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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
2018-05-02make symlinking python3->python optional (#7960)Elizabeth Fischer1-1/+5
* Make symlinking python3->python optional * Added reference to PEP 394
2018-05-02mvapich2: add 2.3rc2 (#7976)Adam Moody1-0/+1
2018-05-02sphinx: Updated to v1.7.4 (#7977)Elizabeth Fischer1-0/+6
* sphinx: Updated to v1.7.4 * Update package.py
2018-05-02Added BookLeaf_Cpp and Typhon packages. (#7969)Tim Law2-0/+105
2018-05-02Add libcint version 3.0.12 (#7972)Michael F. Herbst1-0/+1
2018-05-02bedops: Create new package (#7956)Eric1-0/+42
* bedops: Create new package * fix install method
2018-05-02Fix Spectrum MPI package spec file for PGI compilers (#7964)David Wootton1-0/+10
* Added magma package * Incorporated Serban's change * Remove deleted files * argparse.py * Sync forked Spack repo in github * Use reported version of IBM XL Fortran compiler for compiler versions >= 16.0. Starting with the April 2018 release, the IBM XL C and Fortran compilers report the same version, 16.0. Consequently, there is no need to downgrade the Fortran compiler version to match that of the C compiler. * Eliminate blank lines. * Update the Spectrum MPI package.py file to specify the correct compilation scripts for the PGI compilers.
2018-05-02openmc is not a proxy (#7968)Christoph Junghans1-2/+0
https://github.com/spack/spack/issues/7965#issuecomment-385953224
2018-04-30mvapich2: add registration cache and file systems variants (#7948)Adam Moody1-2/+36
* mvapich2: add registration cache and file systems variants, avoid empty --with-pm= if no process manager is specified, add missing leading dash in --disable-silent-rules
2018-04-30mpifileutils: roll back to dtcmp v1.0.3, add option to build master branch ↵Adam Moody1-1/+6
(#7949) * mpifileutils: roll back to dtcmp v1.0.3 due to API change, add option to build master branch * add comment to explain why certain dtcmp is required, rename version for git branch * dtcmp v1.0.2 is missing github tarball
2018-04-30vt: Create new package (#7947)Eric1-0/+38
2018-04-30Build shared libs for tinyxml. (#7914)健美猫2-9/+20
2018-04-29Patch eospac package to allow compilation with %clang. (#7928)Kelly (KT) Thompson2-0/+65
When building eospac with %clang, spack's Fortran compiler wrapper is called 'flang', which is rejected by the eospac build system..Allow compilation with %clang by patching the eospac build system. My testing only covers %clang where flang is actually gfortran. However, this patch only registers 'flang' as a known Fortran compiler and does not set any flags or options that are compiler specific. .
2018-04-28mfem: fix concretization (#7923)Christoph Junghans1-2/+2
* mfem: fix concretization * Fix hypre deps again * Update package.py
2018-04-27Update with recent versions through 4.8.3 and add variants. (#7933)Chris Green2-1/+68
Add configurable HTTP, Python and readline support. Add previously missing dependencies. Minor patch to improve Python support (see https://github.com/xrootd/xrootd/pull/695).
2018-04-26bcftools: new version (#7930)Levi Baber1-0/+2
2018-04-26add versions 3.4.3. and 3.5.0 (#7929)Sinan1-0/+2
2018-04-26samtools: new version (#7921)Levi Baber1-0/+4
2018-04-26Use GitLab's API endpoint for fetching a git snapshot. (#7881)Sergey Kosukhin9-15/+19
* Use GitLab's API endpoint for fetching a git snapshot. * More GitLab packages use the API. * find_list_url for GitLab's API URLs. * Flake8 * Url for 'hacckernels'. * Check GitLab API regexps before the non-API ones.
2018-04-26add patch to get aspell to build on OSX (#7919)healther2-0/+22
2018-04-26Add Trinity package (#7828)Simon Flood1-0/+74
* Add Trinity package New package to install Trinity - another odd installer (assumes installation to /usr/local/bin and doesn't copy dot files hence deleting them) * Update package.py added dependencies from https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity * Update package.py Copy tree to prefix.bin so that PATH can correctly be set for the Trinity command - can't split it off as it seems everything needs to stay together. * Update package.py Fixed over-length lines and space before comma
2018-04-26Package 'gdbm': do not set CC. (#7912)Sergey Kosukhin1-8/+1
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