Closed johnbradley closed 3 years ago
@wodanaz I created an example project in DDS named sars-cov2-example and gave you permissions. It contains a small fastq.gz file downloaded from https://registry.opendata.aws/ncbi-covid-19/. From this branch you could test it like so using the directory you mentioned in #12:
sbatch run-dds-escape-variants.sh -g MT246667.fasta -d /data/wraycompute/alejo/sars2_genotype/assembling_results -i sars-cov2-example
@wodanaz I created an example project in DDS named sars-cov2-example and gave you permissions. It contains a small fastq.gz file downloaded from https://registry.opendata.aws/ncbi-covid-19/. From this branch you could test it like so using the directory you mentioned in #12:
sbatch run-dds-escape-variants.sh -g MT246667.fasta -d /data/wraycompute/alejo/sars2_genotype/assembling_results -i sars-cov2-example
Ok... one question.
For this to work properly, do I have to clone the github repository to the following directory?
data/wraycompute/alejo/sars2_genotype/assembling_results
ok I think, it's working now
For this to work properly, do I have to clone the github repository to the following directory? data/wraycompute/alejo/sars2_genotype/assembling_results
You should not need to.
For this to work properly, do I have to clone the github repository to the following directory? data/wraycompute/alejo/sars2_genotype/assembling_results
You should not need to.
yeah, I didn't have the genome but it seems to be working now.
Fantastic work!!! Thank you.
I have learned a lot about automation of scripts.
I think its good for now. I will start cranking some data soon.
Will let you know how it goes or if I have any questions!
Adds
run-dds-escape-variants.sh
sbatch script that willThe output DDS project name is created by adding "_results" to the input ddsproject name. Users of this script must first setup their ddsclient credentials.
Help for
run-dds-escape-variants.sh
looks like so:The
datadir
will have aninput
andoutput
subdirectories created. Theinput
subdirectory will hold downloaded DDS projects in project specific subdirectories. Theoutput
subdirectory will hold results and logs in project specific subdirectories.See #12 for more discussion.
The script can be run with sbatch and notify completion via email like so:
To be notified via email you can add the sbatch email flags like so:
Fixes #12