Merge pull request #59 from compbiocore/develop

New feature and bug fixes

docs/src/installation.md

@@ -5,7 +5,7 @@ Download [Julia]("https://julialang.org/downloads/")
 
 ### Supported Operating Systems:
 
-#### macOS 
+#### macOS
 
 Sierra, High Sierra, and Mojave.
 
@@ -32,9 +32,67 @@ Windows 10, Windows 7.
 2. Download the [VIVA Jupyter Notebook](https://github.com/compbiocore/VariantVisualization.jl/blob/master/VIVA.ipynb).
 3. Follow the in-notebook instructions to generate your plots.
 
+------
+
+## Using Docker and Docker Compose
+
+If you don't want to install Julia and VariantVisualization, you can use the Docker images provided.
+For that, first [install Docker](https://docs.docker.com/install/).
+
+#### Using Docker
+
+We provide two images, one with a Jupyter Notebook and one with a command line script for VIVA.
+
+Create a project folder and navigate to it:
+```shell
+mkdir project_x
+cd project_x
+```
+
+Make sure to add your project VCF files to that folder. That directory will be mapped to `/notebook/data` inside of the container.
+
+Then, to run the Jupyter Notebook, from the terminal or Windows PowerShell:
+```shell
+docker run --rm -p 8888:8888 -e JUPYTER_ENABLE_LAB=yes -v "$PWD":/notebook/data compbiocore/viva-notebook
+```
+Go to `http://0.0.0.0:8888/?token=<enter token here>`
+
+[Click here](https://jupyter-docker-stacks.readthedocs.io/en/latest/index.html) for more information about Jupyter Docker Images.
+
+To run VIVA Command Line Tool:
+
+On Mac or Linux:
+```shell
+docker run -it --rm -v "$PWD":/data compbiocore/viva-cli arg1 arg2 arg3
+```
+
+On Windows:
+```shell
+docker run -it --rm -v "${pwd}":/data compbiocore/viva-cli arg1 arg2 arg3
+```
+
+#### Using Docker Compose
+
+To run the images with Docker Compose, copy the [`docker-compose.yml`](https://github.com/compbiocore/viva-docker/blob/master/docker-compose.yml) file to a local directory. From that same directory, run the commandas below.
+
+!!! Note  
+Your current directory will mount to `/notebook/data` in the notebook image and to `/data` in the CLI image.
+
+- Notebook
+```shell
+docker-compose up viva-notebook
+```
+
+- Command Line Tool
+```shell
+docker-compose run viva -f /data/file.vcf arg2 arg3 ...
+```
+
+-----
+
 ### Latest Features
 
-To stay up to date with cutting edge development features install VariantVisualization.jl from the Master branch. 
+To stay up to date with cutting edge development features install VariantVisualization.jl from the Master branch.
 
 Using git from the command line:
 
@@ -58,4 +116,3 @@ Developers may contribute to these open source tools by using [functions contain
 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.
-

src/VariantVisualization.jl

@@ -10,27 +10,18 @@ using ArgParse
 using DelimitedFiles
 using Test
 
-#using Base.Filesystem
-
-#include("vcf_utils.jl")
-#include("plot_utils.jl")
-
-#end #module
-
 export
+    test_parse_main,
     format_reader,
     load_vcf,
     clean_column1!,
-    genotype_cell_searcher_maf_correction,
-    genotype_cell_searcher,
-    dp_cell_searcher,
     load_siglist,
-    sig_list_vcf_filter,
-    genomic_range_vcf_filter,
-    load_sort_phenotype_matrix,
-    reorder_columns,
+    #sig_list_vcf_filter,
+    #genomic_range_vcf_filter,
+    #load_sort_phenotype_matrix,
+    #reorder_columns,
     select_columns,
-    genotype_heatmap2,
+    #genotype_heatmap2,
     dp_heatmap2,
     avg_sample_dp_scatter,
     avg_variant_dp_line_chart,
@@ -72,14 +63,12 @@ export
     add_pheno_matrix_to_dp_data_for_plotting,
     generate_hover_text_array,
     generate_hover_text_array_grouped,
-    save_graphic
+    save_graphic,
+    build_set_from_list
 
-#include("vcf_utils.jl")
 include("vcf_utils_complete.jl")
 include("plot_utils.jl")
 include("new_notebook_utils.jl")
 include("init.jl")
-#include("v1_VIVA_notebook_utils.jl")
-#include("io_filters.jl")
 
 end # module