updating documentation

Author: rchau88

.github/404.md

@@ -0,0 +1,3 @@
+# Page not found (404)
+
+Please use the links in the navigation bar.

NEWS.md

@@ -1,56 +1,59 @@
-
-# MIRA 2.0.0
-* Github Repo: https://github.com/CDCgov/MIRA
-* Documentation: https://cdcgov.github.io/MIRA
-
-### v2.0.0
-- Single container distribution (previously 4 docker images)
-- RSV Illumina module
-- RSV Nanopore module
-- Alternative Command-line interface running of MIRA
-- Associated .html result files generated from command-line pipeline
-- Documentation overhaul
-
-
-### v1.1.4
-- Empty Illumina fastq error-handling
-- Illumina fastq reads less than 70 bases error-handling
-
-### v1.1.3
-- MIRA version displayed in app and in IRMA summary table (along with config)
-- IRMA version bump 1.1.4
-- fixed pulp version
-- Turn off padding for S gene module
-- Packaged fastq in irma .tar.gz
-- Error fixes for single-sample runs
-
-### v1.1.2
-- Whole-Genome SC2 Nanopore module
-- Illumina 2x75 support for Flu and SC2 whole-genome modules
-- Java instability fixed
-- New Version Checking
-- Lab protocols published on documentation website
-- Docker compose steps added to quickstart on documentation website
-- Quality control checks for S-gene specific metrics added to Whole-Genome SC2 modules
-- IRMA container V1.1.1
-- [Final sorted, amended .bams](https://wonder.cdc.gov/amd/flu/irma/output.html) included in tarball. This is in addition to the F1 .bam, which is the first iteration of alignment before reference editing.
-  
-#### v1.1.1
-- Pandas version --> 1.1.0
-- Mac docs updated to show Rosetta usage in Docker Desktop
-- More thorough error and status messaging during assembly
-
-#### v1.1.0
-- Illumina sequencing for WGS SC2 and Flu
-- Auto-samplesheet building
-- Samplesheet download/upload functionality
-- Button added to refresh run listing
-- Button added to download failed fastas
-- Downloaded fasta for FLU now changes the flu segment numbers to the gene name
-- Allow numeric samplenames, and allow "-" in sample names
-- Toss broken reads for ONT fastqs
-- Return only closer Flu B reference in amino acid variants table
-- Better error handling for empty/failed nanopore barcodes
-- Indel table filtered to >20%, Minor variant table filtered to >5%
-- Archive previous run logs in the even of a re-run
-
+
+# MIRA 2.0.0
+
+* Github Repo: https://github.com/CDCgov/MIRA
+* Documentation: https://cdcgov.github.io/MIRA
+
+### v2.0.0
+- Single container distribution (previously 4 docker images)
+- RSV Illumina module
+- RSV Nanopore module
+- Alternative Command-line interface running of MIRA
+- Associated .html result files generated from command-line pipeline
+- Documentation overhaul
+
+
+# MIRA 1.0.0
+
+### v1.1.4
+- Empty Illumina fastq error-handling
+- Illumina fastq reads less than 70 bases error-handling
+
+### v1.1.3
+- MIRA version displayed in app and in IRMA summary table (along with config)
+- IRMA version bump 1.1.4
+- fixed pulp version
+- Turn off padding for S gene module
+- Packaged fastq in irma .tar.gz
+- Error fixes for single-sample runs
+
+### v1.1.2
+- Whole-Genome SC2 Nanopore module
+- Illumina 2x75 support for Flu and SC2 whole-genome modules
+- Java instability fixed
+- New Version Checking
+- Lab protocols published on documentation website
+- Docker compose steps added to quickstart on documentation website
+- Quality control checks for S-gene specific metrics added to Whole-Genome SC2 modules
+- IRMA container V1.1.1
+- [Final sorted, amended .bams](https://wonder.cdc.gov/amd/flu/irma/output.html) included in tarball. This is in addition to the F1 .bam, which is the first iteration of alignment before reference editing.
+  
+#### v1.1.1
+- Pandas version --> 1.1.0
+- Mac docs updated to show Rosetta usage in Docker Desktop
+- More thorough error and status messaging during assembly
+
+#### v1.1.0
+- Illumina sequencing for WGS SC2 and Flu
+- Auto-samplesheet building
+- Samplesheet download/upload functionality
+- Button added to refresh run listing
+- Button added to download failed fastas
+- Downloaded fasta for FLU now changes the flu segment numbers to the gene name
+- Allow numeric samplenames, and allow "-" in sample names
+- Toss broken reads for ONT fastqs
+- Return only closer Flu B reference in amino acid variants table
+- Better error handling for empty/failed nanopore barcodes
+- Indel table filtered to >20%, Minor variant table filtered to >5%
+- Archive previous run logs in the even of a re-run
+

_pkgdown.yml

@@ -1,33 +1,42 @@
-url: https://github.com/CDCgov/MIRA/, https://cdcgov.github.io/MIRA/
+url: https://github.com/CDCgov/MIRA/
 
 template:
-  params:
-    bootstrap: 5
-    bootswatch: cosmo
+  bootstrap: 5
+  light-switch: true
 
 authors:
+  Ben Rambo-Martin:
+    href: https://github.com/nbx0
   Kristine Lacek:
     href: https://github.com/kristinelacek
   Reina Chau:
     href: https://github.com/rchau88
   Amanda Sullivan:
     href: https://github.com/mandysulli
-  Ben Rambo-Martin:
-    href: https://github.com/nbx0
 
 news:
   one_page: false
 
 home:
+  title: MIRA Documentation
   sidebar:
-    structure: [license, citation, authors]
-    
+    structure: [license, citation, authors, resources]
+    components:
+      resources:
+        title: "Resources"
+        text: "<a href='mailto:[email protected]'><span class='fa fa-envelope'></span> Contact Us</a>"
+          
 navbar:
   title: "MIRA"
-  left:
-    - icon: fa-home
+  structure:
+    left: [home, mira_desktop, mira_cli, lab_protocols, help, legacy]
+    right: [search, change_log, issue, github, lightswitch]
+  components:
+    home:
+      icon: fa-home
       href: index.html
-    - text: "MIRA in Docker Desktop"
+    mira_desktop:
+      text: "MIRA in Docker Desktop"
       menu:
         - text: Getting Started and Installation
           href: articles/mira-dd-getting-started.html
@@ -39,7 +48,8 @@ navbar:
           href: articles/data-transfer.html  
         - text: Upgrading MIRA Docker Desktop
           href: articles/upgrading-mira-dd.html
-    - text: "MIRA-CLI"
+    mira_cli:
+      text: "MIRA-CLI"
       menu:
         - text: Quick Start in Ubuntu
           href: articles/quick-start-ubuntu.html
@@ -55,7 +65,8 @@ navbar:
           href: articles/running-mira-cli-illumina.html
         - text: Upgrading MIRA-CLI
           href: articles/upgrading-mira-cli.html
-    - text: "Lab Protocols"
+    lab_protocols:
+      text: "Lab Protocols"
       menu:
         - text: Sequencing Template Generation
         - text: Automated RNA Extraction using QIAcube HT
@@ -84,20 +95,23 @@ navbar:
         - text: Oxford Nanopore Library Preparation and Sequencing
         - text: Library Preparation and Nanopore Sequencing of Influenza and SARS-COV-2 S-gene Amplicons
           icon: fa-star
-          href: articles/influenza-sars-cov-2-s-gene-amplicons-nanopore.html          
-    - text: Help
+          href: articles/influenza-sars-cov-2-s-gene-amplicons-nanopore.html 
+          
+    help:
+      text: "Help"
       menu:
-      - text: FAQs
-        href: articles/FAQs.html
-      - text: Troubleshooting
-        href: articles/troubleshooting.html
-      - text: QC Standards
-        href: articles/sequence-qc.html
-      - text: Development Tips
-        href: articles/development-tips.html
-      - text: Nanopore Frameshift Correction
-        href: articles/nanopore-frameshift-correction.html
-    - text: Legacy
+        - text: FAQs
+          href: articles/FAQs.html
+        - text: Troubleshooting
+          href: articles/troubleshooting.html
+        - text: QC Standards
+          href: articles/sequence-qc.html
+        - text: Development Tips
+          href: articles/development-tips.html
+        - text: Nanopore Frameshift Correction
+          href: articles/nanopore-frameshift-correction.html
+    legacy:
+      text: "Legacy"
       menu:
         - text: Retired PC Getting Started
           href: articles/getting-started.html
@@ -113,17 +127,16 @@ navbar:
           href: articles/running-mira-illumina.html
         - text: Retired Post MIRA sequence analysis with Nextclade
           href: articles/training-post-mira.html
-  search:
-    exclude: ['news/index.html']
-  right:
-    - text: "Change Log"
+    change_log:
+      text: "Change Log"
       href: news/index.html
-    - icon: fa-envelope
-      href: "mailto:[email protected]"
-    - icon: fa-comments
+    issue:
+      icon: fa-comments
       href: https://github.com/CDCgov/MIRA/issues
-    - icon: fa-github
+    github:
+      icon: fa-github
       href: https://github.com/CDCgov/MIRA
+      
 footer:
   structure: 
     left: developed_by

docker-compose-dev.yml

@@ -0,0 +1,40 @@
+version: "3.9"
+
+x-spyne-image:
+  &spyne-image
+  spyne_image: cdcgov/spyne-dev:v2.0.0
+
+x-mira-volume:
+  &mira-volume
+  type: bind
+  source: /home/snu3/Github/MIRA
+  target: /MIRA
+
+x-spyne-volume:
+  &spyne-volume
+  type: bind
+  source: /home/snu3/Github/spyne
+  target: /spyne
+
+x-data-volume:
+  &data-volume
+  type: bind
+  source: /home/snu3/Github/FLU_SC2_SEQUENCING
+  target: /data
+
+services:
+  mira:
+    container_name: mira
+    image: mira:latest
+    build:
+      context: .
+      dockerfile: Dockerfile
+      args:
+        << : [*spyne-image]
+    restart: always
+    ports:
+      - 8020:8050
+    volumes:
+      - *data-volume
+      - *mira-volume
+      - *spyne-volume