diff --git a/docs/img/DRB1-3123_sorting_layouting.png b/docs/img/DRB1-3123_sorting_layouting.png index f001bd45..45c2192c 100644 Binary files a/docs/img/DRB1-3123_sorting_layouting.png and b/docs/img/DRB1-3123_sorting_layouting.png differ diff --git a/docs/index.rst b/docs/index.rst index 4615dbba..1e7adf14 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -79,7 +79,7 @@ Core Functionalities :target: rst/tutorials/extract_selected_loci.html .. |sorting_layouting| image:: img/DRB1-3123_sorting_layouting.png - :target: rst/tutorials/sorting_layouting.html + :target: rst/tutorials/sort_layout.html .. |navigating_and_annotating_graphs| image:: img/nav_welcome.png :target: rst/tutorials/navigating_and_annotating_graphs.html diff --git a/docs/rst/quick_start.rst b/docs/rst/quick_start.rst index c61a171c..b8da269e 100644 --- a/docs/rst/quick_start.rst +++ b/docs/rst/quick_start.rst @@ -18,12 +18,12 @@ version 1 (`GFAv1 `_) Build graph from GFA ---------------------------- -Assuming that your current working directory is the root of the ``odgi`` project, to construct an ``odgi`` file from a -``GFA`` file, execute: +To construct an ``odgi`` file from a ``GFA`` file, execute: .. code-block:: bash - odgi build -g test/DRB1-3123.gfa -o DRB1-3123.og + wget https://raw.githubusercontent.com/pangenome/odgi/master/test/DRB1-3123.gfa + odgi build -g DRB1-3123.gfa -o DRB1-3123.og The command creates a file called ``DRB1-3123.og``, which contains the input graph in ``odgi`` format. diff --git a/docs/rst/tutorials/sort_layout.rst b/docs/rst/tutorials/sort_layout.rst index 8cbf5dd6..2ce086d1 100644 --- a/docs/rst/tutorials/sort_layout.rst +++ b/docs/rst/tutorials/sort_layout.rst @@ -39,12 +39,12 @@ to take a look at the calculated layout using static and interactive tools. Build the unsorted DRB1-3123 graph ---------------------------------- -Assuming that your current working directory is the root of the ``odgi`` project, to construct an ``odgi`` graph from the -``DRB1-3123`` dataset in ``GFA`` format, execute: +To construct an ``odgi`` graph from the ``DRB1-3123`` dataset in ``GFA`` format, execute: .. code-block:: bash - odgi build -g test/DRB1-3123_unsorted.gfa -o DRB1-3123_unsorted.og + wget https://raw.githubusercontent.com/pangenome/odgi/master/test/DRB1-3123_unsorted.gfa + odgi build -g DRB1-3123_unsorted.gfa -o DRB1-3123_unsorted.og The command creates a file called ``DRB1-3123_unsorted.og``, which contains the input graph in ``odgi`` format. This graph contains 12 ALT sequences of the `HLA-DRB1 gene `_ from the GRCh38 reference genome.