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| author | CoprDistGit <infra@openeuler.org> | 2023-06-20 07:26:38 +0000 |
|---|---|---|
| committer | CoprDistGit <infra@openeuler.org> | 2023-06-20 07:26:38 +0000 |
| commit | f03e496462d2986490b411282bb62935410ecf63 (patch) | |
| tree | cdbe4aaa6e8126fe05cb818dcc78a9aa2dfa012b | |
| parent | ec304311a318c2f90a54b819b596bd22e04c9922 (diff) | |
automatic import of python-eggnog-mapperopeneuler20.03
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-eggnog-mapper.spec | 225 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 227 insertions, 0 deletions
@@ -0,0 +1 @@ +/eggnog-mapper-2.1.11.tar.gz diff --git a/python-eggnog-mapper.spec b/python-eggnog-mapper.spec new file mode 100644 index 0000000..b0ba1bf --- /dev/null +++ b/python-eggnog-mapper.spec @@ -0,0 +1,225 @@ +%global _empty_manifest_terminate_build 0 +Name: python-eggnog-mapper +Version: 2.1.11 +Release: 1 +Summary: Fast functional annotation of novel sequences using eggNOG orthology assignments. +License: GPLv3 +URL: http://eggnog-mapper.embl.de +Source0: https://mirrors.aliyun.com/pypi/web/packages/7e/bc/f316df0761266c54b59fc1513d08486aeef68e02b61837375ed7113c8642/eggnog-mapper-2.1.11.tar.gz +BuildArch: noarch + +Requires: python3-biopython +Requires: python3-psutil +Requires: python3-xlsxwriter + +%description +[](https://travis-ci.com/eggnogdb/eggnog-mapper) +[](https://usegalaxy.eu/root?tool_id=eggnog_mapper) + +# Overview +**EggNOG-mapper** is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. + +Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. + +The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches (i.e. BLAST searches), as it avoids transferring annotations from close paralogs (duplicate genes with a higher chance of being involved in functional divergence). + +Benchmarks comparing different eggNOG-mapper options against BLAST and InterProScan [can be found here](https://github.com/jhcepas/emapper-benchmark/blob/master/benchmark_analysis.ipynb). + +EggNOG-mapper is also available as a public online resource: http://eggnog-mapper.embl.de + +# Documentation +https://github.com/jhcepas/eggnog-mapper/wiki + +# Citation + +If you use this software, please cite: +``` +[1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain + prediction at the metagenomic scale. Carlos P. Cantalapiedra, + Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021. + Molecular Biology and Evolution, msab293, https://doi.org/10.1093/molbev/msab293 + +[2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated + orthology resource based on 5090 organisms and 2502 viruses. Jaime + Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia + K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars + J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8; + 47(Database issue): D309–D314. doi: 10.1093/nar/gky1085 +``` + +Please, cite also the underlying algorithm used for the search step of eggNOG-mapper, and Prodigal if it was used for gene prediction: +``` +[HMMER] Accelerated Profile HMM Searches. + Eddy SR. 2011. PLoS Comput. Biol. 7:e1002195. + +[DIAMOND] Sensitive protein alignments at tree-of-life scale using DIAMOND. + Buchfink B, Reuter K, Drost HG. 2021. + Nature Methods 18, 366–368 (2021). https://doi.org/10.1038/s41592-021-01101-x + +[MMSEQS2] MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. + Steinegger M & Söding J. 2017. Nat. Biotech. 35, 1026–1028. https://doi.org/10.1038/nbt.3988 + +[PRODIGAL] Prodigal: prokaryotic gene recognition and translation initiation site identification. + Hyatt et al. 2010. BMC Bioinformatics 11, 119. https://doi.org/10.1186/1471-2105-11-119. + +``` + + +%package -n python3-eggnog-mapper +Summary: Fast functional annotation of novel sequences using eggNOG orthology assignments. +Provides: python-eggnog-mapper +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-eggnog-mapper +[](https://travis-ci.com/eggnogdb/eggnog-mapper) +[](https://usegalaxy.eu/root?tool_id=eggnog_mapper) + +# Overview +**EggNOG-mapper** is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. + +Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. + +The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches (i.e. BLAST searches), as it avoids transferring annotations from close paralogs (duplicate genes with a higher chance of being involved in functional divergence). + +Benchmarks comparing different eggNOG-mapper options against BLAST and InterProScan [can be found here](https://github.com/jhcepas/emapper-benchmark/blob/master/benchmark_analysis.ipynb). + +EggNOG-mapper is also available as a public online resource: http://eggnog-mapper.embl.de + +# Documentation +https://github.com/jhcepas/eggnog-mapper/wiki + +# Citation + +If you use this software, please cite: +``` +[1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain + prediction at the metagenomic scale. Carlos P. Cantalapiedra, + Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021. + Molecular Biology and Evolution, msab293, https://doi.org/10.1093/molbev/msab293 + +[2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated + orthology resource based on 5090 organisms and 2502 viruses. Jaime + Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia + K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars + J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8; + 47(Database issue): D309–D314. doi: 10.1093/nar/gky1085 +``` + +Please, cite also the underlying algorithm used for the search step of eggNOG-mapper, and Prodigal if it was used for gene prediction: +``` +[HMMER] Accelerated Profile HMM Searches. + Eddy SR. 2011. PLoS Comput. Biol. 7:e1002195. + +[DIAMOND] Sensitive protein alignments at tree-of-life scale using DIAMOND. + Buchfink B, Reuter K, Drost HG. 2021. + Nature Methods 18, 366–368 (2021). https://doi.org/10.1038/s41592-021-01101-x + +[MMSEQS2] MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. + Steinegger M & Söding J. 2017. Nat. Biotech. 35, 1026–1028. https://doi.org/10.1038/nbt.3988 + +[PRODIGAL] Prodigal: prokaryotic gene recognition and translation initiation site identification. + Hyatt et al. 2010. BMC Bioinformatics 11, 119. https://doi.org/10.1186/1471-2105-11-119. + +``` + + +%package help +Summary: Development documents and examples for eggnog-mapper +Provides: python3-eggnog-mapper-doc +%description help +[](https://travis-ci.com/eggnogdb/eggnog-mapper) +[](https://usegalaxy.eu/root?tool_id=eggnog_mapper) + +# Overview +**EggNOG-mapper** is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. + +Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. + +The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches (i.e. BLAST searches), as it avoids transferring annotations from close paralogs (duplicate genes with a higher chance of being involved in functional divergence). + +Benchmarks comparing different eggNOG-mapper options against BLAST and InterProScan [can be found here](https://github.com/jhcepas/emapper-benchmark/blob/master/benchmark_analysis.ipynb). + +EggNOG-mapper is also available as a public online resource: http://eggnog-mapper.embl.de + +# Documentation +https://github.com/jhcepas/eggnog-mapper/wiki + +# Citation + +If you use this software, please cite: +``` +[1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain + prediction at the metagenomic scale. Carlos P. Cantalapiedra, + Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021. + Molecular Biology and Evolution, msab293, https://doi.org/10.1093/molbev/msab293 + +[2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated + orthology resource based on 5090 organisms and 2502 viruses. Jaime + Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia + K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars + J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8; + 47(Database issue): D309–D314. doi: 10.1093/nar/gky1085 +``` + +Please, cite also the underlying algorithm used for the search step of eggNOG-mapper, and Prodigal if it was used for gene prediction: +``` +[HMMER] Accelerated Profile HMM Searches. + Eddy SR. 2011. PLoS Comput. Biol. 7:e1002195. + +[DIAMOND] Sensitive protein alignments at tree-of-life scale using DIAMOND. + Buchfink B, Reuter K, Drost HG. 2021. + Nature Methods 18, 366–368 (2021). https://doi.org/10.1038/s41592-021-01101-x + +[MMSEQS2] MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. + Steinegger M & Söding J. 2017. Nat. Biotech. 35, 1026–1028. https://doi.org/10.1038/nbt.3988 + +[PRODIGAL] Prodigal: prokaryotic gene recognition and translation initiation site identification. + Hyatt et al. 2010. BMC Bioinformatics 11, 119. https://doi.org/10.1186/1471-2105-11-119. + +``` + + +%prep +%autosetup -n eggnog-mapper-2.1.11 + +%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-eggnog-mapper -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Tue Jun 20 2023 Python_Bot <Python_Bot@openeuler.org> - 2.1.11-1 +- Package Spec generated @@ -0,0 +1 @@ +0267b269d772e260753de4b38dd92b7d eggnog-mapper-2.1.11.tar.gz |