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diff --git a/python-consreg.spec b/python-consreg.spec new file mode 100644 index 0000000..27a6568 --- /dev/null +++ b/python-consreg.spec @@ -0,0 +1,569 @@ +%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 +[](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 +[](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 +[](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 |