@pjotrp pjotrp released this Dec 27, 2017 · 15 commits to master since this release

Assets 6

Second stable release. This is a bug fix release with many improvements.

Binary executable gemma.macosx was built on a MacBook Pro (3.5 Ghz Intel Core i7) with Mac OS X 10.12.6, gcc Apple LLVM version 8.1.0, Eigen 3.3.4 and statically linked against gsl 2.4 and zlib 1.2.11 (both installed using Homebrew).

For Linux, we recommend using the provided Guix installers gemma-git-gn2-0.97-*. See here for the installation instructions. Use the optimized haswell installer on Intel Haswell computers, otherwise use the generic installer.

We also provide a Linux binary executable gemma.linux.gz for those that prefer not to use the Guix installer. However, we recommend that all Linux users first try the Guix installer. It was built on a machine with CentOS 6.6, gcc 4.9.2 and Eigen 3.3.4 and statically linked against gsl 2.3, zlib 1.2.8 and OpenBLAS 0.2.18.

Speedup of GEMMA by using optimized OpenBlas

  • Providing a binary release with OpenBlas optimization for Intel Haswell.
  • Dropped using standard LAPACK and gslcblas libraries.
  • Fixed NaN bug caused by GSL 2.x and made recent GSL libraries the default.
  • Minimized use of Eigen libraries (which can slow compilation and matrix computation).
  • -legacy switch provides v0.96 behaviour (including Eigen)

Added Leave One Chromosome Out (LOCO) support for Bimbam (K and LMM)

  • See commit 449d882
  • -snps [filename] option allows selecting a subset of SNPs for analysis.
  • -loco [chr] option for K and LMM computations.
  • Added gemma-wrapper to make using LOCO easy.
  • LOCO examples

Added checks for matrices

  • #72 and #45 implements
    1. Fail if K has negative eigen values
    2. Fail if K is not symmetric
    3. Fail if K is not positive definite
    4. Warn in eigen values are very small
    5. Warn if K is ill conditioned
  • Check for NaN values

Added test framework and unit tests

  • Added integration and unit tests, as well as
    Travis-CI support.
  • Improved debug information and testing of input files.

Other

  • #81 printing out beta, se(beta) and logl_H1 under -lmm 2.
  • Improved README and INSTALL docs.
  • Added support info and code of conduct.
  • Updated copyright banner, info and license information for included software.
  • Reformatted the full source tree with commit 3935ba3
  • Merged LMM computation for PLINK and BIMBAM formats.
  • Fixed progress bar issues.
  • #46 removed support for Oxford format.
  • Got rid of all compiler warnings.
  • Started a discussion list.

@pcarbo pcarbo released this May 17, 2017 · 281 commits to master since this release

Assets 5

First stable release.

Executable gemma.linux was built with an Intel Xeon E5-2680v4 ("Broadwell") 2.4GHz processor, Scientific Linux 7 (64-bit) and gcc 4.8.5, and statically linked to glibc 2.14, atlas 3.10.3 and gsl 1.16.

Executable gemma.macosx was built on a MacBook Pro (2.53 Ghz Intel Core 2 Duo) with Mac OS X 10.11.6, gcc Apple LLVM version 8.0.0, and statically linked to gsl 1.16 (installed using Homebrew).

@pcarbo pcarbo released this May 10, 2017 · 282 commits to master since this release

Assets 4

Various miscellaneous bug fixes, and Issue #36 is now closed.

Executable gemma.linux was built with Scientific Linux 7 and gcc 4.8.5, and statically linked to glibc 2.14, atlas 3.10.3 and gsl 2.2.1.

Executable gemma.macosx was built on a MacBook Pro (2.53 Ghz Intel Core 2 Duo) with Mac OS X 10.11.6, gcc Apple LLVM version 8.0.0, and statically linked to gsl 1.16 (installed using Homebrew).

@pcarbo pcarbo released this May 9, 2017 · 290 commits to master since this release

Assets 2

Creating release of GEMMA 0.95a following the request in Issue #33; more stable releases forthcoming.