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diff --git a/python-treesapp.spec b/python-treesapp.spec new file mode 100644 index 0000000..a68842e --- /dev/null +++ b/python-treesapp.spec @@ -0,0 +1,357 @@ +%global _empty_manifest_terminate_build 0 +Name: python-treesapp +Version: 0.11.4 +Release: 1 +Summary: TreeSAPP is a functional and taxonomic annotation tool for genomes and metagenomes. +License: GPL-3.0 +URL: https://github.com/hallamlab/TreeSAPP +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/c9/22/768e33057257389a7d4e234e7910768a8ab3a44017e76990be5cca8712a4/treesapp-0.11.4.tar.gz +BuildArch: noarch + +Requires: python3-biopython +Requires: python3-ete3 +Requires: python3-joblib +Requires: python3-numpy +Requires: python3-packaging +Requires: python3-pyfastx +Requires: python3-pygtrie +Requires: python3-samsum +Requires: python3-scikit-learn +Requires: python3-scipy +Requires: python3-six +Requires: python3-seaborn +Requires: python3-tqdm +Requires: python3-pytest +Requires: python3-pandas +Requires: python3-matplotlib +Requires: python3-pytest +Requires: python3-pytest-cov + +%description +# TreeSAPP: Tree-based Sensitive and Accurate Phylogenetic Profiler + + +[](https://badge.fury.io/py/treesapp) +[](https://anaconda.org/bioconda/treesapp) +[](https://anaconda.org/bioconda/treesapp) +[](https://quay.io/repository/hallamlab/treesapp) + +[](https://www.codacy.com/gh/hallamlab/TreeSAPP?utm_source=github.com&utm_medium=referral&utm_content=hallamlab/TreeSAPP&utm_campaign=Badge_Grade) +[](http://bioconda.github.io/recipes/treesapp/README.html) +[](https://img.shields.io/pypi/pyversions/) +[](https://codecov.io/gh/hallamlab/TreeSAPP) +[](https://anaconda.org/bioconda/treesapp) + +## Overview + +TreeSAPP is a python package for functional and taxonomic annotation of proteins + from genomes and metagenomes using phylogenetic placement. + +## Quick start + +We recommend installing TreeSAPP into its own conda environment with the following command: + +```bash +conda create -n treesapp_cenv -c bioconda -c conda-forge treesapp +conda activate treesapp_cenv +``` + +To list all the sub-commands run `treesapp`. + +To test the `assign` workflow, run: +```bash +treesapp assign -i TreeSAPP/tests/test_data/marker_test_suite.faa -m prot --trim_align -o assign_test -t McrA,DsrAB +``` + +To classify sequences in your genome of interest: +```bash +treesapp assign -i my.fasta -o ~/path/to/output/directory/ +``` + +TreeSAPP comes installed with 33 reference packages involved in a variety of biogeochemical and cellular processes. +We also have many more reference packages available on our [RefPkgs repository](https://github.com/hallamlab/RefPkgs) +and you can view the complete list [here](https://github.com/hallamlab/RefPkgs/wiki/refpkgs). + +## Tutorials + +All of our tutorials are available on the [GitHub wiki](https://github.com/hallamlab/TreeSAPP/wiki) page. +Here are some specific tutorial examples: + +If we do not yet have a reference package for a gene you are interested in, +please try [building a new reference package](https://github.com/hallamlab/TreeSAPP/wiki/Building-reference-packages-with-TreeSAPP). +Of course, if you run into any problems or would like to collaborate on building many reference packages +don't hesitate to email us or create a new issue with an 'enhancement' label. + +To determine whether the sequences used to build your new reference package are what you think they are, + and whether it might unexpectedly annotate homologous sequences, + see the [purity tutorial](https://github.com/hallamlab/TreeSAPP/wiki/Testing-the-functional-purity-of-reference-packages). + +If you are working with a particularly complex reference package, from an orthologous group for example, or have extra + phylogenetic information you'd like to include in your classifications, + try [annotating extra features](https://github.com/hallamlab/TreeSAPP/wiki/Layering-annotations-onto-classifications) with `treesapp layer`. + +## Citation + +If you found TreeSAPP useful in your work, please cite the following paper: + +Morgan-Lang, C., McLaughlin, R., Armstrong, Z., Zhang, G., Chan, K., & Hallam, S. J. (2020). +[TreeSAPP: The Tree-based Sensitive and Accurate Phylogenetic Profiler](https://doi.org/10.1093/bioinformatics/btaa588). +Bioinformatics, 1–8. + +This was brought to you by the team: + +- Connor Morgan-Lang ([cmorganl](https://github.com/cmorganl), maintainer) +- Ryan McLaughlin ([McGlock](https://github.com/McGlock)) +- Grace Zhang ([grace72](https://github.com/gracez72)) +- Kevin Chan ([kevinxchan](https://github.com/kevinxchan)) +- Zachary Armstrong +- Steven J. Hallam + +### References + +If you're feeling extra citation-happy, please consider citing the following works as well: + +- Eddy, S. R. (1998). Profile hidden Markov models. Bioinformatics (Oxford, England), 14(9), 755–763. +- Criscuolo, A., & Gribaldo, S. (2010). BMGE (Block Mapping and Gathering with Entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evolutionary Biology, 10(1). +- Kozlov, A. M., Darriba, D., Flouri, T., Morel, B., & Stamatakis, A. (2019). RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics, 35(21), 4453–4455. +- Barbera, P., Kozlov, A. M., Czech, L., Morel, B., & Stamatakis, A. (2018). EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences. Systematic Biology, 0(0), 291658. + + + + +%package -n python3-treesapp +Summary: TreeSAPP is a functional and taxonomic annotation tool for genomes and metagenomes. +Provides: python-treesapp +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-treesapp +# TreeSAPP: Tree-based Sensitive and Accurate Phylogenetic Profiler + + +[](https://badge.fury.io/py/treesapp) +[](https://anaconda.org/bioconda/treesapp) +[](https://anaconda.org/bioconda/treesapp) +[](https://quay.io/repository/hallamlab/treesapp) + +[](https://www.codacy.com/gh/hallamlab/TreeSAPP?utm_source=github.com&utm_medium=referral&utm_content=hallamlab/TreeSAPP&utm_campaign=Badge_Grade) +[](http://bioconda.github.io/recipes/treesapp/README.html) +[](https://img.shields.io/pypi/pyversions/) +[](https://codecov.io/gh/hallamlab/TreeSAPP) +[](https://anaconda.org/bioconda/treesapp) + +## Overview + +TreeSAPP is a python package for functional and taxonomic annotation of proteins + from genomes and metagenomes using phylogenetic placement. + +## Quick start + +We recommend installing TreeSAPP into its own conda environment with the following command: + +```bash +conda create -n treesapp_cenv -c bioconda -c conda-forge treesapp +conda activate treesapp_cenv +``` + +To list all the sub-commands run `treesapp`. + +To test the `assign` workflow, run: +```bash +treesapp assign -i TreeSAPP/tests/test_data/marker_test_suite.faa -m prot --trim_align -o assign_test -t McrA,DsrAB +``` + +To classify sequences in your genome of interest: +```bash +treesapp assign -i my.fasta -o ~/path/to/output/directory/ +``` + +TreeSAPP comes installed with 33 reference packages involved in a variety of biogeochemical and cellular processes. +We also have many more reference packages available on our [RefPkgs repository](https://github.com/hallamlab/RefPkgs) +and you can view the complete list [here](https://github.com/hallamlab/RefPkgs/wiki/refpkgs). + +## Tutorials + +All of our tutorials are available on the [GitHub wiki](https://github.com/hallamlab/TreeSAPP/wiki) page. +Here are some specific tutorial examples: + +If we do not yet have a reference package for a gene you are interested in, +please try [building a new reference package](https://github.com/hallamlab/TreeSAPP/wiki/Building-reference-packages-with-TreeSAPP). +Of course, if you run into any problems or would like to collaborate on building many reference packages +don't hesitate to email us or create a new issue with an 'enhancement' label. + +To determine whether the sequences used to build your new reference package are what you think they are, + and whether it might unexpectedly annotate homologous sequences, + see the [purity tutorial](https://github.com/hallamlab/TreeSAPP/wiki/Testing-the-functional-purity-of-reference-packages). + +If you are working with a particularly complex reference package, from an orthologous group for example, or have extra + phylogenetic information you'd like to include in your classifications, + try [annotating extra features](https://github.com/hallamlab/TreeSAPP/wiki/Layering-annotations-onto-classifications) with `treesapp layer`. + +## Citation + +If you found TreeSAPP useful in your work, please cite the following paper: + +Morgan-Lang, C., McLaughlin, R., Armstrong, Z., Zhang, G., Chan, K., & Hallam, S. J. (2020). +[TreeSAPP: The Tree-based Sensitive and Accurate Phylogenetic Profiler](https://doi.org/10.1093/bioinformatics/btaa588). +Bioinformatics, 1–8. + +This was brought to you by the team: + +- Connor Morgan-Lang ([cmorganl](https://github.com/cmorganl), maintainer) +- Ryan McLaughlin ([McGlock](https://github.com/McGlock)) +- Grace Zhang ([grace72](https://github.com/gracez72)) +- Kevin Chan ([kevinxchan](https://github.com/kevinxchan)) +- Zachary Armstrong +- Steven J. Hallam + +### References + +If you're feeling extra citation-happy, please consider citing the following works as well: + +- Eddy, S. R. (1998). Profile hidden Markov models. Bioinformatics (Oxford, England), 14(9), 755–763. +- Criscuolo, A., & Gribaldo, S. (2010). BMGE (Block Mapping and Gathering with Entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evolutionary Biology, 10(1). +- Kozlov, A. M., Darriba, D., Flouri, T., Morel, B., & Stamatakis, A. (2019). RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics, 35(21), 4453–4455. +- Barbera, P., Kozlov, A. M., Czech, L., Morel, B., & Stamatakis, A. (2018). EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences. Systematic Biology, 0(0), 291658. + + + + +%package help +Summary: Development documents and examples for treesapp +Provides: python3-treesapp-doc +%description help +# TreeSAPP: Tree-based Sensitive and Accurate Phylogenetic Profiler + + +[](https://badge.fury.io/py/treesapp) +[](https://anaconda.org/bioconda/treesapp) +[](https://anaconda.org/bioconda/treesapp) +[](https://quay.io/repository/hallamlab/treesapp) + +[](https://www.codacy.com/gh/hallamlab/TreeSAPP?utm_source=github.com&utm_medium=referral&utm_content=hallamlab/TreeSAPP&utm_campaign=Badge_Grade) +[](http://bioconda.github.io/recipes/treesapp/README.html) +[](https://img.shields.io/pypi/pyversions/) +[](https://codecov.io/gh/hallamlab/TreeSAPP) +[](https://anaconda.org/bioconda/treesapp) + +## Overview + +TreeSAPP is a python package for functional and taxonomic annotation of proteins + from genomes and metagenomes using phylogenetic placement. + +## Quick start + +We recommend installing TreeSAPP into its own conda environment with the following command: + +```bash +conda create -n treesapp_cenv -c bioconda -c conda-forge treesapp +conda activate treesapp_cenv +``` + +To list all the sub-commands run `treesapp`. + +To test the `assign` workflow, run: +```bash +treesapp assign -i TreeSAPP/tests/test_data/marker_test_suite.faa -m prot --trim_align -o assign_test -t McrA,DsrAB +``` + +To classify sequences in your genome of interest: +```bash +treesapp assign -i my.fasta -o ~/path/to/output/directory/ +``` + +TreeSAPP comes installed with 33 reference packages involved in a variety of biogeochemical and cellular processes. +We also have many more reference packages available on our [RefPkgs repository](https://github.com/hallamlab/RefPkgs) +and you can view the complete list [here](https://github.com/hallamlab/RefPkgs/wiki/refpkgs). + +## Tutorials + +All of our tutorials are available on the [GitHub wiki](https://github.com/hallamlab/TreeSAPP/wiki) page. +Here are some specific tutorial examples: + +If we do not yet have a reference package for a gene you are interested in, +please try [building a new reference package](https://github.com/hallamlab/TreeSAPP/wiki/Building-reference-packages-with-TreeSAPP). +Of course, if you run into any problems or would like to collaborate on building many reference packages +don't hesitate to email us or create a new issue with an 'enhancement' label. + +To determine whether the sequences used to build your new reference package are what you think they are, + and whether it might unexpectedly annotate homologous sequences, + see the [purity tutorial](https://github.com/hallamlab/TreeSAPP/wiki/Testing-the-functional-purity-of-reference-packages). + +If you are working with a particularly complex reference package, from an orthologous group for example, or have extra + phylogenetic information you'd like to include in your classifications, + try [annotating extra features](https://github.com/hallamlab/TreeSAPP/wiki/Layering-annotations-onto-classifications) with `treesapp layer`. + +## Citation + +If you found TreeSAPP useful in your work, please cite the following paper: + +Morgan-Lang, C., McLaughlin, R., Armstrong, Z., Zhang, G., Chan, K., & Hallam, S. J. (2020). +[TreeSAPP: The Tree-based Sensitive and Accurate Phylogenetic Profiler](https://doi.org/10.1093/bioinformatics/btaa588). +Bioinformatics, 1–8. + +This was brought to you by the team: + +- Connor Morgan-Lang ([cmorganl](https://github.com/cmorganl), maintainer) +- Ryan McLaughlin ([McGlock](https://github.com/McGlock)) +- Grace Zhang ([grace72](https://github.com/gracez72)) +- Kevin Chan ([kevinxchan](https://github.com/kevinxchan)) +- Zachary Armstrong +- Steven J. Hallam + +### References + +If you're feeling extra citation-happy, please consider citing the following works as well: + +- Eddy, S. R. (1998). Profile hidden Markov models. Bioinformatics (Oxford, England), 14(9), 755–763. +- Criscuolo, A., & Gribaldo, S. (2010). BMGE (Block Mapping and Gathering with Entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evolutionary Biology, 10(1). +- Kozlov, A. M., Darriba, D., Flouri, T., Morel, B., & Stamatakis, A. (2019). RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics, 35(21), 4453–4455. +- Barbera, P., Kozlov, A. M., Czech, L., Morel, B., & Stamatakis, A. (2018). EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences. Systematic Biology, 0(0), 291658. + + + + +%prep +%autosetup -n treesapp-0.11.4 + +%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-treesapp -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 0.11.4-1 +- Package Spec generated |