Update README.md

Author: Merritt-Brian

README.md

@@ -107,173 +107,6 @@ mv minikraken2_v2_8GB_201904_UPDATE data/databases/
 docker container run -it --rm -p 8098:80 jhuaplbio/basestack_mytax2  bash -c "nginx; bash "
 ```
 
-## Original Mytax v1.0
-
-
-This is the repository for mytax, a tool for building custom taxonomies, which can aid nucleotide sequence classification.
-
-# Installation
-
-Clone this repo with:
-
-`git clone https://github.com/jhuapl-bio/mytax`
-
-Symbolically link all shell scripts into your path, for example with:
-
-`find v1 -name "*.sh" | while read fn; do sudo ln -s $PWD/$fn /usr/local/bin; done`
-
-# Dependencies
-
- - jellyfish (version 1) - https://www.cbcb.umd.edu/software/jellyfish/
- - kraken (version 1) - https://ccb.jhu.edu/software/kraken/
- - gawk - https://www.gnu.org/software/gawk/manual/html_node/Installation.html
- - perl
- - GNU CoreUtils
-
- - 16 GB of RAM is needed to build the provided influenza kraken database
-
-# Usage
-
-## Building example
-
-This pipeline is built from a central set of scripts located in the `v1` directory
-
-Build flu-kraken example with:
-
-`build_flukraken.sh -k flukraken-$(date +"%F")`
-
-The single script `build_flukraken.sh` functions as an outer wrapper for the influenza classification example using the Kraken classifier published in the mytax paper.
-
-
-`build_flukraken.sh` can also be used as a model to build modified pipelines as desired.  It is built from four main sub-modules:
-```
-	download_IVR.sh -> download references and taxonomy from IVR
-
-	build_IVR_metadata.sh -> build tab-delimited metadata table in format for mytax
-
-	build_taxonomy.sh -> build custom taxonomy from tab-delimited table
-
-	build_krakendb.sh -> add new taxonomic IDs to reference FASTA, build kraken database, post-process database for visualization pipeline
-```
-
-`build_krakendb.sh` currently references three helper scripts, which also need to be in the PATH:
-```
-	fix_references.sh -> adds new taxonomic IDs to reference FASTA
-
-	kraken-build -> builds kraken database
-
-	process_krakendb.sh -> post-processes database for visualization pipeline (not included in this repo yet)
-```
-
-
-
-## Running process script on kraken/kraken2 report and outfiles
-
-### If running from Docker
-
-docker build . -t jhuaplbio/mytax
-
-Unix
-
-`docker container run -it --rm -v $PWD:/data jhuaplbio/mytax bash`
-
-Windows Powershell
-
-`docker container run -it --rm -v $pwd:/data jhuaplbio/mytax bash`
-
-
-
-## Run the installation script
-
-
-# Activate the env, this will contain kraken2 and centrifuge scripts to build the database if needed as well as kraken2 and centrifuge dependencies
-
-`conda activate mytax`
-
-## Lets make a sample.fastq from test-data
-
-### First, download ncbi taxdump
-
-```
-python3 src/generate_hierarchy.py -o $PWD/taxdump --report test-data/sample.report   -download 
-rm taxdump.tar.gz
-```
-
-
-### DEPRECATED Kraken1 
-
-```
-mkdir -p databases/minikraken1
-wget https://ccb.jhu.edu/software/kraken/dl/minikraken_20171019_4GB.tgz -O databases/minikraken1.tgz
-tar -xvzf databases/minikraken1.tgz --directory databases/
-
-export kraken1db=databases/minikraken_20171013_4GB && \
-kraken --db $kraken1db --output test-data/sample.out test-data/sample.fastq && \
-kraken-report --db $kraken1db  test-data/sample.out | tee  test-data/sample.report
-```
-
-
-### Kraken2
-
-### IF you've made flukraken2 in tmp or....
-
-`export KRAKEN2_DEFAULT_DB="tmp/flukraken2`
-
-### IF you have a pre-made minikraken/other kraken db ready 
-
-```
-kraken2 --report output/sample_metagenome.first.report --output output/sample_metagenome.first.out --memory-mapping --db ~/Desktop/mytax/minikraken2 example-data/sample_metagenome.first.fastq 
-```
-
-### Download minikraken2
-
-```
-mkdir -p databases/
-wget ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/old/minikraken2_v2_8GB_201904.tgz -O databases/minikraken2.tgz
-tar -xvzf databases/minikraken2.tgz --directory databases/ 
-```
-
-### Centrifuge 
-
-#### Install 
-
-`bash install.sh`
-
-#### Set up centrifuge env
-
-```
-mkdir -p databases/centrifuge
-wget https://genome-idx.s3.amazonaws.com/centrifuge/p_compressed%2Bh%2Bv.tar.gz -O databases/centrifuge.tgz
-tar -xvzf databases/centrifuge.tgz --directory databases/centrifuge/
-```
-
-
-
-#### Run Centrifuge classify 
-
-```
-## If you need to make a new database, see here: $CONDA_PREFIX/lib/centrifuge/centrifuge-build --taxonomy-tree taxonomy/nodes.dmp --name-table taxonomy/names.dmp  sample.fastq sample
-
-$CONDA_PREFIX/lib/centrifuge/centrifuge -f -x databases/centrifuge/p_compressed+h+v  -q test-data/sample.fastq  --report test-data/sample.centrifuge.report > test-data/sample.out
-$CONDA_PREFIX/lib/centrifuge/centrifuge-kreport  -x databases/centrifuge/p_compressed+h+v test-data/sample.centrifuge.report > test-data/sample.report
-```
-
-####  Next, generate the hierarchy json file
-
-```
-python3 server/src/generate_hierarchy.py \
--o output/sample_metagenome.first.fullstring \
---report output/sample_metagenome.first.report \
--taxdump taxonomy/nodes.dmp
-```
-
-#### Get the json for mytax sunburst plot 
-```
-bash server/src/krakenreport2json.sh -i output/sample_metagenome.first.fullstring -o output/sample_metagenome.first.json
-```
-
-The resulting file can then imported into the sunburst plot at `server/src/sunburst/index.html` rendered with a simple `http.server` protocol like `python3 -m http.server 8080`
-
 # License and copyright
 
 Copyright (c) 2019 Thomas Mehoke