allow relative path for sunbeam_config.yml

[scottdaniel]

What's the feature?
In the config.yaml you have to put the absolute path of the sunbeam_config.yml
This would allow it to simply look in the directory where the config.yaml already resides

e.g.
configfile: "sunbeam4_config.yml" # would be nice if you could do it like this
instead of...
configfile: "/mnt/isilon/microbiome/analysis/danielsg/redding_run_4/Scripts/HPC_cluster/sunbeam4_config.yml"

[Ulthran]

Hi Scott,

Just tested this out and it seems like it probably won't work. The path has to relative to a sunbeamlib script it's read into instead of config.yaml.

sunbeam init should fill this in automatically for you though. I think we talked at some point about making a template file for the team so that you could use sunbeam init instead of copy/pasting.

e.g. this is an old pmacs template:

qc:
  human_genome_fp: "/project/bushmanlab/indexes/GCA_000001405.15_GRCh38_genomic.fna"
  phix_genome_fp: "/project/bushmanlab/indexes/phix174.fasta"

classify:
  kraken_db_fp: "/project/bushmanlab/kraken/standard"

blastdbs:
  root_fp: "/project/bushmanlab/genomeIndexes/blast"
  nucleotide:
    nt: nt/nt

Make a file like this with all the default values you want specified or overridden and then use sunbeam init --defaults /path/to/defaults/file.yml ....

[scottdaniel]

Ok, yeah, it would be neat if sunbeam init could generate the path from the project directory. But I understand if there are limits to the code.

…

On Mon, May 1, 2023, 8:28 AM Charlie ***@***.***> wrote: Hi Scott, Just tested this out and it seems like it probably won't work. The path has to relative to a sunbeamlib script it's read into instead of config.yaml. sunbeam init should fill this in automatically for you though. I think we talked at some point about making a template file for the team so that you could use sunbeam init instead of copy/pasting. e.g. this is an old pmacs template: qc: human_genome_fp: "/project/bushmanlab/indexes/GCA_000001405.15_GRCh38_genomic.fna" phix_genome_fp: "/project/bushmanlab/indexes/phix174.fasta" classify: kraken_db_fp: "/project/bushmanlab/kraken/standard" blastdbs: root_fp: "/project/bushmanlab/genomeIndexes/blast" nucleotide: nt: nt/nt Make a file like this with all the default values you want specified or overridden and then use sunbeam init --defaults /path/to/defaults/file.yml .... — Reply to this email directly, view it on GitHub <#397 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AALMZXWNERIP23QXVTFVJDLXD6T5ZANCNFSM6AAAAAAXPTCU54> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[Ulthran]

Refactored to include this directly in the snakemake call instead of in the config file

sunbeam/sunbeam/scripts/run.py

Line 55 in a0cc09b

configfile = Path(profile) / "sunbeam_config.yml"