automatic import of python-consreg

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@@ -0,0 +1 @@
+/ConSReg-1.1.7.tar.gz
diff --git a/python-consreg.spec b/python-consreg.spec
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+%global _empty_manifest_terminate_build 0
+Name:		python-ConSReg
+Version:	1.1.7
+Release:	1
+Summary:	condition-specific regulation
+License:	MIT
+URL:		https://github.com/LiLabAtVT/ConSReg
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/ad/4e/47edea2d770fd9d0f99b0356cf215361302c7375764256740357e383987c/ConSReg-1.1.7.tar.gz
+BuildArch:	noarch
+
+Requires:	python3-numpy
+Requires:	python3-scipy
+Requires:	python3-pandas
+Requires:	python3-joblib
+Requires:	python3-rpy2
+Requires:	python3-networkx
+Requires:	python3-scikit-learn
+Requires:	python3-intervaltree
+
+%description
+# ConSReg 1.1.4
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+Condition-specific regulations
+- [ConSReg 1.1.4](#consreg-114)
+- [Getting Started](#getting-started)
+  * [1. Installation](#1-installation)
+    + [1.1 Required packages](#11-required-packages)
+      - [1.1.1 Python](#111-python)
+      - [1.1.2 R](#112-r)
+    + [1.2 Easy installation by Anaconda (recommended)](#12-easy-installation-by-anaconda--recommended-)
+    + [1.3 Manual installation (Skip this section if 1.2 is successful)](#13-manual-installation--skip-this-section-if-12-is-successful-)
+    + [1.3.1 R installation](#131-r-installation)
+      - [install R](#install-r)
+      - [install R packages](#install-r-packages)
+    + [1.3.2 Python installation](#132-python-installation)
+  * [2. Sample datasets](#2-sample-datasets)
+  * [3. Analysis](#3-analysis)
+  * [4. Publication](#4-publication)
+
+<small><i><a href='http://ecotrust-canada.github.io/markdown-toc/'>Table of contents generated with markdown-toc</a></i></small>
+
+# Getting Started
+## 1. Installation
+### 1.1 Required packages
+#### 1.1.1 Python
+- python = 3.6
+- numpy == 1.16.2
+- scipy == 1.1.0
+- pandas == 0.21.1
+- joblib >= 0.11
+- rpy2==2.8.6
+- networkx >= 2
+- sklearn >= 0.19.1
+- intervaltree == 2.1.0
+#### 1.1.2 R
+- ChIPSeeker == 1.16.1
+- CoReg == 1.0.1
+- gglasso == 1.4
+- RRF == 1.9
+- R >= 3.5.1
+### 1.2 Easy installation by Anaconda (recommended)
+Since ConSReg is dependent on both Python and R packages, we recommend installing ConSReg by Anaconda to easily set up the running environment. You may retrive Anaconda from [here](https://www.anaconda.com/) and install the version corresponding to your OS.  
+Once Anaconda is installed in your OS, run the following commands to create an new environment and install ConSReg and all its dependencies into the new environment:
+```bash
+conda create -y -n consreg python=3.6 # The new environment name is 'consreg'. You may use other name instead.
+conda activate consreg
+conda install -y -c bioconda --no-channel-priority bioconductor-chipseeker
+conda install -y --no-channel-priority r-base r-essentials
+conda install -y --no-channel-priority -c conda-forge r-gglasso r-rrf r-devtools
+pip install ConSReg
+```
+Then ConSReg environment can be activated by `conda activate consreg` and disabled by `conda deactivate`
+### 1.3 Manual installation (Skip this section if 1.2 is successful)
+### 1.3.1 R installation
+#### install R
+If R is not already installed， you may follow these steps to build R from source code. Otherwise, you may skip this section and start from 1.2.2
+
+First, disable any conda environment, if there is an active one.
+```shell
+conda deactivate
+```
+Download R source code from CRAN (https://cran.r-project.org/). You may use any version you like. It is recommended to use R version > 3.0.0. This ensures that rpy2 works correctly with R.
+```shell
+# Download R 3.6.1
+wget https://cran.r-project.org/src/base/R-3/R-3.6.1.tar.gz
+```
+Decompress the downloaded file
+```shell
+tar -zvxf R-3.6.1
+```
+In the decompressed folder, configure R by:
+```shell
+./configure prefix=path_to_install_R --enable-R-shlib
+```
+`--prefix=` specifies a writeable directory to install R into. `--enable-R-shlib` flag was added to build R shared libraries.
+
+In the decompressed folder, compile R
+```shell
+make
+```
+Install R into the specified directory:
+```shell
+make install
+```
+Add a line to ~/.bashrc to tell the OS where to look for R 
+```shell
+export PATH=path_to_R_bin_directory:$PATH
+```
+Add the following line to ~/.bashrc. This is for telling rpy2 where to look for dynamic libraries.
+```shell
+export LD_LIBRARY_PATH=/home/alexsong/R/3.6.1/lib64/R/lib:$LD_LIBRARY_PATH
+```
+Apply the changes to environment variables `PATH` and `LD_LIBRARY_PATH`:
+```shell
+source ~/.bashrc
+```
+#### install R packages
+ConSReg requires several R packages: `ChIPseeker`, `CoReg`, `gglasso` and `RRF`.
+
+It is recommended to deactivate any conda environment when installing R packages, as it may add the environment-specific path which may fail the installation. If any conda environment is active, you may deactivate it by:
+```shell
+conda deactivate
+```
+To install `ChIPSeeker` from bioconductor, type the following commands in R (for R 3.6 or higher version):
+```R
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+BiocManager::install("ChIPseeker")
+```
+For older version of R, type the following commands in R:
+```R
+source("https://bioconductor.org/biocLite.R")
+biocLite("ChIPseeker")
+```
+Please refer to the instructions described [here](https://www.bioconductor.org/packages/release/bioc/html/ChIPseeker.html) for more details.
+
+To install `CoReg` pakcage from GitHub, type the following commands in R environment:
+```R
+install.packages("devtools")
+library(devtools)
+install_github("LiLabAtVT/CoReg")
+```
+Please refer to the GitHub page of `CoReg` project for more details: 
+[link](https://github.com/LiLabAtVT/CoReg)
+
+To install `gglasso` package from CRAN, type the following commands in R environment:
+```R
+install.pacakges("gglasso")
+```
+Please refer to the link [here](https://cran.r-project.org/web/packages/gglasso/index.html) for more details.
+
+To install `RRF` package from CRAN, type the following commands in R environment:
+```R
+install.pacakges("RRF")
+```
+Please refer to the link [here](https://cran.r-project.org/web/packages/RRF/index.html) for more details.
+### 1.3.2 Python installation
+ConSReg can be installed by pip:
+```shell
+pip install ConSReg
+```
+Sometime rpy2 may throw out error message when imported in Python. This problem may arise because rpy2 was built with the R version that is different from the one it is linked to when imported in Python. To fix this, you may remove rpy2 package then reinstall it with 'no-cache-dir' flag:
+
+```shell
+pip install ConSReg --no-cache-dir
+```
+
+Alternatively, you may want to install ConSReg in development mode to be able to edit the package by yourself. To do so, simply `git clone` this repository and then under the directory that contains `setup.py`, type in:
+```shell
+pip install -e .
+```
+## 2. Sample datasets
+Sample datasets can be found in `data` folder.
+
+## 3. Analysis
+We provide code for analyzing the sample datasets in two jupyter notebooks located in the root folder of this project: **bulk_analysis.ipynb** (for bulk RNA-seq data) and **single_cell_analysis.ipynb** (for single cell RNA-seq data).
+
+## 4. Publication
+Please cite the followint paper if you use ConSReg in your research:  
+Qi Song, Jiyoung Lee, Shamima Akter, Ruth Grene, Song Li. "Prediction of condition-specific regulatory genes using machine learning." Nucleic acids research 48.11 (2020): e62-e62.
+
+
+
+
+%package -n python3-ConSReg
+Summary:	condition-specific regulation
+Provides:	python-ConSReg
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-ConSReg
+# ConSReg 1.1.4
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+Condition-specific regulations
+- [ConSReg 1.1.4](#consreg-114)
+- [Getting Started](#getting-started)
+  * [1. Installation](#1-installation)
+    + [1.1 Required packages](#11-required-packages)
+      - [1.1.1 Python](#111-python)
+      - [1.1.2 R](#112-r)
+    + [1.2 Easy installation by Anaconda (recommended)](#12-easy-installation-by-anaconda--recommended-)
+    + [1.3 Manual installation (Skip this section if 1.2 is successful)](#13-manual-installation--skip-this-section-if-12-is-successful-)
+    + [1.3.1 R installation](#131-r-installation)
+      - [install R](#install-r)
+      - [install R packages](#install-r-packages)
+    + [1.3.2 Python installation](#132-python-installation)
+  * [2. Sample datasets](#2-sample-datasets)
+  * [3. Analysis](#3-analysis)
+  * [4. Publication](#4-publication)
+
+<small><i><a href='http://ecotrust-canada.github.io/markdown-toc/'>Table of contents generated with markdown-toc</a></i></small>
+
+# Getting Started
+## 1. Installation
+### 1.1 Required packages
+#### 1.1.1 Python
+- python = 3.6
+- numpy == 1.16.2
+- scipy == 1.1.0
+- pandas == 0.21.1
+- joblib >= 0.11
+- rpy2==2.8.6
+- networkx >= 2
+- sklearn >= 0.19.1
+- intervaltree == 2.1.0
+#### 1.1.2 R
+- ChIPSeeker == 1.16.1
+- CoReg == 1.0.1
+- gglasso == 1.4
+- RRF == 1.9
+- R >= 3.5.1
+### 1.2 Easy installation by Anaconda (recommended)
+Since ConSReg is dependent on both Python and R packages, we recommend installing ConSReg by Anaconda to easily set up the running environment. You may retrive Anaconda from [here](https://www.anaconda.com/) and install the version corresponding to your OS.  
+Once Anaconda is installed in your OS, run the following commands to create an new environment and install ConSReg and all its dependencies into the new environment:
+```bash
+conda create -y -n consreg python=3.6 # The new environment name is 'consreg'. You may use other name instead.
+conda activate consreg
+conda install -y -c bioconda --no-channel-priority bioconductor-chipseeker
+conda install -y --no-channel-priority r-base r-essentials
+conda install -y --no-channel-priority -c conda-forge r-gglasso r-rrf r-devtools
+pip install ConSReg
+```
+Then ConSReg environment can be activated by `conda activate consreg` and disabled by `conda deactivate`
+### 1.3 Manual installation (Skip this section if 1.2 is successful)
+### 1.3.1 R installation
+#### install R
+If R is not already installed， you may follow these steps to build R from source code. Otherwise, you may skip this section and start from 1.2.2
+
+First, disable any conda environment, if there is an active one.
+```shell
+conda deactivate
+```
+Download R source code from CRAN (https://cran.r-project.org/). You may use any version you like. It is recommended to use R version > 3.0.0. This ensures that rpy2 works correctly with R.
+```shell
+# Download R 3.6.1
+wget https://cran.r-project.org/src/base/R-3/R-3.6.1.tar.gz
+```
+Decompress the downloaded file
+```shell
+tar -zvxf R-3.6.1
+```
+In the decompressed folder, configure R by:
+```shell
+./configure prefix=path_to_install_R --enable-R-shlib
+```
+`--prefix=` specifies a writeable directory to install R into. `--enable-R-shlib` flag was added to build R shared libraries.
+
+In the decompressed folder, compile R
+```shell
+make
+```
+Install R into the specified directory:
+```shell
+make install
+```
+Add a line to ~/.bashrc to tell the OS where to look for R 
+```shell
+export PATH=path_to_R_bin_directory:$PATH
+```
+Add the following line to ~/.bashrc. This is for telling rpy2 where to look for dynamic libraries.
+```shell
+export LD_LIBRARY_PATH=/home/alexsong/R/3.6.1/lib64/R/lib:$LD_LIBRARY_PATH
+```
+Apply the changes to environment variables `PATH` and `LD_LIBRARY_PATH`:
+```shell
+source ~/.bashrc
+```
+#### install R packages
+ConSReg requires several R packages: `ChIPseeker`, `CoReg`, `gglasso` and `RRF`.
+
+It is recommended to deactivate any conda environment when installing R packages, as it may add the environment-specific path which may fail the installation. If any conda environment is active, you may deactivate it by:
+```shell
+conda deactivate
+```
+To install `ChIPSeeker` from bioconductor, type the following commands in R (for R 3.6 or higher version):
+```R
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+BiocManager::install("ChIPseeker")
+```
+For older version of R, type the following commands in R:
+```R
+source("https://bioconductor.org/biocLite.R")
+biocLite("ChIPseeker")
+```
+Please refer to the instructions described [here](https://www.bioconductor.org/packages/release/bioc/html/ChIPseeker.html) for more details.
+
+To install `CoReg` pakcage from GitHub, type the following commands in R environment:
+```R
+install.packages("devtools")
+library(devtools)
+install_github("LiLabAtVT/CoReg")
+```
+Please refer to the GitHub page of `CoReg` project for more details: 
+[link](https://github.com/LiLabAtVT/CoReg)
+
+To install `gglasso` package from CRAN, type the following commands in R environment:
+```R
+install.pacakges("gglasso")
+```
+Please refer to the link [here](https://cran.r-project.org/web/packages/gglasso/index.html) for more details.
+
+To install `RRF` package from CRAN, type the following commands in R environment:
+```R
+install.pacakges("RRF")
+```
+Please refer to the link [here](https://cran.r-project.org/web/packages/RRF/index.html) for more details.
+### 1.3.2 Python installation
+ConSReg can be installed by pip:
+```shell
+pip install ConSReg
+```
+Sometime rpy2 may throw out error message when imported in Python. This problem may arise because rpy2 was built with the R version that is different from the one it is linked to when imported in Python. To fix this, you may remove rpy2 package then reinstall it with 'no-cache-dir' flag:
+
+```shell
+pip install ConSReg --no-cache-dir
+```
+
+Alternatively, you may want to install ConSReg in development mode to be able to edit the package by yourself. To do so, simply `git clone` this repository and then under the directory that contains `setup.py`, type in:
+```shell
+pip install -e .
+```
+## 2. Sample datasets
+Sample datasets can be found in `data` folder.
+
+## 3. Analysis
+We provide code for analyzing the sample datasets in two jupyter notebooks located in the root folder of this project: **bulk_analysis.ipynb** (for bulk RNA-seq data) and **single_cell_analysis.ipynb** (for single cell RNA-seq data).
+
+## 4. Publication
+Please cite the followint paper if you use ConSReg in your research:  
+Qi Song, Jiyoung Lee, Shamima Akter, Ruth Grene, Song Li. "Prediction of condition-specific regulatory genes using machine learning." Nucleic acids research 48.11 (2020): e62-e62.
+
+
+
+
+%package help
+Summary:	Development documents and examples for ConSReg
+Provides:	python3-ConSReg-doc
+%description help
+# ConSReg 1.1.4
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+Condition-specific regulations
+- [ConSReg 1.1.4](#consreg-114)
+- [Getting Started](#getting-started)
+  * [1. Installation](#1-installation)
+    + [1.1 Required packages](#11-required-packages)
+      - [1.1.1 Python](#111-python)
+      - [1.1.2 R](#112-r)
+    + [1.2 Easy installation by Anaconda (recommended)](#12-easy-installation-by-anaconda--recommended-)
+    + [1.3 Manual installation (Skip this section if 1.2 is successful)](#13-manual-installation--skip-this-section-if-12-is-successful-)
+    + [1.3.1 R installation](#131-r-installation)
+      - [install R](#install-r)
+      - [install R packages](#install-r-packages)
+    + [1.3.2 Python installation](#132-python-installation)
+  * [2. Sample datasets](#2-sample-datasets)
+  * [3. Analysis](#3-analysis)
+  * [4. Publication](#4-publication)
+
+<small><i><a href='http://ecotrust-canada.github.io/markdown-toc/'>Table of contents generated with markdown-toc</a></i></small>
+
+# Getting Started
+## 1. Installation
+### 1.1 Required packages
+#### 1.1.1 Python
+- python = 3.6
+- numpy == 1.16.2
+- scipy == 1.1.0
+- pandas == 0.21.1
+- joblib >= 0.11
+- rpy2==2.8.6
+- networkx >= 2
+- sklearn >= 0.19.1
+- intervaltree == 2.1.0
+#### 1.1.2 R
+- ChIPSeeker == 1.16.1
+- CoReg == 1.0.1
+- gglasso == 1.4
+- RRF == 1.9
+- R >= 3.5.1
+### 1.2 Easy installation by Anaconda (recommended)
+Since ConSReg is dependent on both Python and R packages, we recommend installing ConSReg by Anaconda to easily set up the running environment. You may retrive Anaconda from [here](https://www.anaconda.com/) and install the version corresponding to your OS.  
+Once Anaconda is installed in your OS, run the following commands to create an new environment and install ConSReg and all its dependencies into the new environment:
+```bash
+conda create -y -n consreg python=3.6 # The new environment name is 'consreg'. You may use other name instead.
+conda activate consreg
+conda install -y -c bioconda --no-channel-priority bioconductor-chipseeker
+conda install -y --no-channel-priority r-base r-essentials
+conda install -y --no-channel-priority -c conda-forge r-gglasso r-rrf r-devtools
+pip install ConSReg
+```
+Then ConSReg environment can be activated by `conda activate consreg` and disabled by `conda deactivate`
+### 1.3 Manual installation (Skip this section if 1.2 is successful)
+### 1.3.1 R installation
+#### install R
+If R is not already installed， you may follow these steps to build R from source code. Otherwise, you may skip this section and start from 1.2.2
+
+First, disable any conda environment, if there is an active one.
+```shell
+conda deactivate
+```
+Download R source code from CRAN (https://cran.r-project.org/). You may use any version you like. It is recommended to use R version > 3.0.0. This ensures that rpy2 works correctly with R.
+```shell
+# Download R 3.6.1
+wget https://cran.r-project.org/src/base/R-3/R-3.6.1.tar.gz
+```
+Decompress the downloaded file
+```shell
+tar -zvxf R-3.6.1
+```
+In the decompressed folder, configure R by:
+```shell
+./configure prefix=path_to_install_R --enable-R-shlib
+```
+`--prefix=` specifies a writeable directory to install R into. `--enable-R-shlib` flag was added to build R shared libraries.
+
+In the decompressed folder, compile R
+```shell
+make
+```
+Install R into the specified directory:
+```shell
+make install
+```
+Add a line to ~/.bashrc to tell the OS where to look for R 
+```shell
+export PATH=path_to_R_bin_directory:$PATH
+```
+Add the following line to ~/.bashrc. This is for telling rpy2 where to look for dynamic libraries.
+```shell
+export LD_LIBRARY_PATH=/home/alexsong/R/3.6.1/lib64/R/lib:$LD_LIBRARY_PATH
+```
+Apply the changes to environment variables `PATH` and `LD_LIBRARY_PATH`:
+```shell
+source ~/.bashrc
+```
+#### install R packages
+ConSReg requires several R packages: `ChIPseeker`, `CoReg`, `gglasso` and `RRF`.
+
+It is recommended to deactivate any conda environment when installing R packages, as it may add the environment-specific path which may fail the installation. If any conda environment is active, you may deactivate it by:
+```shell
+conda deactivate
+```
+To install `ChIPSeeker` from bioconductor, type the following commands in R (for R 3.6 or higher version):
+```R
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+
+BiocManager::install("ChIPseeker")
+```
+For older version of R, type the following commands in R:
+```R
+source("https://bioconductor.org/biocLite.R")
+biocLite("ChIPseeker")
+```
+Please refer to the instructions described [here](https://www.bioconductor.org/packages/release/bioc/html/ChIPseeker.html) for more details.
+
+To install `CoReg` pakcage from GitHub, type the following commands in R environment:
+```R
+install.packages("devtools")
+library(devtools)
+install_github("LiLabAtVT/CoReg")
+```
+Please refer to the GitHub page of `CoReg` project for more details: 
+[link](https://github.com/LiLabAtVT/CoReg)
+
+To install `gglasso` package from CRAN, type the following commands in R environment:
+```R
+install.pacakges("gglasso")
+```
+Please refer to the link [here](https://cran.r-project.org/web/packages/gglasso/index.html) for more details.
+
+To install `RRF` package from CRAN, type the following commands in R environment:
+```R
+install.pacakges("RRF")
+```
+Please refer to the link [here](https://cran.r-project.org/web/packages/RRF/index.html) for more details.
+### 1.3.2 Python installation
+ConSReg can be installed by pip:
+```shell
+pip install ConSReg
+```
+Sometime rpy2 may throw out error message when imported in Python. This problem may arise because rpy2 was built with the R version that is different from the one it is linked to when imported in Python. To fix this, you may remove rpy2 package then reinstall it with 'no-cache-dir' flag:
+
+```shell
+pip install ConSReg --no-cache-dir
+```
+
+Alternatively, you may want to install ConSReg in development mode to be able to edit the package by yourself. To do so, simply `git clone` this repository and then under the directory that contains `setup.py`, type in:
+```shell
+pip install -e .
+```
+## 2. Sample datasets
+Sample datasets can be found in `data` folder.
+
+## 3. Analysis
+We provide code for analyzing the sample datasets in two jupyter notebooks located in the root folder of this project: **bulk_analysis.ipynb** (for bulk RNA-seq data) and **single_cell_analysis.ipynb** (for single cell RNA-seq data).
+
+## 4. Publication
+Please cite the followint paper if you use ConSReg in your research:  
+Qi Song, Jiyoung Lee, Shamima Akter, Ruth Grene, Song Li. "Prediction of condition-specific regulatory genes using machine learning." Nucleic acids research 48.11 (2020): e62-e62.
+
+
+
+
+%prep
+%autosetup -n ConSReg-1.1.7
+
+%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-ConSReg -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Mon May 29 2023 Python_Bot <Python_Bot@openeuler.org> - 1.1.7-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..8e52458
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+4dc693cc1bdd33c4b198ad987d2eed17  ConSReg-1.1.7.tar.gz