Regular Singularity Community meeting, 2nd/4th Tuesdays, 8am Pacific

[Dave Dykstra]

The poll results are in and the choice was Tuesdays at 8am Pacific time.
I have a conflict on 2nd Tuesdays, so I'll be setting it to 1st and 3rd
Tuesdays, beginning next Tuesday June 18.

If you want to attend at least some of the time please send me your name
and email address. I will send out calendar invitations including the
Zoom URL to those that contact me with their info. It will be two
separate invitations for the two different weeks of the month since
calendar invites don't generally support that style in one event.

Dave

On Mon, Jun 07, 2021 at 01:58:59PM -0500, Dave Dykstra wrote:
> I am organizing a regular Singularity Community meeting. If you are
> interested in participating, please fill out the doodle poll:
> https://doodle.com/poll/584fr7hh275396my
>
> The limited choices are due to trying to fit into Greg´s schedule while
> still allowing participation from Cedric in Europe.
>
> Dave

[Dave Dykstra]

Of course that first meeting is June 15, not June 18.

Dave

[Bogdan Tanasa]

Dear all, i am posting a question as a response to Dave, as i have not found yet a way to post new questions on the group website. 

would you please help : I am working with a singularity container that "sees" as input my $HOME (i.e /home/btanasa) folder on a SLURM cluster that has limited storage (32GB) (the singularity container is https://github.com/t-neumann/slamdunk)

a question please : how can i change this $HOME folder that the singularity "sees" with other location on the cluster e.g./labs/zzz/data ? many many thanks !

bogdan

[Thomas Hartmann]

Hi Bogdan,

you can set the ${HOME} path with the `--home` flag, e.g.,
singularity CMD --home /labs/zzz/data ...
that should point ${HOME} in the container to this directory. The flag
also accepts another target path separated by ":" like
singularity CMD --home /labs/zzz/data:/new/path/in/the/container ...

For other paths, you can use also the `--bind` flag to bind-mount
directories from outside a container onto paths inside the container.

Cheers,
Thomas

[Bogdan Tanasa]

Dear Thomas, 

i have used the command below (given that the input file  "8_R1_001.fastq.gz" is in the folder "--home /labs/jlgoldbe/MASSY_data_SLAMseq/the_SAMPLES_MAY2021:/input"

singularity exec \
/labs/jlgoldbe/MASSY_data_SLAMseq/the_SAMPLES_MAY2021/SLAMDUNK_SINGULARITY/slamdunk_latest.sif slamdunk all \
--bind /local/scratch/btanasa:/output8 \
--home /labs/jlgoldbe/MASSY_data_SLAMseq/the_SAMPLES_MAY2021:/input \
-r /home/btanasa/GRCm38.primary_assembly.genome.fa \
-b /home/btanasa/3UTRs_vM14_github_repository.27aug2020.sortdesc.LONG.with.SYMBOLS.to.use.bed \
-o /output8 \
-t 8 \

./8_R1_001.fastq.gz

and i am receiving some error messages : 

INFO:    Converting SIF file to temporary sandbox...
usage: slamdunk [-h] [--version] {map,filter,snp,count,all} ...
slamdunk: error: unrecognized arguments: --bind --home /labs/jlgoldbe/MASSY_data_SLAMseq/the_SAMPLES_MAY2021:/input ./8_R1_001.fastq.gz
INFO:    Cleaning up image...

it would be great of you could help please. thanks a lot !

[Bogdan Tanasa]

in the continuation of my previous email : the input file is "8_R1_001.fastq.gz" in the folder "  /labs/jlgoldbe/MASSY_data_SLAMseq/the_SAMPLES_MAY2021" that i fo bind, and i am still getting an error message : 

singularity exec /labs/jlgoldbe/MASSY_data_SLAMseq/the_SAMPLES_MAY2021/SLAMDUNK_SINGULARITY/slamdunk_latest.sif slamdunk all \

--bind /local/scratch/btanasa:/output8  /labs/jlgoldbe/MASSY_data_SLAMseq/the_SAMPLES_MAY2021:/input \

-r /home/btanasa/GRCm38.primary_assembly.genome.fa \

-b /home/btanasa/3UTRs_vM14_github_repository.27aug2020.sortdesc.LONG.with.SYMBOLS.to.use.bed \

-o /output8 \

-t 8 \

./8_R1_001.fastq.gz

INFO:    Converting SIF file to temporary sandbox...
usage: slamdunk [-h] [--version] {map,filter,snp,count,all} ...

slamdunk: error: unrecognized arguments: --bind ./8_R1_001.fastq.gz

[Jason Stover]

Hi Bogdan,

Move any Singularity options to before the `slamdunk all` ...
Preferable just after the `exec` command. The way Singularity parses
the command line, that is getting passed as an option to slamdunk, and
not as a run option. So something like:

singularity exec --bind /local/scratch/btanasa:/output8
/labs/jlgoldbe/MASSY_data_SLAMseq/the_SAMPLES_MAY2021:/input \
-H /input \
/labs/jlgoldbe/MASSY_data_SLAMseq/the_SAMPLES_MAY2021/SLAMDUNK_SINGULARITY/slamdunk_latest.sif
\
slamdunk all \

-r /home/btanasa/GRCm38.primary_assembly.genome.fa \
-b /home/btanasa/3UTRs_vM14_github_repository.27aug2020.sortdesc.LONG.with.SYMBOLS.to.use.bed
\
-o /output8 \
-t 8 \
./8_R1_001.fastq.gz

-J

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[Bogdan Tanasa]

Dear Jason, thank you very very much ! Many thanks to Thomas too ! 

it has started now :) cheers :)

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[Nadas, Stephen]

Hi Dave,

I will try to attend, although not next week.

Stephen Nadas
na...@bu.edu

Thanks for setting this up.

Regards,
Steve

Stephen Nadas | System Architect | na...@bu.edu
College of Arts and Sciences | Department of Computer Science
Boston University | (617) 358-8450 | he/him/his

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[Ser Heang Tan]

Hi Dave,
I will try to attend.  Please send me invites too.

Thank you.
Warmest regards,
Ser Heang TAN