Skip to content

Improving automation #2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
thepatientwait wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Improving automation #2

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 0 additions & 6 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,12 +33,6 @@ First, download the reference databases for each tool
snakemake --snakefile gather_tool_databases.smk --use-conda -c 8
```

The Metabuli R207 database is downloaded separately. Download the tar.gz file from https://connectqutedu.sharepoint.com/:u:/s/metabuli_gtdb_207/EYk7N71mp-NAtET5_X_fBDABM6AC_DCbxGiDc2rdVVlNiw?e=Ra5rVZ and put it into a new folder `tool_reference_data/metabuli`. Then extract it with

```bash
tar -xvf metabuli.tar.gz
```

Then run the benchmarking, for instance #1

```bash
Expand Down
27 changes: 25 additions & 2 deletions gather_tool_databases.smk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,9 +33,9 @@ map2b_db = os.path.join(map2b_checkout_dir, 'database/GTDB')
# metabuli_db_dir = join(output_directory, 'metabuli')
# metabuli_db = join(metabuli_db_dir, 'gtdb')

# tools = ['singlem', 'metaphlan', 'motus', 'kraken', 'sourmash', 'kaiju', 'map2b', 'metabuli']
tools = ['singlem', 'metaphlan', 'motus', 'kraken', 'sourmash', 'kaiju', 'map2b', 'metabuli']
## metabuli download is not scripted because it is via sharepoint, which gives an indirect link.
tools = ['singlem', 'metaphlan', 'motus', 'kraken', 'sourmash', 'kaiju', 'map2b']
# tools = ['singlem', 'metaphlan', 'motus', 'kraken', 'sourmash', 'kaiju', 'map2b']

rule all:
input:
Expand Down Expand Up @@ -385,3 +385,26 @@ rule bench2_genomes_extract:
"""
cd 2_phylogenetic_novelty && tar -xzf bench2_genomes.tar.gz &> ../{log}
"""

rule download_metabuli:
output:
metabuli_tar = join(output_directory, 'metabuli', 'metabuli.tar.gz'),
log:
join(output_directory, 'metabuli.log')
shell:
"""
mkdir -p {output_directory}/metabuli
wget https://connectqutedu.sharepoint.com/:u:/s/metabuli_gtdb_207/EYk7N71mp-NAtET5_X_fBDABM6AC_DCbxGiDc2rdVVlNiw?download=1 -O {output.metabuli_tar} &> {log}
"""

rule extract_metabuli:
input:
metabuli_tar = join(output_directory, 'metabuli', 'metabuli.tar.gz'),
params:
output_directory = join(output_directory, 'metabuli'),
output:
done=touch(join(output_directory, 'metabuli.done')),
log:
join(output_directory, 'metabuli-extract.log')
shell:
'tar -xzf {input.metabuli_tar} -C {params.output_directory} &> {log}'