Merge pull request #11 from sunbeam-labs/codex/clean-up-extension-and-rename-to-sbx_cenote_taker

Rename extension to sbx_cenote_taker and drop VirSorter integration

Author: Ulthran

README.md

@@ -1,69 +1,48 @@
 <img src="https://github.com/sunbeam-labs/sunbeam/blob/stable/docs/images/sunbeam_logo.gif" width=120, height=120 align="left" />
 
-# sbx_virus_id
+# sbx_cenote_taker
 
 <!-- badges: start -->
-[![Tests](https://github.com/sunbeam-labs/sbx_virus_id/actions/workflows/tests.yml/badge.svg)](https://github.com/sunbeam-labs/sbx_virus_id/actions/workflows/tests.yml)
-[![DockerHub](https://img.shields.io/docker/pulls/sunbeamlabs/sbx_virus_id)](https://hub.docker.com/repository/docker/sunbeamlabs/sbx_virus_id/)
+[![Tests](https://github.com/sunbeam-labs/sbx_cenote_taker/actions/workflows/tests.yml/badge.svg)](https://github.com/sunbeam-labs/sbx_cenote_taker/actions/workflows/tests.yml)
+[![DockerHub](https://img.shields.io/docker/pulls/sunbeamlabs/sbx_cenote_taker)](https://hub.docker.com/repository/docker/sunbeamlabs/sbx_cenote_taker/)
 <!-- badges: end -->
 
 ## Introduction
 
-sbx_virus_id is a [sunbeam](https://github.com/sunbeam-labs/sunbeam) extension for identifying viruses in samples. This pipeline uses [MEGAHIT](https://github.com/voutcn/megahit) or [SPAdes](https://github.com/ablab/spades) for assembly of contigs and [Cenote-Taker2](https://github.com/mtisza1/Cenote-Taker2) or [Virsorter2](https://github.com/jiarong/VirSorter2) for viral identification.
+sbx_cenote_taker is a [sunbeam](https://github.com/sunbeam-labs/sunbeam) extension for identifying viruses in samples with [Cenote-Taker3](https://github.com/jedvachey/Cenote-Taker3). This pipeline uses [MEGAHIT](https://github.com/voutcn/megahit) for assembly of contigs and then processes assemblies with Cenote-Taker3.
 
-N.B. If using Megahit for assembly, this extension requires also having sbx_assembly installed.
+N.B. This extension requires also having sbx_assembly installed.
 
 ### Installation
 
 ```
-sunbeam extend https://github.com/sunbeam-labs/sbx_virus_id.git
+sunbeam extend https://github.com/sunbeam-labs/sbx_assembly.git
+sunbeam extend https://github.com/sunbeam-labs/sbx_cenote_taker.git
 ```
 
-# Installing blast dbs
+### Cenote-Taker database
 
-Install blast db:
+sbx_cenote_taker expects the Cenote-Taker3 reference database to be available locally. Download the database following the official instructions, for example:
 
 ```
-conda create -n blast
-conda activate blast
-conda install -c bioconda blast
-mkdir refseq_select_prot/
-cd refseq_select_prot/
-perl `which update_blastdb.pl` --decompress refseq_select_prot
+conda activate cenote-taker
+get_ct3_dbs -o /path/to/ct3_db --hmm T --hallmark_tax T --refseq_tax T --mmseqs_cdd T --domain_list T --hhCDD T --hhPFAM T --hhPDB T
 ```
 
-Install viral blast db:
+Update the `cenote_taker_db` entry in your Sunbeam configuration to point at the resulting directory.
 
-```
-conda stuff from above ^^^
-mkdir viral_prot/ && cd viral_prot/
-wget https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.1.protein.faa.gz && gzip -d viral.1.protein.faa.gz
-makeblastdb -in viral.1.protein.faa -parse_seqids -title "viral" -dbtype prot
-```
+### Running
 
-## Running
-
-Run with sunbeam on the target `all_virus_id`,
+Run with sunbeam on the target `all_cenote_taker`:
 
 ```
-sunbeam run --profile /path/to/project/ all_virus_id
+sunbeam run --profile /path/to/project/ all_cenote_taker
 ```
 
 ### Options for config.yml
 
   - blast_db: path to blast db (default: "") (NOTE: this should be the database file not just the directory it's in)
   - blastx_threads: number of threads for running blastx (default: 4)
   - bowtie2_build_threads: number of threads for running bowtie2-build (default: 4)
-  - cenote_taker2_db: path to cenote-taker2 db (default: "") (NOTE: this should be a directory)
-  - virsorter_db: path to virsorter2 db (default: "") (NOTE: this should be a directory)
+  - cenote_taker_db: path to cenote-taker3 db (default: "") (NOTE: this should be a directory)
   - include_phages: Whether to include phages in the output (default: False)
-  - use_spades: Whether to use SPAdes instead of MEGAHIT (default: False)
-  - use_virsorter: Whether to use Virsorter2 instead of Cenote-Taker2 (default: False)
-
-## Legacy Installation
-
-```
-git clone https://github.com/sunbeam-labs/sbx_virus_id.git extensions/sbx_virus_id
-cd extensions/sbx_virus_id
-cat config.yml >> /path/to/sunbeam_config.yml
-```

VERSION

@@ -1 +1 @@
-0.0.1
+0.1.0

config.yml

@@ -1,10 +1,6 @@
-sbx_virus_id:
+sbx_cenote_taker:
   blast_db: ''
   blastx_threads: 4
   bowtie2_build_threads: 4
   cenote_taker_db: ''
-  cenote_taker_extra_dbs: True # Download hhsuite databases (True, ~70GB) or only basic (False, ~3GB)
-  virsorter_db: ''
   include_phages: False
-  use_spades: False # Default: Megahit
-  use_virsorter: False # Default: Cenote-Taker2

envs/cenote_taker_env.Dockerfile

@@ -1,17 +1,17 @@
-FROM condaforge/mambaforge:latest
-
-# Setup
-WORKDIR /home/sbx_virus_id_env
-
-COPY envs/cenote_taker_env.yml ./
-
-# Install environment
-RUN conda env create --file cenote_taker_env.yml --name cenote_taker
-
-ENV PATH="/opt/conda/envs/cenote_taker/bin/:${PATH}"
-
-# "Activate" the environment
-SHELL ["conda", "run", "-n", "cenote_taker", "/bin/bash", "-c"]
-
-# Run
-CMD "bash"
+FROM condaforge/mambaforge:latest
+
+# Setup
+WORKDIR /home/sbx_cenote_taker_env
+
+COPY envs/cenote_taker_env.yml ./
+
+# Install environment
+RUN conda env create --file cenote_taker_env.yml --name cenote_taker
+
+ENV PATH="/opt/conda/envs/cenote_taker/bin/:${PATH}"
+
+# "Activate" the environment
+SHELL ["conda", "run", "-n", "cenote_taker", "/bin/bash", "-c"]
+
+# Run
+CMD "bash"

envs/sbx_cenote_taker.Dockerfile

@@ -0,0 +1,17 @@
+FROM condaforge/mambaforge:latest
+
+# Setup
+WORKDIR /home/sbx_cenote_taker_env
+
+COPY envs/sbx_cenote_taker.yml ./
+
+# Install environment
+RUN conda env create --file sbx_cenote_taker.yml --name sbx_cenote_taker
+
+ENV PATH="/opt/conda/envs/sbx_cenote_taker/bin/:${PATH}"
+
+# "Activate" the environment
+SHELL ["conda", "run", "-n", "sbx_cenote_taker", "/bin/bash", "-c"]
+
+# Run
+CMD "bash"

envs/sbx_virus_id.linux-64.pin.txt renamed to envs/sbx_cenote_taker.linux-64.pin.txt

@@ -1,4 +1,4 @@
-name: sbx_virus_id
+name: sbx_cenote_taker
 channels:
   - conda-forge
   - bioconda
@@ -7,4 +7,4 @@ dependencies:
   - blast
   - bowtie2
   - samtools
-  - python>=3.10
+  - python>=3.10