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authorCoprDistGit <infra@openeuler.org>2023-05-10 03:51:49 +0000
committerCoprDistGit <infra@openeuler.org>2023-05-10 03:51:49 +0000
commite279258a3d20146ff33d9d47c32e3ca068f907a6 (patch)
tree67df06bf7604cdb205362fe2b9acaaeb50bb9c1c
parent051265b0a7194d365b0ec51046f4f46e2d068473 (diff)
automatic import of python-download-giabopeneuler20.03
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-rw-r--r--python-download-giab.spec220
-rw-r--r--sources1
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diff --git a/.gitignore b/.gitignore
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+/download_giab-0.7.0.tar.gz
diff --git a/python-download-giab.spec b/python-download-giab.spec
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+%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
diff --git a/sources b/sources
new file mode 100644
index 0000000..9e09162
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+687ed6646b6e6aaf55e18b41918ed212 download_giab-0.7.0.tar.gz