pha4ge / hamronization_workflow Goto Github PK

I got amrfinder_update: command not found when following the installation instructions.
I ran: bash get_dbs.sh. I'm guessing amrfinder is installed via execution.

https://www.frontiersin.org/articles/10.3389/fmicb.2020.00052/full

• test folder, get data bash script
• run test yml file

https://bench.cs.vt.edu/deeparg

Hi, after running:

git clone https://github.com/pha4ge/hAMRonization_workflow
conda env create -n hamronization_workflow --file envs/hamronization_workflow.yaml
conda activate hamronization_workflow
snakemake --configfile config/config.yaml --use-conda --jobs 2 --use-singularity --singularity-args "-B $PWD:/data"

I'm getting the error:
KeyError in line 16 of .../hAMR/test/hAMRonization_workflow/rules/staramr.smk:
'pointfinder'
File ".../hAMR/test/hAMRonization_workflow/Snakefile", line 75, in
File ".../hAMR/test/hAMRonization_workflow/rules/staramr.smk", line 16, in

After deleting "include: "rules/staramr.smk"" in the Snakefile, it seems ok but then getting:
Building DAG of jobs...
MissingInputException in line 19 of .../hAMR/test/hAMRonization_workflow/rules/ariba.smk:
Missing input files for rule run_ariba:
data/test/SAMEA6634591/ERR4008003_R1.fastq.gz
data/test/SAMEA6634591/ERR4008003_R2.fastq.gz

One more question: if I have only assembly, in isolate_list.txt info on reads, read1 and read2 can be just left blank?

Thanks,
Svetlana

kma silently fails when executed by kmerresistance: specifically no error just a non-zero exit code and no output.

I can only reproduce this in the container (based off debian) and have made sure zlib headers are available but it still causes an issue.

For the interactive report or tabular report possibly have an option to just summarise results (genome, gene, tool, versions, phenotype annotation) and the full genomics results (i.e., the whole spec with start/stop contig coverage etc).

The information on the README file for installing via git clone does not clone the hAMRonization_workflow git page but rather the hAMRonization page. Kindly look into correcting this.
Thanks

ShortBRED
https://bitbucket.org/biobakery/shortbred/wiki/Home

Would it be possible to add one more tool to the list?

https://github.com/phac-nml/staramr

Cleaning up temporary files/uneeded outputs only at the end of pipeline execution means A LOT of disk space gets used when running on many isolates.

Move clean up of files to the specific tool execution.

The conda recipe for srst2 is currently broken because the pinned samtools version (0.1.18) is failing to dynamically link in libncurses.so.5

Either the srst2 recipe needs updated to use a newer working version of samtools or someone needs to try and fix the samtools 0.1.18 bioconda recipe.