add required phrases and clean up installation docs

Author: andrewprzh

README.md

@@ -74,13 +74,14 @@ You can leave your comments and bug reports at our [GitHub repository tracker](h
 
 *   Full IsoQuant documentation is available at [ablab.github.io/IsoQuant](https://ablab.github.io/IsoQuant/).
 
-*   IsoQuant can be downloaded from [github.com/ablab/IsoQuant](https://github.com/ablab/IsoQuant) or installed via conda:
+*   IsoQuant can be downloaded from [github.com/ablab/IsoQuant](https://github.com/ablab/IsoQuant) or installed via conda (typically takes a few minutes):
 
-        conda create -c conda-forge -c bioconda -n isoquant python=3.8 isoquant
+        conda create -c conda-forge -c bioconda -n isoquant python=3.12 isoquant
 
 *   If installing manually, you will need Python3 (3.8 or higher), [gffutils](https://pythonhosted.org/gffutils/installation.html), [pysam](https://pysam.readthedocs.io/en/latest/index.html), [pybedtools](https://daler.github.io/pybedtools/), [biopython](https://biopython.org/) and some other common Python libraries to be installed. See `requirements.txt` for details. You will also need to have [minimap2](https://github.com/lh3/minimap2) and [samtools](http://www.htslib.org/download/) to be in your `$PATH` variable.
+All required Python libraries can be installed via `pip install -r requirements.txt`.
 
-*   Verify your installation by running:
+*   Verify your installation by running (typically takes less than 1 minute):
 
         isoquant.py --test
 

docs/installation.md

@@ -1,25 +1,35 @@
 # Installation
 
 IsoQuant requires a 64-bit Linux system or Mac OS and Python (3.8 and higher) to be pre-installed on it.
+Note that IsoQuant 3.11.x and earlier versions are not well compatible with Python 3.14.
+No special hardware is required. 
+
 You will also need
 
 -   [gffutils](https://pythonhosted.org/gffutils/installation.html)
 -   [pysam](https://pysam.readthedocs.io/en/latest/index.html)
 -   [pyfaidx](https://pypi.org/project/pyfaidx/)
--   [pandas](https://pandas.pydata.org/)
--   [pyyaml](https://pypi.org/project/PyYAML/)
+-   [ssw-py](https://pypi.org/project/ssw-py/)
+-   [editdistance](https://pypi.org/project/editdistance/)
+-   [biopython](https://biopython.org/)
+-   [numba](https://numba.pydata.org/)
 -   [minimap2](https://github.com/lh3/minimap2)
 -   [samtools](http://www.htslib.org/download/)
 -   [STAR](https://github.com/alexdobin/STAR) (optional)
 
+and some other common Python libraries. 
+The full requirements list can be found in [requirements.txt](https://github.com/ablab/IsoQuant/blob/master/requirements.txt).
+
+
 ## Installing from conda
 IsoQuant can be installed with conda:
 ```bash
-conda create -c conda-forge -c bioconda -n isoquant python=3.8 isoquant
+conda create -c conda-forge -c bioconda -n isoquant python=3.12 isoquant
 ```
+Typically, conda installation takes a few minutes.
 
 ## Installing from GitHub
-To obtain IsoQuant you can download repository and install requirements.  
+To obtain IsoQuant you can download the repository and install the requirements.  
 Clone IsoQuant repository and switch to the latest release:
 ```bash
 git clone https://github.com/ablab/IsoQuant.git
@@ -30,15 +40,18 @@ Install requirements:
 ```bash
 pip install -r requirements.txt
 ```
+Typically, package installation takes a few minutes.
 
 You also need [samtools](http://www.htslib.org/download/) and [minimap2](https://github.com/lh3/minimap2) to be in the `$PATH` variable.
 
 ## Verifying your installation
-To verify IsoQuant installation type
+To verify IsoQuant installation run
 ```bash
 isoquant.py --test
 ```
-to run on toy dataset.  
+to run on toy dataset. This should typically take less than 1 minute.  
+
+
 If the installation is successful, you will find the following information at the end of the log:
 ```bash
 === IsoQuant pipeline finished ===