automatic import of python-xicra

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diff --git a/.gitignore b/.gitignore
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+++ b/.gitignore
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+/XICRA-1.4.5.tar.gz
diff --git a/python-xicra.spec b/python-xicra.spec
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+%global _empty_manifest_terminate_build 0
+Name:		python-XICRA
+Version:	1.4.5
+Release:	1
+Summary:	Small RNAseq pipeline for paired-end reads
+License:	MIT License
+URL:		https://github.com/HCGB-IGTP/XICRA/
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/90/42/890d7a8e2dbb1c7f4d00228004fe891644ee405e8ca37e07772a309482c8/XICRA-1.4.5.tar.gz
+BuildArch:	noarch
+
+Requires:	python3-pandas
+Requires:	python3-termcolor
+Requires:	python3-cutadapt
+Requires:	python3-mirtop
+Requires:	python3-pysam
+Requires:	python3-pybedtools
+Requires:	python3-biopython
+Requires:	python3-multiqc
+Requires:	python3-HCGB
+Requires:	python3-future
+Requires:	python3-networkx
+Requires:	python3-numpy
+Requires:	python3-gitdir
+
+%description
+# XICRA: Small RNAseq pipeline for paired-end reads
+
+## Description
+
+XICRA is a python pipeline developed in multiple separated modules that it is designed to take 
+paired end fastq reads, trim adapters and low-quality base pairs positions, and merge reads (R1 & R2) 
+that overlap. Using joined reads it describes all major RNA biotypes present in the samples including 
+miRNA and isomiRs, tRNA fragments (tRFs) and piwi associated RNAs (piRNAs).
+
+So far, XICRA produces a miRNA analysis at the isomiR level using joined reads, multiple software at the 
+user selection and following a standardization procedure. Results are generated for each sample analyzed and 
+summarized for all samples in a single expression matrix. This information can be processed at the miRNA or 
+isomiR level (single sequence) but also summarizing for each isomiR variant type. This information can be 
+easily accessed using the accompanied R package XICRA.stats. Although the pipeline is designed to take 
+paired-end reads, it also accepts single-end reads.
+
+## Installation
+
+XICRA will require python v3.7 and java (we tested in openjdk 14 2020-03-17).
+
+The XICRA python pipeline is available in `pip` and also available using `conda`.
+
+XICRA depends on multiple third party software that we have listed below.
+
+### Dependencies 
+
+Python XICRA module will install itself along some python modules dependencies (pandas, multiqc, pybedtools, biopython etc.). 
+
+But additionally, XICRA depends on third party software that we listed in the following [table](https://github.com/HCGB-IGTP/XICRA/blob/master/XICRA_pip/XICRA/config/software/soft_dependencies.csv).
+
+### Conda environment
+
+We encourage you to install XICRA and all dependencies using the `conda` environment we created and following these instructions. 
+
+To create a new conda environment, install third party software, install XICRA and missing dependencies, do as follows: 
+
+1) Get requirements file from XICRA git repo
+
+```sh
+wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/devel/conda/environment.yml
+```
+
+2) Create environment named XICRA and install required packages using conda: 
+
+```sh
+conda env create -f environment.yml
+```
+
+3) Activate environment and install XICRA
+```sh
+## activate
+conda activate XICRA
+
+## install latest python code
+pip install XICRA
+```
+
+4) Install missing software:  Unfortunately, a couple of executables are not available neither as a `conda` or `pip` packages. These packages are `miraligner`, `sRNAbench` and 'MINTmap'. We have generated a `bash` script to retrieve and include within your `conda environment`.
+
+```sh
+## install missing software
+wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/XICRA/config/software/installer.sh
+sh installer.sh
+```
+
+To check everything is fine, try executing the `config` module:
+```sh
+XICRA config
+```
+
+## Documentation
+
+See a full documentation, user guide and manual in [here](https://readthedocs.org/)
+
+## Example
+Here we include a brief example on how to use XICRA.
+
+First, we create a python environment and will install XICRA and dependencies. See example details shown before.
+Then, we can test XICRA by using an example of 100 miRNA simulated and provideded within the repository as an example of simulation.
+
+```sh
+## run XICRA example
+ln -s ~/BMC_bioinformatics_paper/simulation/example/reads/
+
+## prepare reads
+XICRA prep --input reads/ --output_folder test_XICRA
+
+## join reads
+XICRA join --input test_XICRA --noTrim
+
+## create miRNA analysis
+XICRA miRNA --input test_XICRA --software miraligner sRNAbench
+
+## explore results
+ls test_XICRA/report/
+```
+
+## Documentation
+For a full documentation and details visit Read the Docs site [here](https://xicra.readthedocs.io/). 
+
+See a brief example on how to install and run XICRA [here](https://github.com/HCGB-IGTP/XICRA/tree/master/XICRA_pip#example)
+
+## License 
+
+MIT License
+
+Copyright (c) 2020-2022 HCGB-IGTP
+
+See additional details [here](XICRA_pip/LICENSE)
+
+Developed and maintained by Jose F. Sanchez-Herrero and Lauro Sumoy at HCGB-IGTP
+
+http://www.germanstrias.org/technology-services/genomica-bioinformatica/
+
+## Citation
+Sanchez Herrero, J.F., Pluvinet, R., Luna de Haro, A. et al. Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis. BMC Bioinformatics 22, 215 (2021). https://doi.org/10.1186/s12859-021-04128-1
+
+## Authors
+Antonio Luna de Haro (v0.1)
+Jose F Sanchez-Herrero (v1.0)	
+
+
+
+
+%package -n python3-XICRA
+Summary:	Small RNAseq pipeline for paired-end reads
+Provides:	python-XICRA
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-XICRA
+# XICRA: Small RNAseq pipeline for paired-end reads
+
+## Description
+
+XICRA is a python pipeline developed in multiple separated modules that it is designed to take 
+paired end fastq reads, trim adapters and low-quality base pairs positions, and merge reads (R1 & R2) 
+that overlap. Using joined reads it describes all major RNA biotypes present in the samples including 
+miRNA and isomiRs, tRNA fragments (tRFs) and piwi associated RNAs (piRNAs).
+
+So far, XICRA produces a miRNA analysis at the isomiR level using joined reads, multiple software at the 
+user selection and following a standardization procedure. Results are generated for each sample analyzed and 
+summarized for all samples in a single expression matrix. This information can be processed at the miRNA or 
+isomiR level (single sequence) but also summarizing for each isomiR variant type. This information can be 
+easily accessed using the accompanied R package XICRA.stats. Although the pipeline is designed to take 
+paired-end reads, it also accepts single-end reads.
+
+## Installation
+
+XICRA will require python v3.7 and java (we tested in openjdk 14 2020-03-17).
+
+The XICRA python pipeline is available in `pip` and also available using `conda`.
+
+XICRA depends on multiple third party software that we have listed below.
+
+### Dependencies 
+
+Python XICRA module will install itself along some python modules dependencies (pandas, multiqc, pybedtools, biopython etc.). 
+
+But additionally, XICRA depends on third party software that we listed in the following [table](https://github.com/HCGB-IGTP/XICRA/blob/master/XICRA_pip/XICRA/config/software/soft_dependencies.csv).
+
+### Conda environment
+
+We encourage you to install XICRA and all dependencies using the `conda` environment we created and following these instructions. 
+
+To create a new conda environment, install third party software, install XICRA and missing dependencies, do as follows: 
+
+1) Get requirements file from XICRA git repo
+
+```sh
+wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/devel/conda/environment.yml
+```
+
+2) Create environment named XICRA and install required packages using conda: 
+
+```sh
+conda env create -f environment.yml
+```
+
+3) Activate environment and install XICRA
+```sh
+## activate
+conda activate XICRA
+
+## install latest python code
+pip install XICRA
+```
+
+4) Install missing software:  Unfortunately, a couple of executables are not available neither as a `conda` or `pip` packages. These packages are `miraligner`, `sRNAbench` and 'MINTmap'. We have generated a `bash` script to retrieve and include within your `conda environment`.
+
+```sh
+## install missing software
+wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/XICRA/config/software/installer.sh
+sh installer.sh
+```
+
+To check everything is fine, try executing the `config` module:
+```sh
+XICRA config
+```
+
+## Documentation
+
+See a full documentation, user guide and manual in [here](https://readthedocs.org/)
+
+## Example
+Here we include a brief example on how to use XICRA.
+
+First, we create a python environment and will install XICRA and dependencies. See example details shown before.
+Then, we can test XICRA by using an example of 100 miRNA simulated and provideded within the repository as an example of simulation.
+
+```sh
+## run XICRA example
+ln -s ~/BMC_bioinformatics_paper/simulation/example/reads/
+
+## prepare reads
+XICRA prep --input reads/ --output_folder test_XICRA
+
+## join reads
+XICRA join --input test_XICRA --noTrim
+
+## create miRNA analysis
+XICRA miRNA --input test_XICRA --software miraligner sRNAbench
+
+## explore results
+ls test_XICRA/report/
+```
+
+## Documentation
+For a full documentation and details visit Read the Docs site [here](https://xicra.readthedocs.io/). 
+
+See a brief example on how to install and run XICRA [here](https://github.com/HCGB-IGTP/XICRA/tree/master/XICRA_pip#example)
+
+## License 
+
+MIT License
+
+Copyright (c) 2020-2022 HCGB-IGTP
+
+See additional details [here](XICRA_pip/LICENSE)
+
+Developed and maintained by Jose F. Sanchez-Herrero and Lauro Sumoy at HCGB-IGTP
+
+http://www.germanstrias.org/technology-services/genomica-bioinformatica/
+
+## Citation
+Sanchez Herrero, J.F., Pluvinet, R., Luna de Haro, A. et al. Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis. BMC Bioinformatics 22, 215 (2021). https://doi.org/10.1186/s12859-021-04128-1
+
+## Authors
+Antonio Luna de Haro (v0.1)
+Jose F Sanchez-Herrero (v1.0)	
+
+
+
+
+%package help
+Summary:	Development documents and examples for XICRA
+Provides:	python3-XICRA-doc
+%description help
+# XICRA: Small RNAseq pipeline for paired-end reads
+
+## Description
+
+XICRA is a python pipeline developed in multiple separated modules that it is designed to take 
+paired end fastq reads, trim adapters and low-quality base pairs positions, and merge reads (R1 & R2) 
+that overlap. Using joined reads it describes all major RNA biotypes present in the samples including 
+miRNA and isomiRs, tRNA fragments (tRFs) and piwi associated RNAs (piRNAs).
+
+So far, XICRA produces a miRNA analysis at the isomiR level using joined reads, multiple software at the 
+user selection and following a standardization procedure. Results are generated for each sample analyzed and 
+summarized for all samples in a single expression matrix. This information can be processed at the miRNA or 
+isomiR level (single sequence) but also summarizing for each isomiR variant type. This information can be 
+easily accessed using the accompanied R package XICRA.stats. Although the pipeline is designed to take 
+paired-end reads, it also accepts single-end reads.
+
+## Installation
+
+XICRA will require python v3.7 and java (we tested in openjdk 14 2020-03-17).
+
+The XICRA python pipeline is available in `pip` and also available using `conda`.
+
+XICRA depends on multiple third party software that we have listed below.
+
+### Dependencies 
+
+Python XICRA module will install itself along some python modules dependencies (pandas, multiqc, pybedtools, biopython etc.). 
+
+But additionally, XICRA depends on third party software that we listed in the following [table](https://github.com/HCGB-IGTP/XICRA/blob/master/XICRA_pip/XICRA/config/software/soft_dependencies.csv).
+
+### Conda environment
+
+We encourage you to install XICRA and all dependencies using the `conda` environment we created and following these instructions. 
+
+To create a new conda environment, install third party software, install XICRA and missing dependencies, do as follows: 
+
+1) Get requirements file from XICRA git repo
+
+```sh
+wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/devel/conda/environment.yml
+```
+
+2) Create environment named XICRA and install required packages using conda: 
+
+```sh
+conda env create -f environment.yml
+```
+
+3) Activate environment and install XICRA
+```sh
+## activate
+conda activate XICRA
+
+## install latest python code
+pip install XICRA
+```
+
+4) Install missing software:  Unfortunately, a couple of executables are not available neither as a `conda` or `pip` packages. These packages are `miraligner`, `sRNAbench` and 'MINTmap'. We have generated a `bash` script to retrieve and include within your `conda environment`.
+
+```sh
+## install missing software
+wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/XICRA/config/software/installer.sh
+sh installer.sh
+```
+
+To check everything is fine, try executing the `config` module:
+```sh
+XICRA config
+```
+
+## Documentation
+
+See a full documentation, user guide and manual in [here](https://readthedocs.org/)
+
+## Example
+Here we include a brief example on how to use XICRA.
+
+First, we create a python environment and will install XICRA and dependencies. See example details shown before.
+Then, we can test XICRA by using an example of 100 miRNA simulated and provideded within the repository as an example of simulation.
+
+```sh
+## run XICRA example
+ln -s ~/BMC_bioinformatics_paper/simulation/example/reads/
+
+## prepare reads
+XICRA prep --input reads/ --output_folder test_XICRA
+
+## join reads
+XICRA join --input test_XICRA --noTrim
+
+## create miRNA analysis
+XICRA miRNA --input test_XICRA --software miraligner sRNAbench
+
+## explore results
+ls test_XICRA/report/
+```
+
+## Documentation
+For a full documentation and details visit Read the Docs site [here](https://xicra.readthedocs.io/). 
+
+See a brief example on how to install and run XICRA [here](https://github.com/HCGB-IGTP/XICRA/tree/master/XICRA_pip#example)
+
+## License 
+
+MIT License
+
+Copyright (c) 2020-2022 HCGB-IGTP
+
+See additional details [here](XICRA_pip/LICENSE)
+
+Developed and maintained by Jose F. Sanchez-Herrero and Lauro Sumoy at HCGB-IGTP
+
+http://www.germanstrias.org/technology-services/genomica-bioinformatica/
+
+## Citation
+Sanchez Herrero, J.F., Pluvinet, R., Luna de Haro, A. et al. Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis. BMC Bioinformatics 22, 215 (2021). https://doi.org/10.1186/s12859-021-04128-1
+
+## Authors
+Antonio Luna de Haro (v0.1)
+Jose F Sanchez-Herrero (v1.0)	
+
+
+
+
+%prep
+%autosetup -n XICRA-1.4.5
+
+%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-XICRA -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Mon May 29 2023 Python_Bot <Python_Bot@openeuler.org> - 1.4.5-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..aeb5417
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+7a19d59dee80d32161fa60b9b38b92ca  XICRA-1.4.5.tar.gz