Merge pull request #257 from idiv-biodiversity/doc-spell-check

fixes spelling in docs

docs/content/frozenbinary.rst

@@ -21,7 +21,7 @@ In attempt to further simplify the MetAMOS installation process, we are happy to
 - R 2.11.1 (or newer)
 - 64-bit \*nix OS or Mac OSX 10.7+ (you may need to install MacPorts for full functionality)
 
-**Disclaimer: The frozen binary is provided as-is and has limited support and reduced functionality/features compared to installing from source. If you encouter issues with a frozen binary, please try installing the latest release.**
+**Disclaimer: The frozen binary is provided as-is and has limited support and reduced functionality/features compared to installing from source. If you encounter issues with a frozen binary, please try installing the latest release.**
 
 First, select your flavor (DBs below are required but provided separately):
 
@@ -77,9 +77,9 @@ The frozen binary is actually a collection of programs that extracts/runs/cleans
  * The directory named by the TEMP environment variable.
  * The directory named by the TMP environment variable.
 
-If your system is missing all of the above, does not have sufficient space, or is missing write-premissions, runPipeline will not be able to extract itself and will report: INTERNAL ERROR: cannot create temporary directory!. The extracted runPipeline requires at least 4GB of free temporary disk space. You will get a "No DBs found ERROR!" if you do not download any DBs. The DB dir needs to be placed inside of the frozen binary install dir. 
+If your system is missing all of the above, does not have sufficient space, or is missing write-permissions, runPipeline will not be able to extract itself and will report: INTERNAL ERROR: cannot create temporary directory!. The extracted runPipeline requires at least 4GB of free temporary disk space. You will get a "No DBs found ERROR!" if you do not download any DBs. The DB dir needs to be placed inside of the frozen binary install dir. 
 
-If you encouter the messages:
+If you encounter the messages:
 
 .. code-block:: bash
 

docs/content/imetamos.rst

@@ -32,7 +32,7 @@ To install iMetAMOS without using a frozen binary, run:
 
     $ python INSTALL.py iMetAMOS
 
-To enable iMetAMOS, specify it as an option to initPipelien using the -W flag. Below is a simple example of running of iMetAMOS to assemble an SRA dataset::
+To enable iMetAMOS, specify it as an option to initPipeline using the -W flag. Below is a simple example of running of iMetAMOS to assemble an SRA dataset::
 
     initPipeline -q -1 SRR987657 -d projectDir -W iMetAMOS
     runPipeline -d projectDir -p 16

docs/content/installation.rst

@@ -11,7 +11,7 @@ See below sections for further details.
 Prerequisites
 ==============
 MetAMOS has several dependencies/prerequisites, the large majority of which are automatically downloaded
-and installed when running INSTALL.py (see next section). In addition, several dependences/prerequisites 
+and installed when running INSTALL.py (see next section). In addition, several dependencies/prerequisites
 are not installed by INSTALL.py and must be available on your system:
 
     * Java (6+)
@@ -57,7 +57,7 @@ MetAMOS contains an automated installation script which installs
 MetAMOS along with required Python dependencies, third party software
 and necessary data files. If you encounter issues during installation, you can 
 try installing the required dependencies manually and re-running INSTALL.py. If you 
-continue to encounter issues, plase provide the output from INSTALL.py as a new `issue <https://github.com/marbl/metAMOS/issues?state=open>`_.
+continue to encounter issues, please provide the output from INSTALL.py as a new `issue <https://github.com/marbl/metAMOS/issues?state=open>`_.
 
 To download the software release package:
 

docs/content/quickstart.rst

@@ -226,7 +226,7 @@ Common use-cases
 
     -a idba_ud
 
-* To use Kraken for read classifcation::
+* To use Kraken for read classification::
 
     -c kraken