updated getting started readme

docs/run_chronqc.rst

@@ -20,22 +20,22 @@ This example demonstrates generating ChronQC plots from a custom database,
 ..
 
 
-Run following command to generate interactive plots in html,
+Run following command to generate interactive plots in HTML,
 
 .. code-block:: shell   
 
  chronqc plot chronqc_custom_db.sqlite Somatic config.json  
  
 ..
 
-The types of created plots and their properties are specified in "config.json" file. For details on creating the config file visit `documentation. <http://chronqc.readthedocs.io/en/latest/plots/plot_options.html>`__
+The types of created plots and their properties are specified in "config.json" file. For details on creating the `config . <http://chronqc.readthedocs.io/en/latest/run_chronqc.html#chronqc-config-files>`__ file visit `documentation. <http://chronqc.readthedocs.io/en/latest/plots/plot_options.html>`__
 Interactive html report is created under ``chronqc_output`` directory
 
 
 Using the output of MultiQC
 ---------------------------
 
-**Creating ChronQC database and plots**
+**1. Creating ChronQC database and plots**
 
 For creating ChronQC database and plots, see the example below. 
 This example demonstrates generating a ChronQC database and creating ChronQC graphs using the database.
@@ -54,7 +54,7 @@ Step 1: Create a ChronQC database
  
 ..    
 
-A sqlite database ``chronqc.stats.sqlite`` and ``chronqc.stats.cols.txt`` file are created in ``chronqc_db`` folder under the ``.`` (current) directory. 
+A sqlite database ``chronqc.stats.sqlite``, ``chronqc.default.json`` and ``chronqc.stats.cols.txt`` file are created in ``chronqc_db`` folder under the ``.`` (current) directory. 
 
 Step 2: Create ChronQC plots
 
@@ -71,7 +71,7 @@ Interactive html report is created in ``chronqc_output`` under the ``.`` (curren
 
 *Customizing the JSON*
 
-It is strongly adviced to create custom JSON file, based on the laboratories assay tracking strategy. A sample of custom JSON is included in the folder. `chronqc.stats.cols.txt` file contains column names present in the database, and can be used to create the config file. For details on creating the config file visit `documentation. <http://chronqc.readthedocs.io/en/latest/plots/plot_options.html>`__
+It is strongly adviced to create custom JSON file, based on the laboratories assay tracking strategy. A sample of custom JSON is included in the folder. `chronqc.stats.cols.txt` file contains column names present in the database, and can be used to create the config file. For details on creating the `config . <http://chronqc.readthedocs.io/en/latest/run_chronqc.html#chronqc-config-files>`__ file visit `documentation. <http://chronqc.readthedocs.io/en/latest/plots/plot_options.html>`__
 
 .. code-block:: shell
 
@@ -82,10 +82,10 @@ It is strongly adviced to create custom JSON file, based on the laboratories ass
 Interactive html report is created in ``chronqc_output`` under the ``.`` (current) directory.
 
 
-**Creating, updating ChronQC database and plots**
+**2. Creating and updating ChronQC database and creating plots**
 
 
-For creating, updating ChronQC database and plots, see the example below*
+For creating, updating ChronQC database and plots, see the example below.
 This example demonstrates generating a ChronQC database, updating the generated database with new data and creating ChronQC graphs using the database.
 
 .. code-block:: shell
@@ -102,7 +102,7 @@ Step 1: Create a ChronQC database
  
 ..
 
-A sqlite database ``chronqc.stats.sqlite`` and `chronqc.stats.cols.txt` file are created in ``chronqc_db`` folder under the ``.`` (current) directory. 
+A sqlite database ``chronqc.stats.sqlite``, ``chronqc.default.json`` and `chronqc.stats.cols.txt` file are created in ``chronqc_db`` folder under the ``.`` (current) directory. 
 A default JSON file named ``chronqc.default.json`` is also created in chronqc_db under the ``.`` (current) directory.
 
 Step 2: Update existing ChronQC database
@@ -128,7 +128,7 @@ Interactive html report is created in ``chronqc_output`` under the ``.`` (curren
 
 *Customizing the JSON*
 
-It is strongly adviced to create custom JSON file, based on the laboratories assay tracking strategy. A sample of custom JSON is included in the folder. `chronqc.stats.cols.txt` file contains column names present in the database, and can be used to create the config file. For details on creating the config file visit `documentation. <http://chronqc.readthedocs.io/en/latest/plots/plot_options.html>`__
+It is strongly adviced to create custom JSON file, based on the laboratories assay tracking strategy. A sample of custom JSON is included in the folder. `chronqc.stats.cols.txt` file contains column names present in the database, and can be used to create the config file. For details on creating the `config . <http://chronqc.readthedocs.io/en/latest/run_chronqc.html#chronqc-config-files>`__ file visit `documentation. <http://chronqc.readthedocs.io/en/latest/plots/plot_options.html>`__
 
 .. code-block:: shell    
 

examples/custom_db_example/readme.md

@@ -8,12 +8,12 @@ Run following command to generate interactive plots in html
 
 `chronqc plot chronqc_custom_db.sqlite Somatic config.json`
 
-The types of created plots and their properties are specified in "config.json" file. For details on creating the config file visit [documentation](https://chronqc.readthedocs.io/en/latest/plots/plot_options.html).
+The types of created plots and their properties are specified in "config.json" file. For details on creating the [config](http://chronqc.readthedocs.io/en/latest/run_chronqc.html#chronqc-config-files) file visit [documentation](https://chronqc.readthedocs.io/en/latest/plots/plot_options.html).
 Interactive html report is created under `chronqc_output`.
 
 ## Using the ChronQC plots
 
 ChronQC is designed to be interactive. ChronQC plots can be adjusted to a time period and are zoomable. Mousing over a point displays its associated data such as run ID, sample IDs, and corresponding values. 
 To use the annotation feature of ChronQC plots, start the annotation database connectivity by using `chronqc annotation` command. Default port used for annotation server is 8000, this can be customized by using --port option. 
 Then open the ChronQC output html in a recent browser (tested on: Google Chrome and Mozilla Firefox).
-Users can record notes and corrective actions on the plots by clicking on a point or selecting a date. User notes and corrective actions are stored for long-term recordkeeping in the SQLite ChronQC annotations database. The plots are interlinked so that when an individual point or date is annotated in one graph, the same annotation appears on other graphs. By using the ChronQC report with the ChronQC annotations data-base (by starting the annotation server with "chronqc annotation" command), users can see the notes that have been recorded previously.
+Users can record notes and corrective actions on the plots by clicking on a point or selecting a date. User notes and corrective actions are stored for long-term recordkeeping in the SQLite ChronQC annotations database. The plots are interlinked so that when an individual point or date is annotated in one graph, the same annotation appears on other graphs. By using the ChronQC report with the ChronQC annotations data-base (by starting the annotation server with "chronqc annotation" command), users can see the notes that have been recorded previously.

examples/multiqc_example_1/readme.md

@@ -7,7 +7,7 @@ This example demonstrates generating a ChronQC database and creating ChronQC gra
 ### Step 1: Create a ChronQC database
 `chronqc database --create --run-date-info run_date_info.csv -o . multiqc_data/multiqc_general_stats.txt SOMATIC`
 
-A sqlite database `chronqc.stats.sqlite` and `chronqc.stats.cols.txt` file are created in  `chronqc_db` folder  under the `.` (current) directory. 
+A sqlite database `chronqc.stats.sqlite`, `chronqc.default.json` and `chronqc.stats.cols.txt` file are created in  `chronqc_db` folder  under the `.` (current) directory. 
 
 ### Step 2: Create ChronQC plots
 The types of created plots and their properties are specified in JSON file.
@@ -18,7 +18,7 @@ Plots can be generated using the default ``chronqc.default.json`` file,
 Interactive html report is created in `chronqc_output` under the `.` (current) directory.
 
 #### Customizing the JSON
-It is strongly adviced to create custom JSON file, based on the laboratories assay tracking strategy. A sample of custom JSON is included in the folder. `chronqc.stats.cols.txt` file contains column names present in the database, and can be used to create the config file. For details on creating the config file visit [documentation](https://chronqc.readthedocs.io/en/latest/plots/plot_options.html).
+It is strongly adviced to create custom JSON file, based on the laboratories assay tracking strategy. A sample of custom JSON is included in the folder. `chronqc.stats.cols.txt` file contains column names present in the database, and can be used to create the config file. For details on creating the [config](http://chronqc.readthedocs.io/en/latest/run_chronqc.html#chronqc-config-files) file visit [documentation](https://chronqc.readthedocs.io/en/latest/plots/plot_options.html).
 
 `chronqc plot -o . chronqc_db/chronqc.stats.sqlite SOMATIC sample.json`
 
@@ -29,4 +29,4 @@ Interactive html report is created in `chronqc_output` under the `.` (current) d
 ChronQC is designed to be interactive. ChronQC plots can be adjusted to a time period and are zoomable. Mousing over a point displays its associated data such as run ID, sample IDs, and corresponding values. 
 To use the annotation feature of ChronQC plots, start the annotation database connectivity by using `chronqc annotation` command. Default port used for annotation server is 8000, this can be customized by using --port option. 
 Then open the ChronQC output html in a recent browser (tested on: Google Chrome and Mozilla Firefox).
-Users can record notes and corrective actions on the plots by clicking on a point or selecting a date. User notes and corrective actions are stored for long-term recordkeeping in the SQLite ChronQC annotations database. The plots are interlinked so that when an individual point or date is annotated in one graph, the same annotation appears on other graphs. By using the ChronQC report with the ChronQC annotations data-base (by starting the annotation server with "chronqc annotation" command), users can see the notes that have been recorded previously.
+Users can record notes and corrective actions on the plots by clicking on a point or selecting a date. User notes and corrective actions are stored for long-term recordkeeping in the SQLite ChronQC annotations database. The plots are interlinked so that when an individual point or date is annotated in one graph, the same annotation appears on other graphs. By using the ChronQC report with the ChronQC annotations database (by starting the annotation server with "chronqc annotation" command), users can see the notes that have been recorded previously.

examples/multiqc_example_2/readme.md

@@ -7,8 +7,7 @@ This example demonstrates generating a ChronQC database, updating the generated
 ### Step 1: Create a ChronQC database
 `chronqc database --create --run-date-info year_2016/run_date_info.csv -o . year_2016/multiqc_data/multiqc_general_stats.txt Germline`
 
-A sqlite database `chronqc.stats.sqlite` and `chronqc.stats.cols.txt` file are created in `chronqc_db` folder under the `.` (current) directory.
-A default JSON file named ``chronqc.default.json`` is also created in `chronqc_db` under the `.` (current) directory.
+A sqlite database `chronqc.stats.sqlite`, `chronqc.default.json` and `chronqc.stats.cols.txt` file are created in `chronqc_db` folder under the `.` (current) directory.
 
 ### Step 2: Update existing ChronQC database 
 `chronqc database --update --db chronqc_db/chronqc.stats.sqlite --run-date-info year_2017/run_date_info.csv year_2017/multiqc_data/multiqc_general_stats.txt Germline`
@@ -22,7 +21,7 @@ Interactive html report is created in `chronqc_output` under the `.` (current) d
 
 #### Customizing the JSON
 
-It is strongly adviced to create custom JSON file, based on the laboratories assay tracking strategy. A sample of custom JSON is included in the folder. `chronqc.stats.cols.txt` file contains column names present in the database, and can be used to create the config file. For details on creating the config file visit [documentation](https://chronqc.readthedocs.io/en/latest/plots/plot_options.html).
+It is strongly adviced to create custom JSON file, based on the laboratories assay tracking strategy. A sample of custom JSON is included in the folder. `chronqc.stats.cols.txt` file contains column names present in the database, and can be used to create the config file. For details on creating the [config](http://chronqc.readthedocs.io/en/latest/run_chronqc.html#chronqc-config-files) file visit [documentation](https://chronqc.readthedocs.io/en/latest/plots/plot_options.html).
 
 `chronqc plot -o . chronqc_db/chronqc.stats.sqlite Germline sample.json`
 
@@ -33,4 +32,4 @@ Interactive html report is created in `chronqc_output` under the `.` (current) d
 ChronQC is designed to be interactive. ChronQC plots can be adjusted to a time period and are zoomable. Mousing over a point displays its associated data such as run ID, sample IDs, and corresponding values. 
 To use the annotation feature of ChronQC plots, start the annotation database connectivity by using `chronqc annotation` command. Default port used for annotation server is 8000, this can be customized by using --port option.  
 Then open the ChronQC output html in a recent browser (tested on: Google Chrome and Mozilla Firefox).
-Users can record notes and corrective actions on the plots by clicking on a point or selecting a date. User notes and corrective actions are stored for long-term recordkeeping in the SQLite ChronQC annotations database. The plots are interlinked so that when an individual point or date is annotated in one graph, the same annotation appears on other graphs. By using the ChronQC report with the ChronQC annotations data-base (by starting the annotation server with "chronqc annotation" command), users can see the notes that have been recorded previously.
+Users can record notes and corrective actions on the plots by clicking on a point or selecting a date. User notes and corrective actions are stored for long-term recordkeeping in the SQLite ChronQC annotations database. The plots are interlinked so that when an individual point or date is annotated in one graph, the same annotation appears on other graphs. By using the ChronQC report with the ChronQC annotations database (by starting the annotation server with "chronqc annotation" command), users can see the notes that have been recorded previously.