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diff --git a/python-besst.spec b/python-besst.spec new file mode 100644 index 0000000..30fce3a --- /dev/null +++ b/python-besst.spec @@ -0,0 +1,90 @@ +%global _empty_manifest_terminate_build 0 +Name: python-BESST +Version: 2.2.8 +Release: 1 +Summary: Scaffolder for genomic assemblies. +License: GPLv3 +URL: https://github.com/ksahlin/BESST +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/4e/77/8e3ef4977dafc1c270b87f465b2850a346e9529077934ae3f8c520f3608d/BESST-2.2.8.tar.gz +BuildArch: noarch + + +%description +Supported on Linux / OSX with python2 (versions >= 2.7) and python3 (versions >=3.4) [](https://travis-ci.org/ksahlin/BESST) +BESST is a package for scaffolding genomic assemblies. BESST v1.0.4 is first described in [2] with various improvements in v2.0 (e.g. [3]). BESST is based on GapEst [1]. +For installation, see docs/INSTALL.md. Manual is found in docs/MANUAL.md. +Please cite [2] and later manuscripts when using BESST! BiBTeX entries are available in the file besst.bib. +1. Sahlin K, Street N, Lundeberg J, Arvestad L (2012) "Improved gap size estimation for scaffolding algorithms." Bioinformatics 28(17), 2215-2222 [Link](http://bioinformatics.oxfordjournals.org/content/28/17/2215.long) +2. Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L (2014) "BESST--efficient scaffolding of large fragmented assemblies." BMC Bioinformatics 15, 281 [Link](http://www.biomedcentral.com/1471-2105/15/281) +3. Sahlin K, Chikhi R, Arvestad L (2016) "Assembly scaffolding with PE-contaminated mate-pair libraries." Bioinformatics [Link](https://bioinformatics.oxfordjournals.org/content/early/2016/03/09/bioinformatics.btw064) + +%package -n python3-BESST +Summary: Scaffolder for genomic assemblies. +Provides: python-BESST +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-BESST +Supported on Linux / OSX with python2 (versions >= 2.7) and python3 (versions >=3.4) [](https://travis-ci.org/ksahlin/BESST) +BESST is a package for scaffolding genomic assemblies. BESST v1.0.4 is first described in [2] with various improvements in v2.0 (e.g. [3]). BESST is based on GapEst [1]. +For installation, see docs/INSTALL.md. Manual is found in docs/MANUAL.md. +Please cite [2] and later manuscripts when using BESST! BiBTeX entries are available in the file besst.bib. +1. Sahlin K, Street N, Lundeberg J, Arvestad L (2012) "Improved gap size estimation for scaffolding algorithms." Bioinformatics 28(17), 2215-2222 [Link](http://bioinformatics.oxfordjournals.org/content/28/17/2215.long) +2. Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L (2014) "BESST--efficient scaffolding of large fragmented assemblies." BMC Bioinformatics 15, 281 [Link](http://www.biomedcentral.com/1471-2105/15/281) +3. Sahlin K, Chikhi R, Arvestad L (2016) "Assembly scaffolding with PE-contaminated mate-pair libraries." Bioinformatics [Link](https://bioinformatics.oxfordjournals.org/content/early/2016/03/09/bioinformatics.btw064) + +%package help +Summary: Development documents and examples for BESST +Provides: python3-BESST-doc +%description help +Supported on Linux / OSX with python2 (versions >= 2.7) and python3 (versions >=3.4) [](https://travis-ci.org/ksahlin/BESST) +BESST is a package for scaffolding genomic assemblies. BESST v1.0.4 is first described in [2] with various improvements in v2.0 (e.g. [3]). BESST is based on GapEst [1]. +For installation, see docs/INSTALL.md. Manual is found in docs/MANUAL.md. +Please cite [2] and later manuscripts when using BESST! BiBTeX entries are available in the file besst.bib. +1. Sahlin K, Street N, Lundeberg J, Arvestad L (2012) "Improved gap size estimation for scaffolding algorithms." Bioinformatics 28(17), 2215-2222 [Link](http://bioinformatics.oxfordjournals.org/content/28/17/2215.long) +2. Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L (2014) "BESST--efficient scaffolding of large fragmented assemblies." BMC Bioinformatics 15, 281 [Link](http://www.biomedcentral.com/1471-2105/15/281) +3. Sahlin K, Chikhi R, Arvestad L (2016) "Assembly scaffolding with PE-contaminated mate-pair libraries." Bioinformatics [Link](https://bioinformatics.oxfordjournals.org/content/early/2016/03/09/bioinformatics.btw064) + +%prep +%autosetup -n BESST-2.2.8 + +%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-BESST -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 2.2.8-1 +- Package Spec generated |