Update precluster branch

.github/workflows/test-ibis.yml → .github/workflows/test-binchicken.yml

@@ -1,4 +1,4 @@
-name: Test Ibis with Setup-Miniconda From Marketplace
+name: Test Bin chicken with Setup-Miniconda From Marketplace
 on: [push]
 
 jobs:
@@ -17,7 +17,7 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: test
-          environment-file: ibis.yml
+          environment-file: binchicken.yml
           python-version: ${{ matrix.python-version }}
           miniforge-variant: Mambaforge
           auto-activate-base: false
@@ -33,7 +33,7 @@ jobs:
           sudo rm -rf /opt/ghc
           sudo rm -rf "/usr/local/share/boost"
           sudo rm -rf "$AGENT_TOOLSDIRECTORY"
-      - name: Install Ibis
+      - name: Install Bin chicken
         run: |
           pip install -e .
       - name: Run unit tests

MANIFEST.in

@@ -1,2 +1,3 @@
 include LICENSE
-recursive-include ibis *.yaml *.yml *.smk ibis_logo.png
+include binchicken_logo.png
+recursive-include binchicken *.yaml *.yml *.smk

README.md

@@ -1,34 +1,60 @@
-# Ibis
+# Bin chicken
 
-[<img src="ibis_logo.png" width="50%" />](ibis_logo.png)
+[<img src="binchicken_logo.png" width="50%" />](binchicken_logo.png)
 
-Ibis (bin chicken) - targeted recovery of low abundance genomes through intelligent coassembly.
+Bin chicken - targeted recovery of low abundance metagenome assembled genomes through intelligent coassembly.
 
 ## Installation options
 
+### Install from Bioconda
+
+Install latest release via bioconda.
+
+```bash
+conda create -n binchicken -c bioconda binchicken
+```
+
+### Install from pip
+
+Install latest release via pip.
+
+```bash
+pip install binchicken
+```
+
 ### Install from source
 
-Create conda env from `ibis.yml` and install from source.
+Create conda env from `binchicken.yml` and install from source.
 
 ```bash
-git clone https://github.com/AroneyS/ibis.git
-cd ibis
-conda env create -f ibis.yml
-conda activate ibis
+git clone https://github.com/AroneyS/binchicken.git
+cd binchicken
+conda env create -f binchicken.yml
+conda activate binchicken
 pip install -e .
 ```
 
+## Environment setup
+
 Create subprocess conda environments and setup environment variables.
+Conda prefix is the directory you want to contain the subprocess conda environments.
+SingleM metapackage is the metapackage downloaded by SingleM using `singlem data` (see <https://github.com/wwood/singlem>).
+
+The latter databases are required only if you want to run Aviary directly using the `--run-aviary` argument.
+GTDB-Tk database is the directory containing the GTDB-Tk release (see <https://github.com/Ecogenomics/GTDBTk>).
+CheckM2 database is the directory containing the CheckM2 database (see <https://github.com/chklovski/CheckM2>).
+These can also be downloaded automatically by Aviary using `aviary configure --download gtdb singlem checkm2` (see <https://github.com/rhysnewell/aviary>).
 
 ```bash
-ibis build \
+binchicken build \
   --conda-prefix /path/to/conda/envs/dir \
   --singlem-metapackage /metapackage/dir \
   --gtdbtk-db /gtdb/release/dir \
   --checkm2-db /checkm2/db/dir
 ```
 
 Alternatively, set directory to contain subprocess conda environments and environment variables manually.
+Subprocess conda environments will be created when required.
 
 ```bash
 conda env config vars set SNAKEMAKE_CONDA_PREFIX="/path/to/conda/envs"
@@ -38,38 +64,32 @@ conda env config vars set GTDBTK_DATA_PATH="/gtdb/release/dir"
 conda env config vars set CHECKM2DB="/checkm2/db/dir"
 ```
 
-### Install from pip
-
-Install latest release via pip.
-
-```bash
-pip install ibis-genome
-```
-
 ## Example workflow
 
 ```bash
-# Assemble and recover from each sample individually with 20 samples used for differential abundance binning
-ibis coassemble \
+# Assemble and recover from each sample individually
+# 20 samples used for differential abundance binning
+binchicken coassemble \
   --forward-list samples_forward.txt --reverse-list samples_reverse.txt \
   --run-aviary --single-assembly \
-  --cores 64 --output ibis_single_assembly
+  --cores 64 --output binchicken_single_assembly
 
-# Assemble and recover from 2-sample coassemblies, prioritising samples with genomes not previously recovered
-ibis iterate \
-  --coassemble-output ibis_single_assembly \
+# Assemble and recover from 2-sample coassemblies
+# Prioritising samples with genomes not previously recovered
+binchicken iterate \
+  --coassemble-output binchicken_single_assembly \
   --run-aviary --assemble-unmapped \
-  --cores 64 --output ibis_2_coassembly
+  --cores 64 --output binchicken_2_coassembly
 
 # Perform another iteration of coassembly, with 3-samples this time
-ibis iterate \
+binchicken iterate \
   --coassembly-samples 3 \
-  --coassemble-output ibis_2_coassembly \
+  --coassemble-output binchicken_2_coassembly \
   --run-aviary --assemble-unmapped \
-  --cores 64 --output ibis_3_coassembly
+  --cores 64 --output binchicken_3_coassembly
 ```
 
-## Ibis coassemble
+## Bin chicken coassemble
 
 Snakemake pipeline to discover coassembly sample clusters based on co-occurrence of single-copy marker genes, excluding those genes present in reference genomes (e.g. previously recovered genomes).
 The taxa of the considered sequences can be filtered to target a specific taxon (e.g. the phylum Planctomycetota).
@@ -80,65 +100,65 @@ Paired end reads of form reads_1.1.fq, reads_1_1.fq and reads_1_R1.fq are automa
 
 ```bash
 # Example: cluster reads into proposed coassemblies
-ibis coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ...
+binchicken coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ...
 
 # Example: cluster reads into proposed coassemblies based on unbinned sequences
-ibis coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --genomes genome_1.fna ...
+binchicken coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --genomes genome_1.fna ...
 
 # Example: cluster reads into proposed coassemblies based on unbinned sequences and coassemble only unbinned reads
-ibis coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --genomes genome_1.fna ... --assemble-unmapped
+binchicken coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --genomes genome_1.fna ... --assemble-unmapped
 
 # Example: cluster reads into proposed coassemblies based on unbinned sequences from a specific taxa
-ibis coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --genomes genome_1.fna ... --taxa-of-interest "p__Planctomycetota"
+binchicken coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --genomes genome_1.fna ... --taxa-of-interest "p__Planctomycetota"
 
 # Example: find relevant samples for differential coverage binning (no coassembly)
-ibis coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --single-assembly
+binchicken coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --single-assembly
 
 # Example: run proposed coassemblies through aviary with cluster submission
 # Create snakemake profile at ~/.config/snakemake/qsub with cluster, cluster-status, cluster-cancel, etc.
 # See https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles
-ibis coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --run-aviary \
+binchicken coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --run-aviary \
   --snakemake-profile qsub --cluster-retries 3 --local-cores 64 --cores 64
 ```
 
-## Ibis evaluate
+## Bin chicken evaluate
 
 Evaluates the recovery of target genes by coassemblies suggested by above, finding the number of target genes present in the newly recovered genomes.
 Compares the recovery by phyla and by single-copy marker gene.
 
 ```bash
 # Example: evaluate a completed coassembly
-ibis evaluate --coassemble-output coassemble_dir --aviary-outputs coassembly_0_dir ...
+binchicken evaluate --coassemble-output coassemble_dir --aviary-outputs coassembly_0_dir ...
 
 # Example: evaluate a completed coassembly by providing genomes directly
-ibis evaluate --coassemble-output coassemble_dir --new-genomes genome_1.fna ... --coassembly-run coassembly_0
+binchicken evaluate --coassemble-output coassemble_dir --new-genomes genome_1.fna ... --coassembly-run coassembly_0
 ```
 
-## Ibis iterate
+## Bin chicken iterate
 
 Run a further iteration of coassemble, including newly recovered bins.
 Defaults to using genomes with at least 70% complete and at most 10% contamination CheckM2.
 Automatically excludes previous coassemblies.
 
 ```bash
 # Example: rerun coassemble, adding new bins to database
-ibis iterate --coassemble-output coassemble_dir
+binchicken iterate --coassemble-output coassemble_dir
 
 # Example: rerun coassemble, adding new bins to database, providing genomes directly
-ibis iterate --coassemble-output coassemble_dir --new-genomes new_genome_1.fna
+binchicken iterate --coassemble-output coassemble_dir --new-genomes new_genome_1.fna
 ```
 
-## Ibis update
+## Bin chicken update
 
-Applies further processing to a previous Ibis coassemble run: downloading SRA reads, generating unmapped reads files, and/or running assembly/recovery commands.
+Applies further processing to a previous Bin chicken coassemble run: downloading SRA reads, generating unmapped reads files, and/or running assembly/recovery commands.
 
 ```bash
 # Example: update previous run to download SRA reads
-ibis update --coassemble-output coassemble_dir --sra --forward SRA000001 ... --genomes genome_1.fna ...
+binchicken update --coassemble-output coassemble_dir --sra --forward SRA000001 ... --genomes genome_1.fna ...
 
 # Example: update previous run to perform unmapping
-ibis update --coassemble-output coassemble_dir --assemble-unmapped --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --genomes genome_1.fna ...
+binchicken update --coassemble-output coassemble_dir --assemble-unmapped --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --genomes genome_1.fna ...
 
 # Example: update previous run to run specific coassemblies
-ibis update --coassemble-output coassemble_dir --run-aviary --coassemblies coassembly_0 ... --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --genomes genome_1.fna ...
+binchicken update --coassemble-output coassemble_dir --run-aviary --coassemblies coassembly_0 ... --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --genomes genome_1.fna ...
 ```

ibis.yml → binchicken.yml

@@ -1,4 +1,4 @@
-name: ibis
+name: binchicken
 channels:
   - conda-forge
   - bioconda
@@ -11,7 +11,7 @@ dependencies:
   - bird_tool_utils_python=0.4.*
   - extern=0.4.*
   - ruamel.yaml=0.17.*
-  - polars=0.19.7
+  - polars=0.20.*
   - pigz=2.3.*
   - pyarrow=12.0.*
   - parallel=20230522

binchicken/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.10.0"