%global _empty_manifest_terminate_build 0 Name: python-bsbolt Version: 1.6.0 Release: 1 Summary: Bisulfite Sequencing Processing Platform License: MIT URL: https://github.com/NuttyLogic/BSBolt Source0: https://mirrors.nju.edu.cn/pypi/web/packages/ca/64/b923da8df7f3e3887fafa6d8a94c0f8c38b785be60aa725c5f0f614b6226/bsbolt-1.6.0.tar.gz BuildArch: noarch Requires: python3-pysam Requires: python3-numpy Requires: python3-tqdm Requires: python3-setuptools %description # **BSBolt (BiSulfite Bolt)** ## A fast and safe bisulfite sequencing analysis platform [BiSuflite Bolt (BSBolt)](https://github.com/NuttyLogic/BSBolt); a fast and scalable bisulfite sequencing analysis platform. BSBolt is an integrated analysis platform that offers support for bisulfite sequencing read simulation, alignment, methylation calling, data aggregation, and data imputation. BSBolt has been validated to work with a wide array of bisulfite sequencing data,including whole genome bisulfite sequencing (WGBS), reduced representative bisulfite sequencing data (RRBS), and targeted methylation sequencing data. BSBolt utilizes forked versions of [BWA](https://github.com/lh3/bwa) and [WGSIM](https://github.com/lh3/wgsim) for read alignment and read simulation respectively. BSBolt is released under the MIT license. ## Publication [Farrell, C., Thompson, M., Tosevska, A., Oyetunde, A. & Pellegrini, M. **BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform.** 2020.10.06.328559 (2020). doi:10.1101/2020.10.06.328559](https://academic.oup.com/gigascience/article/10/5/giab033/6272610) ## Documentation Documentation can be found at [https://bsbolt.readthedocs.io](https://bsbolt.readthedocs.io/en/latest/). ## Release Notes - v1.6.0 - MethyDackel compatibility - Option to output alignment to stdout - v1.5.0 - Improved thread handling for methylation / variant calling. - Experimental bisulfite aware SNP caller. - v1.4.8 - Fixed bug ending alignment when the reference template end greater than reference boundary. - v1.4.7 - Alignment stats fix. - v1.4.6 - Alignment statistics now output as generated. - Fixed bug where alignment would stop when observed mappability was low. - v1.4.5 - Fixed maximum read depth bug that prevented methylation call on site covered by greater than 8000 reads - Refactored build script, with experimental support for M1 Macs - v1.4.4 - The default entry point for BSBolt has changed from **BSBolt** to **bsbolt** for conda compatibility ## **Installation** ### **PyPi Installation** Pre-compiled binaries can be installed using PyPi. Binaries are available for python >=3.6 on unix like systems (macOS >=10.15 and linux). ```shell pip3 install bsbolt --user ``` ### **Conda Installation** BSBolt can be installed using the conda package manager using the instructions below. ```shell conda config --add channels bioconda conda config --add channels conda-forge conda install -c cpfarrell bsbolt ``` ### **Installing from Source** Dependencies * zlib-devel >= 1.2.3-29 * GCC >= 8.3.1 ```shell # clone the repository git clone https://github.com/NuttyLogic/BSBolt.git cd bsbolt # compile and install package pip3 install . ``` ### **Installing from Source on macOS** Dependencies - autoconf - automake - homebrew - xcode Installation from source requires xcode command line utilities, [homebrew](https://brew.sh/) macOS package manager, autoconf, python (>=3.6), and automake.The full installation process is outlined below. ```shell # install xcode utilities xcode-select --install # install homebrew /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" # install autoconf brew install autoconf # install automake brew install automake # optionally install python > 3.5 brew install python3.8 # clone the repository git clone https://github.com/NuttyLogic/BSBolt.git cd BSBolt # compile and install package pip3 install -e . ``` ## Usage Following installation BSBolt can be called using **bsbolt Module**. ```shell python3 -m bsbolt ``` ```shell bsbolt Module Align Alignment Index Index Generation CallMethylation Methylation Calling AggregateMatrix CGmap Matrix Aggregation Simulate bsbolt Illumina Read Simulation Impute kNN Imputation Sort Sort BAM File BamIndex Index BAM file ``` %package -n python3-bsbolt Summary: Bisulfite Sequencing Processing Platform Provides: python-bsbolt BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-bsbolt # **BSBolt (BiSulfite Bolt)** ## A fast and safe bisulfite sequencing analysis platform [BiSuflite Bolt (BSBolt)](https://github.com/NuttyLogic/BSBolt); a fast and scalable bisulfite sequencing analysis platform. BSBolt is an integrated analysis platform that offers support for bisulfite sequencing read simulation, alignment, methylation calling, data aggregation, and data imputation. BSBolt has been validated to work with a wide array of bisulfite sequencing data,including whole genome bisulfite sequencing (WGBS), reduced representative bisulfite sequencing data (RRBS), and targeted methylation sequencing data. BSBolt utilizes forked versions of [BWA](https://github.com/lh3/bwa) and [WGSIM](https://github.com/lh3/wgsim) for read alignment and read simulation respectively. BSBolt is released under the MIT license. ## Publication [Farrell, C., Thompson, M., Tosevska, A., Oyetunde, A. & Pellegrini, M. **BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform.** 2020.10.06.328559 (2020). doi:10.1101/2020.10.06.328559](https://academic.oup.com/gigascience/article/10/5/giab033/6272610) ## Documentation Documentation can be found at [https://bsbolt.readthedocs.io](https://bsbolt.readthedocs.io/en/latest/). ## Release Notes - v1.6.0 - MethyDackel compatibility - Option to output alignment to stdout - v1.5.0 - Improved thread handling for methylation / variant calling. - Experimental bisulfite aware SNP caller. - v1.4.8 - Fixed bug ending alignment when the reference template end greater than reference boundary. - v1.4.7 - Alignment stats fix. - v1.4.6 - Alignment statistics now output as generated. - Fixed bug where alignment would stop when observed mappability was low. - v1.4.5 - Fixed maximum read depth bug that prevented methylation call on site covered by greater than 8000 reads - Refactored build script, with experimental support for M1 Macs - v1.4.4 - The default entry point for BSBolt has changed from **BSBolt** to **bsbolt** for conda compatibility ## **Installation** ### **PyPi Installation** Pre-compiled binaries can be installed using PyPi. Binaries are available for python >=3.6 on unix like systems (macOS >=10.15 and linux). ```shell pip3 install bsbolt --user ``` ### **Conda Installation** BSBolt can be installed using the conda package manager using the instructions below. ```shell conda config --add channels bioconda conda config --add channels conda-forge conda install -c cpfarrell bsbolt ``` ### **Installing from Source** Dependencies * zlib-devel >= 1.2.3-29 * GCC >= 8.3.1 ```shell # clone the repository git clone https://github.com/NuttyLogic/BSBolt.git cd bsbolt # compile and install package pip3 install . ``` ### **Installing from Source on macOS** Dependencies - autoconf - automake - homebrew - xcode Installation from source requires xcode command line utilities, [homebrew](https://brew.sh/) macOS package manager, autoconf, python (>=3.6), and automake.The full installation process is outlined below. ```shell # install xcode utilities xcode-select --install # install homebrew /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" # install autoconf brew install autoconf # install automake brew install automake # optionally install python > 3.5 brew install python3.8 # clone the repository git clone https://github.com/NuttyLogic/BSBolt.git cd BSBolt # compile and install package pip3 install -e . ``` ## Usage Following installation BSBolt can be called using **bsbolt Module**. ```shell python3 -m bsbolt ``` ```shell bsbolt Module Align Alignment Index Index Generation CallMethylation Methylation Calling AggregateMatrix CGmap Matrix Aggregation Simulate bsbolt Illumina Read Simulation Impute kNN Imputation Sort Sort BAM File BamIndex Index BAM file ``` %package help Summary: Development documents and examples for bsbolt Provides: python3-bsbolt-doc %description help # **BSBolt (BiSulfite Bolt)** ## A fast and safe bisulfite sequencing analysis platform [BiSuflite Bolt (BSBolt)](https://github.com/NuttyLogic/BSBolt); a fast and scalable bisulfite sequencing analysis platform. BSBolt is an integrated analysis platform that offers support for bisulfite sequencing read simulation, alignment, methylation calling, data aggregation, and data imputation. BSBolt has been validated to work with a wide array of bisulfite sequencing data,including whole genome bisulfite sequencing (WGBS), reduced representative bisulfite sequencing data (RRBS), and targeted methylation sequencing data. BSBolt utilizes forked versions of [BWA](https://github.com/lh3/bwa) and [WGSIM](https://github.com/lh3/wgsim) for read alignment and read simulation respectively. BSBolt is released under the MIT license. ## Publication [Farrell, C., Thompson, M., Tosevska, A., Oyetunde, A. & Pellegrini, M. **BiSulfite Bolt: A BiSulfite Sequencing Analysis Platform.** 2020.10.06.328559 (2020). doi:10.1101/2020.10.06.328559](https://academic.oup.com/gigascience/article/10/5/giab033/6272610) ## Documentation Documentation can be found at [https://bsbolt.readthedocs.io](https://bsbolt.readthedocs.io/en/latest/). ## Release Notes - v1.6.0 - MethyDackel compatibility - Option to output alignment to stdout - v1.5.0 - Improved thread handling for methylation / variant calling. - Experimental bisulfite aware SNP caller. - v1.4.8 - Fixed bug ending alignment when the reference template end greater than reference boundary. - v1.4.7 - Alignment stats fix. - v1.4.6 - Alignment statistics now output as generated. - Fixed bug where alignment would stop when observed mappability was low. - v1.4.5 - Fixed maximum read depth bug that prevented methylation call on site covered by greater than 8000 reads - Refactored build script, with experimental support for M1 Macs - v1.4.4 - The default entry point for BSBolt has changed from **BSBolt** to **bsbolt** for conda compatibility ## **Installation** ### **PyPi Installation** Pre-compiled binaries can be installed using PyPi. Binaries are available for python >=3.6 on unix like systems (macOS >=10.15 and linux). ```shell pip3 install bsbolt --user ``` ### **Conda Installation** BSBolt can be installed using the conda package manager using the instructions below. ```shell conda config --add channels bioconda conda config --add channels conda-forge conda install -c cpfarrell bsbolt ``` ### **Installing from Source** Dependencies * zlib-devel >= 1.2.3-29 * GCC >= 8.3.1 ```shell # clone the repository git clone https://github.com/NuttyLogic/BSBolt.git cd bsbolt # compile and install package pip3 install . ``` ### **Installing from Source on macOS** Dependencies - autoconf - automake - homebrew - xcode Installation from source requires xcode command line utilities, [homebrew](https://brew.sh/) macOS package manager, autoconf, python (>=3.6), and automake.The full installation process is outlined below. ```shell # install xcode utilities xcode-select --install # install homebrew /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" # install autoconf brew install autoconf # install automake brew install automake # optionally install python > 3.5 brew install python3.8 # clone the repository git clone https://github.com/NuttyLogic/BSBolt.git cd BSBolt # compile and install package pip3 install -e . ``` ## Usage Following installation BSBolt can be called using **bsbolt Module**. ```shell python3 -m bsbolt ``` ```shell bsbolt Module Align Alignment Index Index Generation CallMethylation Methylation Calling AggregateMatrix CGmap Matrix Aggregation Simulate bsbolt Illumina Read Simulation Impute kNN Imputation Sort Sort BAM File BamIndex Index BAM file ``` %prep %autosetup -n bsbolt-1.6.0 %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-bsbolt -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Wed May 10 2023 Python_Bot - 1.6.0-1 - Package Spec generated