RGT installation successful, but rgtdata folder is missing.

[mdu4003]

Hello, I am trying to install rgt on a mac (ventura). I did: $ brew install python boost llvm Warning: python@3.11 3.11.3 is already installed and up-to-date. To reinstall 3.11.3, run: brew reinstall python@3.11 Warning: boost 1.81.0_1 is already installed and up-to-date. To reinstall 1.81.0_1, run: brew reinstall boost Warning: llvm 16.0.5 is already installed and up-to-date. To reinstall 16.0.5, run: brew reinstall llvm $ pip install cython numpy scipy Requirement already satisfied: cython in ./.local/lib/python3.8/site-packages (0.29.35) Requirement already satisfied: numpy in ./.local/lib/python3.8/site-packages (1.24.3) Requirement already satisfied: scipy in ./.local/lib/python3.8/site-packages (1.10.1) $pip install RGT --no-binary RGT Requirement already satisfied: cython in ./.local/lib/python3.8/site-packages (0.29.35) Requirement already satisfied: numpy in ./.local/lib/python3.8/site-packages (1.24.3) Requirement already satisfied: scipy in ./.local/lib/python3.8/site-packages (1.10.1) MAC205928:~ diazmeco$ pip install RGT --no-binary RGT Collecting RGT Using cached RGT-1.0.0-py3-none-any.whl Requirement already satisfied: cython in ./.local/lib/python3.8/site-packages (from RGT) (0.29.35) Requirement already satisfied: numpy>=1.4.0 in ./.local/lib/python3.8/site-packages (from RGT) (1.24.3) Requirement already satisfied: scipy>=1.0.0 in ./.local/lib/python3.8/site-packages (from RGT) (1.10.1) Requirement already satisfied: pysam>=0.12.0 in ./.local/lib/python3.8/site-packages (from RGT) (0.21.0) Requirement already satisfied: pyBigWig in ./.local/lib/python3.8/site-packages (from RGT) (0.3.22) Requirement already satisfied: Biopython>=1.64 in ./.local/lib/python3.8/site-packages (from RGT) (1.81) Requirement already satisfied: fisher>=0.1.5 in ./.local/lib/python3.8/site-packages (from RGT) (0.1.10) Requirement already satisfied: moods-python>=1.9.4.1 in ./.local/lib/python3.8/site-packages (from RGT) (1.9.4.1) Requirement already satisfied: scikit-learn>=0.19.0 in ./.local/lib/python3.8/site-packages (from RGT) (1.2.2) Requirement already satisfied: hmmlearn==0.2.2 in ./.local/lib/python3.8/site-packages (from RGT) (0.2.2) Requirement already satisfied: pandas in ./.local/lib/python3.8/site-packages (from RGT) (2.0.2) Requirement already satisfied: logomaker in ./.local/lib/python3.8/site-packages (from RGT) (0.8) Requirement already satisfied: pyx in ./.local/lib/python3.8/site-packages (from RGT) (0.16) Requirement already satisfied: joblib in ./.local/lib/python3.8/site-packages (from RGT) (1.2.0) Requirement already satisfied: seaborn in ./.local/lib/python3.8/site-packages (from RGT) (0.12.2) Requirement already satisfied: adjustText in ./.local/lib/python3.8/site-packages (from RGT) (0.8) Requirement already satisfied: matplotlib>=1.1.0 in ./.local/lib/python3.8/site-packages (from RGT) (3.7.1) Requirement already satisfied: mpmath in ./.local/lib/python3.8/site-packages (from RGT) (1.3.0) Requirement already satisfied: HTSeq in ./.local/lib/python3.8/site-packages (from RGT) (2.0.3) Requirement already satisfied: matplotlib-venn in ./.local/lib/python3.8/site-packages (from RGT) (0.11.9) Requirement already satisfied: natsort in ./.local/lib/python3.8/site-packages (from RGT) (8.3.1) Requirement already satisfied: contourpy>=1.0.1 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (1.0.7) Requirement already satisfied: cycler>=0.10 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (0.11.0) Requirement already satisfied: fonttools>=4.22.0 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (4.39.4) Requirement already satisfied: kiwisolver>=1.0.1 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (1.4.4) Requirement already satisfied: packaging>=20.0 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (23.1) Requirement already satisfied: pillow>=6.2.0 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (9.5.0) Requirement already satisfied: pyparsing>=2.3.1 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (3.0.9) Requirement already satisfied: python-dateutil>=2.7 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (2.8.2) Requirement already satisfied: importlib-resources>=3.2.0 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (5.12.0) Requirement already satisfied: threadpoolctl>=2.0.0 in ./.local/lib/python3.8/site-packages (from scikit-learn>=0.19.0->RGT) (3.1.0) Requirement already satisfied: pytz>=2020.1 in ./.local/lib/python3.8/site-packages (from pandas->RGT) (2023.3) Requirement already satisfied: tzdata>=2022.1 in ./.local/lib/python3.8/site-packages (from pandas->RGT) (2023.3) Requirement already satisfied: zipp>=3.1.0 in ./.local/lib/python3.8/site-packages (from importlib-resources>=3.2.0->matplotlib>=1.1.0->RGT) (3.15.0) Requirement already satisfied: six>=1.5 in ./.local/lib/python3.8/site-packages (from python-dateutil>=2.7->matplotlib>=1.1.0->RGT) (1.16.0) Installing collected packages: RGT Successfully installed RGT-1.0.0 MAC205928:~ diazmeco$ ls Applications cpdb-venv Creative Cloud Files gsea_home Desktop httpsanalysis.ingenuity.compa_4248295 Documents httpsanalysis.ingenuity.compa_627256 Downloads id_rsa Dropbox id_rsa.pub GSVA igv Library mambaforge MoscatDiazMecoLab med.cornell.edu MoscatDiazMecoLab Dropbox miniconda3 Movies ncbi Music opt OneDrive - med.cornell.edu pathml Pictures pippo Public prefix PycharmProjects rose SEACR src Sites streamlit_apps MAC205928:~ diazmeco$ brew install python boost llvm Warning: python@3.11 3.11.3 is already installed and up-to-date. To reinstall 3.11.3, run: brew reinstall python@3.11 Warning: boost 1.81.0_1 is already installed and up-to-date. To reinstall 1.81.0_1, run: brew reinstall boost Warning: llvm 16.0.5 is already installed and up-to-date. To reinstall 16.0.5, run: brew reinstall llvm MAC205928:~ diazmeco$ pip install cython numpy scipy Requirement already satisfied: cython in ./.local/lib/python3.8/site-packages (0.29.35) Requirement already satisfied: numpy in ./.local/lib/python3.8/site-packages (1.24.3) Requirement already satisfied: scipy in ./.local/lib/python3.8/site-packages (1.10.1) MAC205928:~ diazmeco$ pip install RGT --no-binary RGT Requirement already satisfied: RGT in ./.pyenv/versions/3.8.2/lib/python3.8/site-packages (1.0.0) Requirement already satisfied: cython in ./.local/lib/python3.8/site-packages (from RGT) (0.29.35) Requirement already satisfied: numpy>=1.4.0 in ./.local/lib/python3.8/site-packages (from RGT) (1.24.3) Requirement already satisfied: scipy>=1.0.0 in ./.local/lib/python3.8/site-packages (from RGT) (1.10.1) Requirement already satisfied: pysam>=0.12.0 in ./.local/lib/python3.8/site-packages (from RGT) (0.21.0) Requirement already satisfied: pyBigWig in ./.local/lib/python3.8/site-packages (from RGT) (0.3.22) Requirement already satisfied: Biopython>=1.64 in ./.local/lib/python3.8/site-packages (from RGT) (1.81) Requirement already satisfied: fisher>=0.1.5 in ./.local/lib/python3.8/site-packages (from RGT) (0.1.10) Requirement already satisfied: moods-python>=1.9.4.1 in ./.local/lib/python3.8/site-packages (from RGT) (1.9.4.1) Requirement already satisfied: scikit-learn>=0.19.0 in ./.local/lib/python3.8/site-packages (from RGT) (1.2.2) Requirement already satisfied: hmmlearn==0.2.2 in ./.local/lib/python3.8/site-packages (from RGT) (0.2.2) Requirement already satisfied: pandas in ./.local/lib/python3.8/site-packages (from RGT) (2.0.2) Requirement already satisfied: logomaker in ./.local/lib/python3.8/site-packages (from RGT) (0.8) Requirement already satisfied: pyx in ./.local/lib/python3.8/site-packages (from RGT) (0.16) Requirement already satisfied: joblib in ./.local/lib/python3.8/site-packages (from RGT) (1.2.0) Requirement already satisfied: seaborn in ./.local/lib/python3.8/site-packages (from RGT) (0.12.2) Requirement already satisfied: adjustText in ./.local/lib/python3.8/site-packages (from RGT) (0.8) Requirement already satisfied: matplotlib>=1.1.0 in ./.local/lib/python3.8/site-packages (from RGT) (3.7.1) Requirement already satisfied: mpmath in ./.local/lib/python3.8/site-packages (from RGT) (1.3.0) Requirement already satisfied: HTSeq in ./.local/lib/python3.8/site-packages (from RGT) (2.0.3) Requirement already satisfied: matplotlib-venn in ./.local/lib/python3.8/site-packages (from RGT) (0.11.9) Requirement already satisfied: natsort in ./.local/lib/python3.8/site-packages (from RGT) (8.3.1) Requirement already satisfied: contourpy>=1.0.1 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (1.0.7) Requirement already satisfied: cycler>=0.10 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (0.11.0) Requirement already satisfied: fonttools>=4.22.0 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (4.39.4) Requirement already satisfied: kiwisolver>=1.0.1 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (1.4.4) Requirement already satisfied: packaging>=20.0 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (23.1) Requirement already satisfied: pillow>=6.2.0 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (9.5.0) Requirement already satisfied: pyparsing>=2.3.1 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (3.0.9) Requirement already satisfied: python-dateutil>=2.7 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (2.8.2) Requirement already satisfied: importlib-resources>=3.2.0 in ./.local/lib/python3.8/site-packages (from matplotlib>=1.1.0->RGT) (5.12.0) Requirement already satisfied: threadpoolctl>=2.0.0 in ./.local/lib/python3.8/site-packages (from scikit-learn>=0.19.0->RGT) (3.1.0) Requirement already satisfied: pytz>=2020.1 in ./.local/lib/python3.8/site-packages (from pandas->RGT) (2023.3) Requirement already satisfied: tzdata>=2022.1 in ./.local/lib/python3.8/site-packages (from pandas->RGT) (2023.3) Requirement already satisfied: zipp>=3.1.0 in ./.local/lib/python3.8/site-packages (from importlib-resources>=3.2.0->matplotlib>=1.1.0->RGT) (3.15.0) Requirement already satisfied: six>=1.5 in ./.local/lib/python3.8/site-packages (from python-dateutil>=2.7->matplotlib>=1.1.0->RGT) (1.16.0)

But the rgtdata folder in not in home. I also tried unistall and install using: pip install --user RGT --no-binary rgt and pip install --user RGT --no-binary rgt and pip install --user RGT --use-pep517 RGT and still no rgtdata folder. Would you mind to help me please? Thanks!

[lzj1769]

Hi @mdu4003

What about simply using:

pip install RGT

[priyagaddi]

I have installed RGT package v1.0.0, but it says rgt-hint command not found. Any suggestions ?

[lzj1769]

You need to make sure that the PATH is included in your enviroment variable.

Can you type which python and see where you installed the package?

[mdu4003]

Hi @lzj1769, Thank you very much! I got the installation to install the folder after clearing the pip cache. Also, on my mac (OS Ventura), I had to downgrade numpy from 1.24.3 to 1.20.5 to make it work. Thanks!!!

[lzj1769]

Closed if no further questions and feel free to re-open it when needed.