%global _empty_manifest_terminate_build 0 Name: python-download-giab Version: 0.7.0 Release: 1 Summary: Utility Python package to download Genome-in-a-Bottle data from their index files. License: GPLv3 URL: https://github.com/davidlougheed/download_giab Source0: https://mirrors.nju.edu.cn/pypi/web/packages/9d/6e/0a6a14adce94cf988f3b7c80d7f5b98fce1bbe2dd9cc32a40751c9c46ff6/download_giab-0.7.0.tar.gz BuildArch: noarch Requires: python3-requests %description # download_giab Utility Python package to download Genome-in-a-Bottle (GIAB) data from their [index files](https://github.com/genome-in-a-bottle/giab_data_indexes/). This requires Python 3.6 or later. To install, run the following: ```bash pip install download_giab ``` If you're installing on a cluster, this might be more like: ```bash pip install --user download_giab ``` To use, run something like the following: ```bash download_giab https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/AshkenazimTrio/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG002 ``` This will download everything in the linked index to the directory the utility is run from. It can also download from local index files. If you want to download lots of data and not have the program hang up upon session disconnect, you can use `nohup` and `&`: ```bash nohup download_giab https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/AshkenazimTrio/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG002 & ``` If you are downloading paired-end reads and want to concatenate all FASTQ files into two files, you can use the `--cat-paired` flag. This will generate two files per sample: `[sample]_1.fastq.gz` and `[sample]_2.fastq.gz`. If a sample ID is not present, the literal text `paired` will be used. This will not work for some tools (e.g. `bwa mem`) if the FASTQ files in a pair-set are of different lengths. If instead you want to store the read pairs + a suggested common name, use the `--store-paired-names` flag. This will write to a file called `paired_names.txt`. To filter what files are downloaded, the `--filter` flag can be provided with a case insensitive string or regular expression (in Python syntax.) %package -n python3-download-giab Summary: Utility Python package to download Genome-in-a-Bottle data from their index files. Provides: python-download-giab BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-download-giab # download_giab Utility Python package to download Genome-in-a-Bottle (GIAB) data from their [index files](https://github.com/genome-in-a-bottle/giab_data_indexes/). This requires Python 3.6 or later. To install, run the following: ```bash pip install download_giab ``` If you're installing on a cluster, this might be more like: ```bash pip install --user download_giab ``` To use, run something like the following: ```bash download_giab https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/AshkenazimTrio/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG002 ``` This will download everything in the linked index to the directory the utility is run from. It can also download from local index files. If you want to download lots of data and not have the program hang up upon session disconnect, you can use `nohup` and `&`: ```bash nohup download_giab https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/AshkenazimTrio/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG002 & ``` If you are downloading paired-end reads and want to concatenate all FASTQ files into two files, you can use the `--cat-paired` flag. This will generate two files per sample: `[sample]_1.fastq.gz` and `[sample]_2.fastq.gz`. If a sample ID is not present, the literal text `paired` will be used. This will not work for some tools (e.g. `bwa mem`) if the FASTQ files in a pair-set are of different lengths. If instead you want to store the read pairs + a suggested common name, use the `--store-paired-names` flag. This will write to a file called `paired_names.txt`. To filter what files are downloaded, the `--filter` flag can be provided with a case insensitive string or regular expression (in Python syntax.) %package help Summary: Development documents and examples for download-giab Provides: python3-download-giab-doc %description help # download_giab Utility Python package to download Genome-in-a-Bottle (GIAB) data from their [index files](https://github.com/genome-in-a-bottle/giab_data_indexes/). This requires Python 3.6 or later. To install, run the following: ```bash pip install download_giab ``` If you're installing on a cluster, this might be more like: ```bash pip install --user download_giab ``` To use, run something like the following: ```bash download_giab https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/AshkenazimTrio/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG002 ``` This will download everything in the linked index to the directory the utility is run from. It can also download from local index files. If you want to download lots of data and not have the program hang up upon session disconnect, you can use `nohup` and `&`: ```bash nohup download_giab https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/AshkenazimTrio/sequence.index.AJtrio_Illumina300X_wgs_07292015.HG002 & ``` If you are downloading paired-end reads and want to concatenate all FASTQ files into two files, you can use the `--cat-paired` flag. This will generate two files per sample: `[sample]_1.fastq.gz` and `[sample]_2.fastq.gz`. If a sample ID is not present, the literal text `paired` will be used. This will not work for some tools (e.g. `bwa mem`) if the FASTQ files in a pair-set are of different lengths. If instead you want to store the read pairs + a suggested common name, use the `--store-paired-names` flag. This will write to a file called `paired_names.txt`. To filter what files are downloaded, the `--filter` flag can be provided with a case insensitive string or regular expression (in Python syntax.) %prep %autosetup -n download-giab-0.7.0 %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-download-giab -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Wed May 10 2023 Python_Bot - 0.7.0-1 - Package Spec generated