Updated README & docs with new installation instructions #121

draeger-lab · Aug 28, 2024 · dd50de8 · dd50de8
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diff --git a/README.md b/README.md
@@ -56,14 +56,14 @@ pip install refineGEMs
 
 ```
 
-or to a local conda environment where `refineGEMs` is distributed via this GitHub repository and all dependencies are denoted in the `setup.py` file:
+or to a local conda environment where `refineGEMs` is distributed via this GitHub repository and all dependencies are denoted in the `pyproject.toml` file:
 
 ```bash
 # clone or pull the latest source code
 git clone https://github.com/draeger-lab/refinegems.git
 cd refinegems
 
-conda create -n <EnvName> python=3.9
+conda create -n <EnvName> python=3.10 (or higher)
 
 conda activate <EnvName>
 
@@ -74,6 +74,19 @@ pip install .
 
 ```
 
+``refineGEMs`` depends on the tools [MCC](https://github.com/Biomathsys/MassChargeCuration) and 
+[BOFdat](https://github.com/draeger-lab/BOFdat) which cannot directly be installed via PyPI or the `pyproject.toml`. 
+Please install both tools before using ``refineGEMs``:
+
+```bash
+# For MCC, until hot fix is merged into main:
+pip install "masschargecuration@git+https://github.com/Biomathsys/MassChargeCuration@installation-fix"
+
+# For BOFdat, our fork with hot fix(es):
+pip install "bofdat@git+https://github.com/draeger-lab/BOFdat"
+
+```
+
 ## How to cite
 When using `refineGEMs`, please cite the latest publication:
 

diff --git a/docs/source/development.rst b/docs/source/development.rst
@@ -13,6 +13,22 @@ To maintain or extend the toolbox ``refineGEMs`` please install the package via
 Installation for developers
 ---------------------------
 
+``refineGEMs`` depends on the tools `MCC <https://github.com/Biomathsys/MassChargeCuration>`__ and 
+`BOFdat <https://github.com/draeger-lab/BOFdat>`__ which cannot directly be installed via 
+`PyPI <https://pypi.org/project/refineGEMs/>`__ or the `pyproject.toml`. Please install both tools before using 
+``refineGEMs`` into the corresponding environment:
+
+.. code:: console
+    :class: copyable
+
+    pip install "masschargecuration@git+https://github.com/Biomathsys/MassChargeCuration@installation-fix"
+
+.. code:: console
+    :class: copyable
+
+    pip install "bofdat@git+https://github.com/draeger-lab/BOFdat"
+
+
 Into a Conda environment
 ^^^^^^^^^^^^^^^^^^^^^^^^
 

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -21,6 +21,27 @@ To install refineGEMs as Python package from `PyPI <https://pypi.org/project/ref
 
 The corresponding project site can be found `here <https://pypi.org/project/refineGEMs/>`__.
 
+``refineGEMs`` depends on the tools `MCC <https://github.com/Biomathsys/MassChargeCuration>`__ and 
+`BOFdat <https://github.com/draeger-lab/BOFdat>`__ which cannot directly be installed via 
+`PyPI <https://pypi.org/project/refineGEMs/>`__. Please install both tools before using ``refineGEMs``:
+
+.. hint:: 
+
+   BOFdat should be installed as stated below. The fork contains certain bug fixes such that the program is able 
+   to run. If you have a functional version of BOFdat installed you can try to use it. In case you encounter problems 
+   with your own version, please, install BOFdat as stated below.
+
+.. code:: console
+   :class: copyable
+
+   pip install "masschargecuration@git+https://github.com/Biomathsys/MassChargeCuration@installation-fix"
+
+.. code:: console
+   :class: copyable
+
+   pip install "bofdat@git+https://github.com/draeger-lab/BOFdat"
+
+
 .. hint:: 
 
    For the installation for developers, refer to :ref:`installation for developers`