update documentation, fix #134

CHANGELOG.md

@@ -5,6 +5,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ## [2.3.2] - 2015-03-21
 ### Fixed
 - Refactor ``EntryPointsCLI`` to allow for external subcommands
+- Updated documentation to reflect Chanjo 2.x CLI
 
 ## [2.3.1] - 2015-03-05
 ### Changed

docs/interface.rst

@@ -85,7 +85,7 @@ Chanjo takes advantage of the power behind SQL databases by providing a way to s
 
 .. code-block:: console
 
-	$ chanjo build CCDS.coverage.sqlite3 CCDS.intervals.bed
+	$ chanjo --db="CCDS.coverage.sqlite3" build CCDS.intervals.bed
 
 As shown below, it's very important to sort the BED-formatted input file before running ``chanjo build``. The input stream should be sorted on:
 
@@ -105,7 +105,7 @@ This is a convenience command to export a BED stream of all intervals as defined
 
 .. code-block:: console
 
-	$ chanjo export CCDS.coverage.sqlite3 > CCDS.intervals.min.bed
+	$ chanjo --db="CCDS.coverage.sqlite3" export > CCDS.intervals.min.bed
 
 Exporting intervals from a database can be handy since you only need to store the definitions in *one* place (the database). Otherwise it can be easy to forget which original BED-file was initially used.
 
@@ -154,7 +154,7 @@ Simply speaking, "import" will take the output from ``chanjo annotate`` and impo
 .. code-block:: console
 
 	$ chanjo annotate alignment.bam CCDS.intervals.min.bed [...] \
-	> | chanjo import CCDS.coverage.sqlite3
+	> | chanjo --db="CCDS.coverage.sqlite3" import
 
 **Runtime**: ~1 min (<800 Mb)
 

docs/introduction.rst

@@ -16,7 +16,7 @@ As indicated by the picture, Chanjo is built around streams of data that can be
 
 .. code-block:: console
 
-	$ cat CCDS.txt | chanjo convert | chanjo build coverage.sqlite3
+	$ cat CCDS.txt | chanjo convert | chanjo --db="coverage.sqlite3" build
 
 
 Demo