Additional fixes to documentation

kdm9 · Apr 16, 2018 · 4b985d2 · 4b985d2
1 parent 2dee6b4
commit 4b985d2
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Showing 5 changed files with 7 additions and 8 deletions.
diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
@@ -17,7 +17,7 @@ IF(SPHINXBUILD)
 	COMMAND ${CMAKE_COMMAND} -E remove_directory "${CMAKE_BINARY_DIR}/doc"
         WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
         )
-    ADD_CUSTOM_TARGET(doc ALL DEPENDS doc_man doc_onehtml)
+    ADD_CUSTOM_TARGET(doc ALL DEPENDS doc_man doc_html doc_onehtml)
     INSTALL(FILES ${CMAKE_BINARY_DIR}/doc/man/axe.1 DESTINATION "share/man/man1" RENAME "axe-demux.1")
     SET_DIRECTORY_PROPERTIES(PROPERTY ADDITIONAL_MAKE_CLEAN_FILES doc/)
 ELSE()

diff --git a/docs/algorithm.rst b/docs/algorithm.rst
@@ -46,7 +46,7 @@ referred to  as the 0, 1 and 2-mm tries, for a hamming distance (mismatch) of
 trie. If this prefix is not a valid leaf in the 0mm trie, we find the longest
 prefix in the 1mm trie, and so on for all tries in ascending order. If no
 prefix of the read is a complete sequence in any trie, the read is assigned to
-an "non-indexd" output file.
+an "non-indexed" output file.
 
 This algorithm ensures optimal index matching in many ways, but is also
 extremely fast. In situations with indexes of differing length, we ensure that

diff --git a/docs/index.rst b/docs/index.rst
@@ -15,7 +15,7 @@ indexing schemes.
 Contents:
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
 
    tutorial
    usage

diff --git a/docs/tutorial.rst b/docs/tutorial.rst
@@ -2,12 +2,10 @@
 Axe Tutorial
 ************
 
-**TODO!**
-
 In this tutorial, we'll use Axe to demultiplex some paired-end,
 combinatorially-index Genotyping-by-Sequencing reads. The data for this
-tutorial is available from figshare
-`here https://figshare.com/articles/axe-tutorial_tar/6143720`_.
+tutorial is available from figshare:
+https://figshare.com/articles/axe-tutorial_tar/6143720 .
 
 Axe should be run as the initial step of any analysis: don't use sequence QC
 tools like AdapterRemoval or Trimmomatic before using axe, as indexes may be
@@ -54,7 +52,7 @@ Then, we need to ensure that axe has somewhere to put the demultiplexed reads.
 Axe outputs one file (or more, depending on pairing) per sample. Axe does so by
 appending the sample name to some prefix (as given by the ``-I``, ``-F``,
 and/or ``-R`` options). If this prefix is a directory, then sample fastq files
-will be created in that subdirectory, but the directory must exist. Let's make
+will be created in that sub-directory, but the directory must exist. Let's make
 an output directory:
 
 .. code-block:: bash

diff --git a/docs/usage.rst b/docs/usage.rst
@@ -18,6 +18,7 @@ For concise reference, the command-line usage of ``axe-demux`` is reproduced
 below:
 
 .. literalinclude:: usage.txt
+   :language: text
 
 Inputs and Outputs
 ------------------