automatic import of python-bcbio-nextgen

3 files changed, 128 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..65cc8fa 100644
--- a/.gitignore
+++ b/.gitignore
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+/bcbio-nextgen-1.1.5.tar.gz
diff --git a/python-bcbio-nextgen.spec b/python-bcbio-nextgen.spec
new file mode 100644
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+%global _empty_manifest_terminate_build 0
+Name:		python-bcbio-nextgen
+Version:	1.1.5
+Release:	1
+Summary:	Best-practice pipelines for fully automated high throughput sequencing analysis
+License:	MIT
+URL:		https://github.com/bcbio/bcbio-nextgen
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/9d/7e/452e1d1051c19c2414f7583c796dc2b165740cf1750f1b6c89226bb8f4c2/bcbio-nextgen-1.1.5.tar.gz
+BuildArch:	noarch
+
+
+%description
+- Community developed: We welcome contributors with the goal of
+  overcoming the biological, algorithmic and computational challenges
+  that face individual developers working on complex pipelines in
+  quickly changing research areas. See our `users page`_ for examples
+  of bcbio-nextgen deployments, and the `developer documentation`_ for
+  tips on contributing.
+- Installation: `A single installer script`_ prepares all
+  third party software, data libraries and system configuration files.
+- `Automated validation`_: Compare variant calls against common reference
+  materials or sample specific SNP arrays to ensure call correctness.
+  Incorporation of multiple approaches for alignment, preparation and
+  variant calling enable unbiased comparisons of algorithms.
+- Distributed: Focus on `parallel analysis and scaling`_ to handle
+  large population studies and whole genome analysis. Runs on single
+  multicore computers, in compute clusters using `IPython parallel`_,
+  or on the Amazon cloud. See the `parallel documentation`_ for full
+  details.
+- Multiple analysis algorithms: bcbio-nextgen provides configurable
+  `variant calling, RNA-seq and small RNA pipelines`_.
+
+%package -n python3-bcbio-nextgen
+Summary:	Best-practice pipelines for fully automated high throughput sequencing analysis
+Provides:	python-bcbio-nextgen
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-bcbio-nextgen
+- Community developed: We welcome contributors with the goal of
+  overcoming the biological, algorithmic and computational challenges
+  that face individual developers working on complex pipelines in
+  quickly changing research areas. See our `users page`_ for examples
+  of bcbio-nextgen deployments, and the `developer documentation`_ for
+  tips on contributing.
+- Installation: `A single installer script`_ prepares all
+  third party software, data libraries and system configuration files.
+- `Automated validation`_: Compare variant calls against common reference
+  materials or sample specific SNP arrays to ensure call correctness.
+  Incorporation of multiple approaches for alignment, preparation and
+  variant calling enable unbiased comparisons of algorithms.
+- Distributed: Focus on `parallel analysis and scaling`_ to handle
+  large population studies and whole genome analysis. Runs on single
+  multicore computers, in compute clusters using `IPython parallel`_,
+  or on the Amazon cloud. See the `parallel documentation`_ for full
+  details.
+- Multiple analysis algorithms: bcbio-nextgen provides configurable
+  `variant calling, RNA-seq and small RNA pipelines`_.
+
+%package help
+Summary:	Development documents and examples for bcbio-nextgen
+Provides:	python3-bcbio-nextgen-doc
+%description help
+- Community developed: We welcome contributors with the goal of
+  overcoming the biological, algorithmic and computational challenges
+  that face individual developers working on complex pipelines in
+  quickly changing research areas. See our `users page`_ for examples
+  of bcbio-nextgen deployments, and the `developer documentation`_ for
+  tips on contributing.
+- Installation: `A single installer script`_ prepares all
+  third party software, data libraries and system configuration files.
+- `Automated validation`_: Compare variant calls against common reference
+  materials or sample specific SNP arrays to ensure call correctness.
+  Incorporation of multiple approaches for alignment, preparation and
+  variant calling enable unbiased comparisons of algorithms.
+- Distributed: Focus on `parallel analysis and scaling`_ to handle
+  large population studies and whole genome analysis. Runs on single
+  multicore computers, in compute clusters using `IPython parallel`_,
+  or on the Amazon cloud. See the `parallel documentation`_ for full
+  details.
+- Multiple analysis algorithms: bcbio-nextgen provides configurable
+  `variant calling, RNA-seq and small RNA pipelines`_.
+
+%prep
+%autosetup -n bcbio-nextgen-1.1.5
+
+%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-bcbio-nextgen -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Mon May 29 2023 Python_Bot <Python_Bot@openeuler.org> - 1.1.5-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..32d2c86
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+01a9ff270a4e3f50d3906a2064e18d73  bcbio-nextgen-1.1.5.tar.gz