018-05-03py-yamlreader: new package (#7997)Elizabeth Fischer1-0/+39
2018-05-03gmp: update (#7999)Elizabeth Fischer1-0/+2
2018-05-03py-scipy: update (#8000)Elizabeth Fischer1-4/+1
2018-05-03py-pyside: update (#8002)Elizabeth Fischer1-0/+14
2018-05-03py-cython: update (#8005)Elizabeth Fischer1-0/+5
2018-05-03genomefinisher: Create new package (#7989)Eric2-0/+65
2018-05-03 py-crispresso: Create new package (#7990)Eric1-0/+46
* py-crispresso: Create new package * py-crispresso: Create new package
2018-05-03New Package: ruby-svn2git (#7979)Kelly (KT) Thompson1-0/+48
* New Package: svn2git https://github.com/nirvdrum/svn2git svn2git is a tiny utility for migrating projects from Subversion to Git while keeping the trunk, branches and tags where they should be. It uses git-svn to clone an svn repository and does some clean-up to make sure branches and tags are imported in a meaningful way, and that the code checked into master ends up being what's currently in your svn trunk rather than whichever svn branch your last commit was in. * Actually requires +perl variant of subversion. * fix style issue.
2018-05-03A new package: nanopb. (#7981)健美猫1-0/+38
* A new package: nanopb. * flake8. * Remove py-pytorch.
2018-05-03Bump pgi to 18.4. (#7980)健美猫1-0/+1
* Bump pgi to 18.4. * Remove the empty line. * Update.
2018-05-03Bump gatk version to 4.0.4.0. (#7985)健美猫1-5/+13
* Bump gatk version to 4.0.4.0. * Update. * Fixed. * Fixed.
2018-05-03A new package: py-openslide-python. (#7907)健美猫1-0/+41
* A new package: py-openslide-python. * Update. * Remove py-pytorch package. * Remove nektar package. * Remove install_time_test_callbacks
2018-05-03go: Update to 1.10.2 (#7982)Michael Kuhn1-0/+1
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