DOCS: updated docs

README.md

@@ -9,19 +9,22 @@ This package is intended to convert a clusters.hdf file with alphasynchro data i
   * alphasynchro.zip
 
 * Steps
-  * Unpack timspeak.zip and alphasynchro.zip
+  * Download timspeak: `git clone https://github.com/MannLabs/timspeak.git`
+  * Download alphasynchro: `git clone https://github.com/MannLabs/alphasynchro.git`
   * Create conda env: `conda create -n synchro python=3.10 -y`
   * Activate: `conda activate synchro`
-  * Install msconvert (mgf->mzml): `conda install -c bioconda proteowizard -y`
   * Install Sage: `conda install -c bioconda -c conda-forge sage-proteomics -y`
   * Install timspeak and alphasynchro: `pip install -e ./timspeak -e ./alphasynchro`
 
 ## Usage
 
 * Required
-  * timspeak.config
-  * sage.config
-  * sample.fasta
+  * Config folder (e.g. [example](example/)) containing:
+    * timspeak.config
+    * sage.config
+    * species.fasta
   * raw_data.d
-
-See the [command-line input](example/cmd.txt) in the [example folder](example/).
+* Usage
+  * Copy-paste [examplary command-line input](example/cmd.sh) in the [example folder](example/) and modify.
+  * Note: if working with regular dia-PASEF rather than synchro-PASEF, use line 15 instead of 14 (add the `--diapasef`, but furtherwise identical).
+  * Run `./example/cmd.sh`