From f318fd8678bac5ae0b11216806df8ea53a38414e Mon Sep 17 00:00:00 2001 From: CoprDistGit Date: Thu, 18 May 2023 06:39:40 +0000 Subject: automatic import of python-fastlmm --- .gitignore | 1 + python-fastlmm.spec | 108 ++++++++++++++++++++++++++++++++++++++++++++++++++++ sources | 1 + 3 files changed, 110 insertions(+) create mode 100644 python-fastlmm.spec create mode 100644 sources diff --git a/.gitignore b/.gitignore index e69de29..e56e8f0 100644 --- a/.gitignore +++ b/.gitignore @@ -0,0 +1 @@ +/fastlmm-0.6.5.tar.gz diff --git a/python-fastlmm.spec b/python-fastlmm.spec new file mode 100644 index 0000000..6d3eee8 --- /dev/null +++ b/python-fastlmm.spec @@ -0,0 +1,108 @@ +%global _empty_manifest_terminate_build 0 +Name: python-fastlmm +Version: 0.6.5 +Release: 1 +Summary: Fast GWAS +License: Apache 2.0 +URL: https://fastlmm.github.io/ +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/80/42/5a96824c1175f63eddc2b8651ec362992002d0aaf2e72038981421b7309a/fastlmm-0.6.5.tar.gz +BuildArch: noarch + + +%description +FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed Models, is a program for performing +genome-wide association studies (GWAS) on datasets of all sizes, up to one millions samples. +This release contains the following features, each illustrated with an IPython notebook. +* Core FaST-LMM ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/FaST-LMM.ipynb)) -- [Lippert *et al.*, *Nature Methods* 2011](http://www.nature.com/nmeth/journal/v8/n10/abs/nmeth.1681.html) +Improvements: +* New features for single_snp (including effect size and multiple phenotype support) and epistasis (including reporting beta and using pre-computed eigenvalue decompositions) ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/fastlmm2021.ipynb)) -- [Lippert *et al.*, *Nature Methods* 2011](http://www.nature.com/nmeth/journal/v8/n10/abs/nmeth.1681.html) +* Ludicrous-Speed GWAS ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/SingleSnpScale.ipynb)) -- [Kadie and Heckerman, *bioRxiv* 2018](https://www.biorxiv.org/content/10.1101/154682v2) +* Heritability with Spatial Correction ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/heritability_si.ipynb)), [Heckerman *et al.*, *PNAS* 2016](http://www.pnas.org/content/113/27/7377.abstract) +* Two Kernels ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/FaST-LMM.ipynb)) -- [Widmer *et al.*, *Scientific Reports* 2014](http://www.nature.com/srep/2014/141112/srep06874/full/srep06874.html) +* Set Analysis ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/FaST-LMM.ipynb)) -- [Lippert *et al.*, *Bioinformatics* 2014](http://bioinformatics.oxfordjournals.org/content/early/2014/09/07/bioinformatics.btu504) +* Epistasis ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/FaST-LMM.ipynb)) -- [Lippert *et al.*, *Scientific Reports,* 2013](http://www.nature.com/srep/2013/130122/srep01099/full/srep01099.html) +* Prediction ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/FaST-LMM.ipynb)) -- [Lippert *et al.*, *Nature Methods* 2011](http://www.nature.com/nmeth/journal/v8/n10/abs/nmeth.1681.html) +*A C++ version, which is generally less functional, is available. See http://fastlmm.github.io/.* + +%package -n python3-fastlmm +Summary: Fast GWAS +Provides: python-fastlmm +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-fastlmm +FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed Models, is a program for performing +genome-wide association studies (GWAS) on datasets of all sizes, up to one millions samples. +This release contains the following features, each illustrated with an IPython notebook. +* Core FaST-LMM ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/FaST-LMM.ipynb)) -- [Lippert *et al.*, *Nature Methods* 2011](http://www.nature.com/nmeth/journal/v8/n10/abs/nmeth.1681.html) +Improvements: +* New features for single_snp (including effect size and multiple phenotype support) and epistasis (including reporting beta and using pre-computed eigenvalue decompositions) ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/fastlmm2021.ipynb)) -- [Lippert *et al.*, *Nature Methods* 2011](http://www.nature.com/nmeth/journal/v8/n10/abs/nmeth.1681.html) +* Ludicrous-Speed GWAS ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/SingleSnpScale.ipynb)) -- [Kadie and Heckerman, *bioRxiv* 2018](https://www.biorxiv.org/content/10.1101/154682v2) +* Heritability with Spatial Correction ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/heritability_si.ipynb)), [Heckerman *et al.*, *PNAS* 2016](http://www.pnas.org/content/113/27/7377.abstract) +* Two Kernels ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/FaST-LMM.ipynb)) -- [Widmer *et al.*, *Scientific Reports* 2014](http://www.nature.com/srep/2014/141112/srep06874/full/srep06874.html) +* Set Analysis ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/FaST-LMM.ipynb)) -- [Lippert *et al.*, *Bioinformatics* 2014](http://bioinformatics.oxfordjournals.org/content/early/2014/09/07/bioinformatics.btu504) +* Epistasis ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/FaST-LMM.ipynb)) -- [Lippert *et al.*, *Scientific Reports,* 2013](http://www.nature.com/srep/2013/130122/srep01099/full/srep01099.html) +* Prediction ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/FaST-LMM.ipynb)) -- [Lippert *et al.*, *Nature Methods* 2011](http://www.nature.com/nmeth/journal/v8/n10/abs/nmeth.1681.html) +*A C++ version, which is generally less functional, is available. See http://fastlmm.github.io/.* + +%package help +Summary: Development documents and examples for fastlmm +Provides: python3-fastlmm-doc +%description help +FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed Models, is a program for performing +genome-wide association studies (GWAS) on datasets of all sizes, up to one millions samples. +This release contains the following features, each illustrated with an IPython notebook. +* Core FaST-LMM ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/FaST-LMM.ipynb)) -- [Lippert *et al.*, *Nature Methods* 2011](http://www.nature.com/nmeth/journal/v8/n10/abs/nmeth.1681.html) +Improvements: +* New features for single_snp (including effect size and multiple phenotype support) and epistasis (including reporting beta and using pre-computed eigenvalue decompositions) ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/fastlmm2021.ipynb)) -- [Lippert *et al.*, *Nature Methods* 2011](http://www.nature.com/nmeth/journal/v8/n10/abs/nmeth.1681.html) +* Ludicrous-Speed GWAS ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/SingleSnpScale.ipynb)) -- [Kadie and Heckerman, *bioRxiv* 2018](https://www.biorxiv.org/content/10.1101/154682v2) +* Heritability with Spatial Correction ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/heritability_si.ipynb)), [Heckerman *et al.*, *PNAS* 2016](http://www.pnas.org/content/113/27/7377.abstract) +* Two Kernels ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/FaST-LMM.ipynb)) -- [Widmer *et al.*, *Scientific Reports* 2014](http://www.nature.com/srep/2014/141112/srep06874/full/srep06874.html) +* Set Analysis ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/FaST-LMM.ipynb)) -- [Lippert *et al.*, *Bioinformatics* 2014](http://bioinformatics.oxfordjournals.org/content/early/2014/09/07/bioinformatics.btu504) +* Epistasis ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/FaST-LMM.ipynb)) -- [Lippert *et al.*, *Scientific Reports,* 2013](http://www.nature.com/srep/2013/130122/srep01099/full/srep01099.html) +* Prediction ([notebook](https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/FaST-LMM.ipynb)) -- [Lippert *et al.*, *Nature Methods* 2011](http://www.nature.com/nmeth/journal/v8/n10/abs/nmeth.1681.html) +*A C++ version, which is generally less functional, is available. See http://fastlmm.github.io/.* + +%prep +%autosetup -n fastlmm-0.6.5 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-fastlmm -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Thu May 18 2023 Python_Bot - 0.6.5-1 +- Package Spec generated diff --git a/sources b/sources new file mode 100644 index 0000000..7407da3 --- /dev/null +++ b/sources @@ -0,0 +1 @@ +6196fc054d09b349f66cfbc676c5c622 fastlmm-0.6.5.tar.gz -- cgit v1.2.3