Updated documentation for HPC integration ?

[loraine-gueguen]

We are deploying sequenceserver to our infrastructure.
First of all thanks for this great tool !

We would be interested in running the blast jobs on our HPC, instead of a local server.

I have seen the documentation here https://sequenceserver.com/doc/#hpc and on the google forum https://groups.google.com/d/msg/sequenceserver/Ed05cYtHyPY/cMNYUxeaBQAJ.

But it seems outdated (2016), and the code has changed, the line number indicated doesn't exist anymore:

And then modify L67 of lib/sequenceserver/blast.rb to
system("/path/to/script #{rfile.path} #{efile.path} #{command}")

Do you have an updated documentation for HPC integration ?
Is it easily achievable ?

Thanks in advance.

[yeban]

The documentation needs updating indeed.

For version 2.0, add the following at line 51 in blast/job.rb:

def run 
  system("/path/to/script #{stdout} #{stderr} #{command}")
end

Please let me know if that works. I will then update the website.

[loraine-gueguen]

We have deployed the last stable release of sequenceserver (1.0.12) and I find out that I was not looking at the right version of code on github: on the tag 1.0.12, the given line number still exists (L67 of lib/sequenceserver/blast.rb). Sorry for the mistake...

But I thank you for the update for version 2.0 !

What are the new features in this version ? Is there a planned release date for this version ?

[yeban]

Sorry I have been slow to respond lately. This google group thread is the best place to learn about version 2.0: https://groups.google.com/d/msg/sequenceserver/2G4_jdAr4-k/tkbRaCovAAAJ

You can try a beta release of version 2.0 now. The stable release should follow hopefully in 2-4 months time.

[loraine-gueguen]

ok. Thanks!

[loraine-gueguen]

The documentation needs updating indeed.

For version 2.0, add the following at line 51 in blast/job.rb:

def run 
  system("/path/to/script #{stdout} #{stderr} #{command}")
end

Please let me know if that works. I will then update the website.

I have tested with 2.0.0rc4 and that works.
Moreover, regarding the script proposed in https://groups.google.com/d/msg/sequenceserver/Ed05cYtHyPY/cMNYUxeaBQAJ, it is needed to add 2 more sed commands to handle outfmt options:

param=`echo "$@" | sed "s/\-db\ /\-db\ \'/" | sed "s/\ \-query\ /\'\ \-query\ /" | sed "s/\-outfmt\ /\-outfmt\ \'/" | sed "s/\ \-num_threads\ /\'\ \-num_threads\ /"`

Regards

[yeban]

Thanks!

[loraine-gueguen]

To be more precise, I deployed sequenceserver in order to run blast searches with sbatch on a slurm cluster. For that, I use 2 scripts. The first one with the sbatch command, whose path is given in the run method at line 52 in blast/job.rb, calls a second one with the blast command. This configuation may be useful to other people.

#!/bin/bash
rfile=$1
efile=$2
shift 2
blast_cmd="$@"
sbatch_cmd="sbatch --wait --cpus-per-task=4 --mem=4GB --output=$rfile --error=$efile /path/to/second_script.sh $blast_cmd"
echo $sbatch_cmd
$sbatch_cmd

#!/bin/bash
blast=$1
shift 1
param=`echo "$@" | sed "s/\-db\ /\-db\ \'/" | sed "s/\ \-query\ /\'\ \-query\ /" | sed "s/\-outfmt\ /\-outfmt\ \'/" | sed "s/\ \-num_threads\ /\'\ \-num_threads\ /"`
module load blast/2.9.0
eval "$blast $param"