Closed Daniel-Mietchen closed 5 years ago
Good mix of people in the room, including some people from iGEM Virginia with whom I was trying to get in touch anyway, following the synthetic biology symposium last week (cf. https://github.com/Daniel-Mietchen/events/issues/568 ).
In the afternoon, there will be room to discuss what software is/ should be running on the UVA HPC cluster Rivanna (see my separate notes on that). I'd like to use a MyBinder/ Docker/ Wikibase combo, and I'd like to learn more about the different file formats used in sequence analysis as well as about dark taxa.
Another thing that's on my mind in this context is how things like http://wikigenomes.org/ can be integrated into sequence analysis workflows, or https://wikidp.org/ into software curation workflows.
popular sequence alignment software:
key sequence alignment algorithms:
I asked about how the environmental footprint of Rivanna is managed, and the VP for IT was mentioned as overseeing that. Will contact them.
as allocation, users can use "rivanna-training" up to certain limits.
For large file transfers, use Globus.
For the hands-on, I am using the Terminal under rivanna-portal, along with instructions from https://workshops.somrc.virginia.edu/lesson/ngs-seq-alignment/ .
The hostname
command gives udc-ba35-36
for me right now.
Gonna avoid that for running my jobs.
after launching the ijob, hostname
gives udc-ba26-28a
.
to get a list of all of a user's Rivanna jobs on that host machine, type
squeue -u UVACOMPUTEID
, where UVACOMPUTEID is their compute id
to get a list of most recently run jobs, type sacct
, or sacct -S 2017-01-30
to get all the jobs run since a given start date. Output format can be specified using things like
sacct --format=jobid,jobname,start,elapsed,end -S 2017-01-30
.
See sacct -h
for details.
echo $SLURM_CPUS_PER_TASK
gives the number of cores requested by the ijob command
If there is no scratch directory, then instead of
cd /scratch/dm7gn/ngs-aln-workshop/ref/
,
one can do
cd /sfs/lustre/scratch/dm7gn/ngs-aln-workshop/ref/
.
met Sarah French. will send email to follow up.
under /project/genomes
, there is a list of genomes for which indexes for alignment have already been built.
Both the iGEM team and Sara are working on styrofoam.
as per https://education.cadre.virginia.edu/#/workshop/1596 and https://workshops.somrc.virginia.edu/lesson/hpc-bioinformatics/