docs(ReadmeAndVariousDocsEditsHyperlinksAndTypos.AlsoChangedManualToV…

…ivaManualInMkdocs): readme and various docs edits hyperlinks and typos. also changed manual to viva manual in mkdocs docs refinement
compbiocore · Mar 28, 2019 · 97e37fc · 97e37fc
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diff --git a/README.md b/README.md
@@ -30,9 +30,9 @@ Windows 10, Windows 7
 
 1. Add VariantVisualization.jl in the Julia Pkg prompt.
 2. Download the [VIVA](https://github.com/compbiocore/VariantVisualization.jl/tree/master/VIVA) tool script and save it to a working directory for your analysis.
-3. Navigate to your working directory and follow the [VIVA manual](https://compbiocore.github.io/VIVA.jl/latest) to generate your plots.
+3. Navigate to your working directory and follow the [VIVA manual](https://compbiocore.github.io/VariantVisualization.jl/latest/) to generate your plots.
 
-### Jupyer Notebook
+### Jupyter Notebook
 
 1. [Install Jupyter](https://jupyter.org/install)
 2. Download the [VIVA Jupyter Notebook](https://github.com/compbiocore/VariantVisualization.jl/tree/master/VIVA.ipynb).
@@ -55,6 +55,17 @@ using Pkg
 Pkg.clone("https://github.com/compbiocore/VariantVisualization.jl")
 ```
 
+### *For Developers*
+
+VIVA Jupyter notebook and the VIVA the command line tool are built with functions contained in our VariantVisualization.jl package.
+
+Developers may contribute to these open source tools by using [functions contained within VariantVisualization.jl](https://github.com/compbiocore/VariantVisualization.jl/tree/master/src/) which are carefully documented with docstrings.
+
+We have included in-line comments within the code for the [VIVA command line tool](https://github.com/compbiocore/VariantVisualization.jl/tree/master/viva).
+
+The ***VIVA Jupyter notebook*** is powered by a [main function](https://github.com/compbiocore/VariantVisualization.jl/tree/master/src/new_notebook_utils.jl) which takes arguments defined by the user in the notebook. We welcome users to post in issues to request a new feature or bug fix.
+
+
 ## Contributing and Questions
 
 Contributions are welcome, as are feature requests and suggestions. Please open an

diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
@@ -26,7 +26,7 @@ docs_dir: 'build'
 
 pages:
 - Home: index.md
-- Manual:
+- VIVA Manual:
   - Filtering Your VCF File: filtering_vcf.md
   - Making Plots: plotting.md
   - Examples: examples.md

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -6,7 +6,7 @@
 
 ## Description
 
-VIVA is a user-friendly command line tool built with our VariantVisualization.jl package for exploratory analysis and generation of publication quality graphics for variant analysis project using Variant Call Format (VCF) files.
+VIVA is a user-friendly command line tool built with our VariantVisualization.jl package for exploratory analysis and generation of publication quality graphics for variant analysis projects using Variant Call Format (VCF) files.
 
 Variant selection and plotting is all executed in a single command.
 
@@ -86,12 +86,3 @@ Use the following steps to use the VIVA Jupyter Notebook utility:
 
 * [Plotting Options](https://github.com/compbiocore/VariantVisualization.jl/tree/master/docs/src/plotting.md)
 
-### *For Developers*
-
-VIVA Jupyter notebook and the VIVA the command line tool are built with functions contained in our VariantVisualization.jl package.
-
-Developers may contribute to these open source tools by using [functions contained within VariantVisualization.jl](https://github.com/compbiocore/VariantVisualization.jl/tree/master/src/) which are carefully documented with docstrings.
-
-We have included in-line comments within the code for the ***[VIVA command line tool]***(https://github.com/compbiocore/VariantVisualization.jl/tree/master/viva).
-
-The ***VIVA Jupyter notebook*** is powered by a [main function](https://github.com/compbiocore/VariantVisualization.jl/tree/master/src/new_notebook_utils.jl) which takes arguments defined by the user in the notebook. We welcome users to post in issues to request a new feature or bug fix.
diff --git a/docs/src/installation.md b/docs/src/installation.md
@@ -1,7 +1,7 @@
 #Installation
 
-##Install Julia v1.1
-Follow the [instructions]("") for installing Julia v1.1 on your system.
+##Install Julia v1.1.0
+Download [Julia]("https://julialang.org/downloads/")
 
 ##Install the VariantVisualization.jl
 Add `VariantVisualization.jl` at the package prompt in the Julia v1.1 REPL.