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author | CoprDistGit <infra@openeuler.org> | 2023-05-10 03:51:49 +0000 |
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committer | CoprDistGit <infra@openeuler.org> | 2023-05-10 03:51:49 +0000 |
commit | e279258a3d20146ff33d9d47c32e3ca068f907a6 (patch) | |
tree | 67df06bf7604cdb205362fe2b9acaaeb50bb9c1c | |
parent | 051265b0a7194d365b0ec51046f4f46e2d068473 (diff) |
automatic import of python-download-giabopeneuler20.03
-rw-r--r-- | .gitignore | 1 | ||||
-rw-r--r-- | python-download-giab.spec | 220 | ||||
-rw-r--r-- | sources | 1 |
3 files changed, 222 insertions, 0 deletions
@@ -0,0 +1 @@ +/download_giab-0.7.0.tar.gz diff --git a/python-download-giab.spec b/python-download-giab.spec new file mode 100644 index 0000000..f3cf3b5 --- /dev/null +++ b/python-download-giab.spec @@ -0,0 +1,220 @@ +%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 <Python_Bot@openeuler.org> - 0.7.0-1 +- Package Spec generated @@ -0,0 +1 @@ +687ed6646b6e6aaf55e18b41918ed212 download_giab-0.7.0.tar.gz |