From f92f29532b45e9619f4b20ab2dee0342f444a4b3 Mon Sep 17 00:00:00 2001 From: Fabio Steffen <35061965+fdsteffen@users.noreply.github.com> Date: Mon, 28 Oct 2024 08:53:39 +0100 Subject: [PATCH] Update README.md --- README.md | 27 +++++---------------------- 1 file changed, 5 insertions(+), 22 deletions(-) diff --git a/README.md b/README.md index f6ff45e..4843d1a 100644 --- a/README.md +++ b/README.md @@ -16,11 +16,11 @@ PAMtools is documented [here](https://fdsteffen.github.io/PAMtools/). Download and install -------------------- -1. Make sure that you have Matlab (including the curvefit and Statistics and machine Learning toolbox installed). +1. Make sure that you have Matlab (including the curvefit and Statistics and machine Learning toolbox installed). **MatPAM** uses the function `jsonencode()` and therefore requires Matlab 2016b (9.1) or newer 2. Install [PAM](https://gitlab.com/PAM-PIE/PAM) -3. Clone or [download](https://github.com/fdsteffen/PAMtools/archive/master.zip) PAMtools into a directory of your choice. +3. Clone PAMtools into a directory of your choice. ``` git clone https://github.com/fdsteffen/PAMtools.git ``` @@ -28,29 +28,12 @@ git clone https://github.com/fdsteffen/PAMtools.git - Add the **MatPAM** folder to the Matlab search path - Install the **PyPAM** module via pip ``` -pip install --user git+https://github.com/fdsteffen/PAMtools.git -or -pip install --user -e +pip install . ``` -4. Copy the file in `matpam/profiles/profile PIE.mat`` into the profiles directory in PAM. +4. Copy the file in `src/pamtools/matpam/profiles/profile PIE.mat` into the profiles directory in PAM. -5. Copy the FCS models in `matpam/models` to the Models directory in PAM - -Dependencies ------------- - -- **MatPAM** uses the function `jsonencode()` and therefore requires Matlab 2016b (9.1) or newer - -- **PyPAM** depends on the following Python packages: - - - numpy - - scipy - - pandas - - matplotlib - - seaborn - - uncertainties - - naturalcolors (get it from [here](https://github.com/fdsteffen/naturalcolors.git)) +5. Copy the FCS models in `src/pamtools/matpam/models` to the Models directory in PAM --- 1 W. Schrimpf, A. Barth, J. Hendrix, D.C. Lamb, *Biophys. J.* **2018**, *114*, 1518–1528. [![](https://img.shields.io/badge/DOI-10.1016/j.bpj.2018.02.035-blue.svg)](https://doi.org/10.1016/j.bpj.2018.02.035)