Update location of the Jannovar ZIP, replace specific SvAnna version …

…by placeholder, add `$` to CLI examples, fix typos

docs/quickstart.rst

@@ -12,24 +12,29 @@ Prerequisites
 SvAnna is written in Java 11 and needs Java 11+ to be present in the runtime environment. Please verify that you are
 using Java 11+ by running::
 
-  java -version
+  $ java -version
 
+If ``java`` is present on your ``$PATH``, then the command above will print a message similar to this one::
+
+  openjdk version "11" 2018-09-25
+  OpenJDK Runtime Environment 18.9 (build 11+28)
+  OpenJDK 64-Bit Server VM 18.9 (build 11+28, mixed mode)
 
 SvAnna setup
 ^^^^^^^^^^^^
 
-SvAnna is install by running the following three steps.
+SvAnna is installed by running the following three steps.
 
 1. Download SvAnna distribution ZIP
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Download and extract SvAnna distribution ZIP archive from `here <https://github.com/TheJacksonLaboratory/SvAnna/releases>`_.
-Expand the *Assets* menu and download the ``svanna-cli-{version}-distribution.zip``. Choose the latest stable version,
+Expand the *Assets* menu and download the ``svanna-cli-${project.version}-distribution.zip``. Choose the latest stable version,
 or a release candidate (RC).
 
 After unzipping the distribution archive, run the following command to display the help message::
 
-  java -jar svanna-cli-1.0.0-RC1.jar --help
+  $ java -jar svanna-cli-${project.version}.jar --help
 
 .. note::
   If things went OK, the command above will print the following help message::
@@ -46,18 +51,20 @@ After unzipping the distribution archive, run the following command to display t
 2. Download SvAnna database files
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Run the following::
+Download SvAnna data files by running::
 
-  wget https://svanna.s3.amazonaws.com/svanna.zip && unzip svanna.zip
-  wget https://squirls.s3.amazonaws.com/jannovar_v0.35.zip && unzip jannovar_v0.35.zip
+  $ wget https://svanna.s3.amazonaws.com/svanna.zip && unzip svanna.zip
+  $ wget ftp://squirls.ielis.xyz/jannovar_v0.35.zip && unzip jannovar_v0.35.zip
 
+.. tip::
+  Use ``curl --output svanna.zip https://svanna.s3.amazonaws.com/svanna.zip`` if ``wget`` is not available in your environment
 
 3. Generate & fill the configuration file
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Generate the configuration file::
 
-  java -jar `pwd`/svanna/svanna-cli-1.0.0-RC1.jar generate-config svanna-config.yml
+  $ java -jar `pwd`/svanna/svanna-cli-${project.version}.jar generate-config svanna-config.yml
 
 Now open the generated file in your favorite text editor and provide absolute paths to the following two resources:
 
@@ -77,7 +84,7 @@ Let's annotate a toy VCF file containing eight SVs reported in the SvAnna manusc
 
 First, let's download the VCF file::
 
-  wget https://github.com/TheJacksonLaboratory/SvAnna/blob/master/svanna-cli/src/examples/example.vcf
+  $ wget https://github.com/TheJacksonLaboratory/SvAnna/blob/master/svanna-cli/src/examples/example.vcf
 
 The variants were sourced from published clinical case reports and each variant led to a Mendelian disease.
 
@@ -90,7 +97,7 @@ sequencing run of a patient presenting with the following clinical symptoms:
 
 Now, let's prioritize the variants::
 
-  java -jar svanna/svanna-cli-1.0.0-RC1.jar prioritize --config svanna-config.yml --output-format html,csv,vcf --vcf example.vcf --term HP:0011890 --term HP:0000978 --term HP:0012147
+  $ java -jar svanna/svanna-cli-${project.version}.jar prioritize --config svanna-config.yml --output-format html,csv,vcf --vcf example.vcf --term HP:0011890 --term HP:0000978 --term HP:0012147
 
 The variant with ID ``Othman-2010-20696945-VWF-index-FigS7`` that disrupts a promoter of the *von Willenbrand factor*
 (*VWF*) gene (`Othman et al., 2010 <https://pubmed.ncbi.nlm.nih.gov/20696945>`_)

docs/running.rst

@@ -22,7 +22,7 @@ stored in one or more :ref:`rstoutputformats`.
 
 To prioritize variants in the `example.vcf`_ file (an example VCF file with 8 variants stored in SvAnna repository), run::
 
-  java -jar svanna-cli.jar prioritize --config svanna-config.yaml --vcf example.vcf --term HP:0011890 --term HP:0000978 --term HP:0012147 --prefix /path/to/output
+  $ java -jar svanna-cli.jar prioritize --config svanna-config.yaml --vcf example.vcf --term HP:0011890 --term HP:0000978 --term HP:0012147 --prefix /path/to/output
 
 After the annotation, the results are stored at ``/path/to/output.html``.
 

docs/setup.rst

@@ -54,7 +54,11 @@ tested to work with SvAnna.
 For your convenience, the files containing *UCSC*, *RefSeq*, or *ENSEMBL* transcripts
 for *hg19* or *hg38* genome assemblies are available for download (~330 MB for download, ~330 MB unpacked).
 
-`Download Jannovar files from here <https://squirls.s3.amazonaws.com/jannovar_v0.35.zip>`_.
+Download Jannovar files from ftp://squirls.ielis.xyz/jannovar_v0.35.zip::
+
+  $ wget ftp://squirls.ielis.xyz/jannovar_v0.35.zip
+  or
+  $ curl --output jannovar_v0.35.zip ftp://squirls.ielis.xyz/jannovar_v0.35.zip
 
 
 Build SvAnna from source
@@ -71,11 +75,11 @@ Run the following commands to download SvAnna source code from GitHub repository
 .. note::
   To build SvAnna from sources, JDK 11 or better must be available in the environment
 
-After the successful build, the JAR file is located at ``svanna-cli/target/svanna-cli-1.0.0-RC1.jar``.
+After the successful build, the JAR file is located at ``svanna-cli/target/svanna-cli-${project.version}.jar``.
 
 To verify that the building process went well, run::
 
-  $ java -jar svanna-cli/target/svanna-cli-1.0.0-RC1.jar --help
+  $ java -jar svanna-cli/target/svanna-cli-${project.version}.jar --help
 
 You should see a message describing how to run the individual commands.
 

docs/tutorial.rst

@@ -39,7 +39,7 @@ It is possible to run SvAnna without phenotype data, i.e., using just a VCF file
 
 .. code-block:: console
 
-    java -jar svanna-cli.jar prioritize --vcf example.vcf -c svanna-config.yml
+    $ java -jar svanna-cli.jar prioritize --vcf example.vcf -c svanna-config.yml
 
 This will output an HTML file called `example.SVANNA.html` in the same directory as the input VCF file.
 SvAnna outputs information about each of the SVs in the VCF file. Two main sections are generated for each SV. The top section