docs: prepare for release

README.md

@@ -26,13 +26,13 @@ This python script generates an interactive summary report from fusion detection
 ### Using Conda
 
 ```bash
-conda install -c bioconda fusion-report=2.0.2
+conda install -c bioconda fusion-report=2.1.0
 ```
 
 ### From source
 
 ```bash
-sudo apt-get install sqlite3 wget
+sudo apt-get install sqlite3
 python3 setup.py install
 ```
 
@@ -61,6 +61,7 @@ Or get help and list all possible parameters.
 fusion_report --help
 fusion_report run --help
 fusion_report download --help
+fusion_report sync --help
 ```
 
 For more info on how to run the script, please see the [documentation](https://matq007.github.io/fusion-report/).
@@ -69,3 +70,7 @@ For more info on how to run the script, please see the [documentation](https://m
 
 * Testing dataset copied from [ndaniel/fusioncatcher](https://github.com/ndaniel/fusioncatcher).
 * DNA icon made by [Freepik](https://www.freepik.com) from [Flaticon](https://www.flaticon.com) is licensed by [CC 3.0 BY](http://creativecommons.org/licenses/by/3.0/).
+
+## TODO
+
+- [ ] documentation

docs/add_database.md

@@ -26,9 +26,8 @@ class Test(Db, metaclass=Singleton):
         return res['fusions']
 ```
 
-2. Create database schema in `fusion_report/schema/{database.sql}`. This is a SQL script which defines a structure 
-of your database.
-3. Update `__enrich()` function in `fusion_report/app.py`
+2. Create database schema in `fusion_report/schema/{database.sql}`. This is a SQL script which defines a structure of your database.
+3. Update `enrich()` function in `fusion_report/app.py`
 
 ```python
 local_fusions: Dict[str, List[str]] = {
@@ -39,28 +38,4 @@ local_fusions: Dict[str, List[str]] = {
 }
 ```
 
-4. Finally, to make sure everyone can use the database, you have to implement steps of how to download your database.
-To do this head over to `fusion_report/download.py`.
-
-    4.1. Create fusion `__get_test()`
-    ```python
-    # file, url = ...
-
-    # You finish the function by calling TestDB() object and running setup function.
-    db = TestDB('.')
-    # This is a in-house function which will:
-    # 1. Create database using your schema
-    # 2. Use provided files as data files which will be imported to the database
-    db.setup(files, delimiter='\t', skip_header=True)
-    ```
-    4.2. Add your function into  `__download_all()`
-    ```python
-    processes = [
-       Process(target=self.get_fusiongdb),
-       Process(target=self.get_mitelman),
-       Process(target=self.get_cosmic),
-       Process(target=self.get_test)
-    ]
-    ```
-
-5. Give yourself a high five for awesome job! :+1:
+4. Give yourself a high five for awesome job! :+1:

docs/templating.md

@@ -11,8 +11,7 @@ available variables which can be used in the report.
 * `modules: Dict[str, Any]`: Dictionary of modules and its variables
 * `menu`: List of menu items
 
-Each `Page` has an option to have a custom extra variables. Therefore, you can observe not mentioned variables like
-i.e: `sample`, `db_path`, `fusion` or `tooL_cutoff`.
+Each `Page` has an option to have a custom extra variables. Therefore, you can observe not mentioned variables like i.e: `sample`, `db_path`, `fusion` or `tooL_cutoff`.
 
 ## Functions
 

docs/usage.md

@@ -3,15 +3,15 @@
 > Before running the tool make sure you have downloaded all the necessary resources!
 
 ## Run all fusion detection tools
-   
+
 ```bash
-fusion_report run "<SAMPLE NAME>" /path/to/output /path/to/db/
-  --arriba tests/test_data/arriba.tsv
-  --ericscript tests/test_data/ericscript.tsv
-  --starfusion tests/test_data/starfusion.tsv
-  --fusioncatcher tests/test_data/fusioncatcher.txt
-  --squid tests/test_data/squid.txt
-  --pizzly tests/test_data/pizzly.tsv
+fusion_report run "<SAMPLE NAME>" /path/to/output /path/to/db/ \
+  --arriba tests/test_data/arriba.tsv \
+  --ericscript tests/test_data/ericscript.tsv \
+  --starfusion tests/test_data/starfusion.tsv \
+  --fusioncatcher tests/test_data/fusioncatcher.txt \
+  --squid tests/test_data/squid.txt \
+  --pizzly tests/test_data/pizzly.tsv \
   --dragen tests/test_data/dragen.tsv
 ```
 
@@ -21,10 +21,10 @@ Each tool has a predefined weight when estimating score of a fusion. On default
 `(100 / NUMBER_OF_RUNNING_TOOLS)`. To change the weights follow the steps below:
 
 ```bash
-fusion_report run "<SAMPLE NAME>" /path/to/output /path/to/db/
-  --ericscript tests/test_data/ericscript.tsv
-  --ericscript_weight 30.5
-  --fusioncatcher tests/test_data/fusioncatcher.txt
+fusion_report run "<SAMPLE NAME>" /path/to/output /path/to/db/ \
+  --ericscript tests/test_data/ericscript.tsv \
+  --ericscript_weight 30.5 \
+  --fusioncatcher tests/test_data/fusioncatcher.txt \
   --fusioncatcher_weight 70.5
 ```
 
@@ -34,4 +34,5 @@ fusion_report run "<SAMPLE NAME>" /path/to/output /path/to/db/
 fusion_report --help
 fusion_report run --help
 fusion_report download --help
-```
+fusion_report sync --help
+```