From 5124d6ff460a1f47837cc63926ae29e116915626 Mon Sep 17 00:00:00 2001
From: Fabio Steffen <35061965+fdsteffen@users.noreply.github.com>
Date: Sat, 28 Oct 2023 17:56:34 +0200
Subject: [PATCH] Update installation instructions

---
 README.md                                           |  10 +++++++++-
 docs/source/README.rst                              |  10 +++++++++-
 .../{extract_2Dplot.PNG => extract_2Dplot.png}      | Bin
 ...{extract_timetrace.PNG => extract_timetrace.png} | Bin
 .../source/_static/{write_FCS.PNG => write_FCS.png} | Bin
 5 files changed, 18 insertions(+), 2 deletions(-)
 rename docs/source/_static/{extract_2Dplot.PNG => extract_2Dplot.png} (100%)
 rename docs/source/_static/{extract_timetrace.PNG => extract_timetrace.png} (100%)
 rename docs/source/_static/{write_FCS.PNG => write_FCS.png} (100%)

diff --git a/README.md b/README.md
index f9d1e31..f6ff45e 100644
--- a/README.md
+++ b/README.md
@@ -16,7 +16,11 @@ PAMtools is documented [here](https://fdsteffen.github.io/PAMtools/).
 Download and install
 --------------------
 
-Clone or [download](https://github.com/fdsteffen/PAMtools/archive/master.zip) PAMtools into a directory of your choice.
+1. Make sure that you have Matlab (including the curvefit and Statistics and machine Learning toolbox installed).
+
+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.
 ```
 git clone https://github.com/fdsteffen/PAMtools.git
 ```
@@ -29,6 +33,10 @@ or
 pip install --user -e <path/to/PAMtools>
 ```
 
+4. Copy the file in `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
 ------------
 
diff --git a/docs/source/README.rst b/docs/source/README.rst
index c3bfbc3..e803d0a 100644
--- a/docs/source/README.rst
+++ b/docs/source/README.rst
@@ -13,7 +13,11 @@ PAMtools is a set of helper functions written in Matlab and Python to export and
 Download and install
 --------------------
 
-Clone or :download:`download <https://github.com/fdsteffen/PAMtools/archive/master.zip>` PAMtools into a directory of your choice. ::
+1. Make sure that you have Matlab (including the curvefit and Statistics and machine Learning toolbox installed).
+
+2. Install [PAM](https://gitlab.com/PAM-PIE/PAM)
+
+3. Clone or :download:`download <https://github.com/fdsteffen/PAMtools/archive/master.zip>` PAMtools into a directory of your choice. ::
 
     git clone https://github.com/fdsteffen/PAMtools.git
 
@@ -22,6 +26,10 @@ Clone or :download:`download <https://github.com/fdsteffen/PAMtools/archive/mast
 
     pip install <path/to/PAMtools>
 
+4. Copy the file in `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
 ------------
diff --git a/docs/source/_static/extract_2Dplot.PNG b/docs/source/_static/extract_2Dplot.png
similarity index 100%
rename from docs/source/_static/extract_2Dplot.PNG
rename to docs/source/_static/extract_2Dplot.png
diff --git a/docs/source/_static/extract_timetrace.PNG b/docs/source/_static/extract_timetrace.png
similarity index 100%
rename from docs/source/_static/extract_timetrace.PNG
rename to docs/source/_static/extract_timetrace.png
diff --git a/docs/source/_static/write_FCS.PNG b/docs/source/_static/write_FCS.png
similarity index 100%
rename from docs/source/_static/write_FCS.PNG
rename to docs/source/_static/write_FCS.png