BRASS installation

[callosciurus]

Would it be possible to install the two packages below? My understanding is that the first depends on the second, and also on PCAP-core (https://github.com/ICGC-TCGA-PanCancer/PCAP-core), which was installed previously for the package called cgpBattenberg.

https://github.com/cancerit/BRASS https://github.com/cancerit/grass

[tatarsky]

I'll take a look at this in a bit. Have a few other items in the queue. I assume it lives in the same perl tree as cgpBattenberg as it appears to be the same author...

[callosciurus]

Yes, you're right. I realized it might depend on another tool from the same group: https://github.com/cancerit/cgpVcf

[tatarsky]

Yeah, already noted that. Out of an abundance of caution, are you running items right now in a way that some unexpected mod to that tree would cause problems?

[callosciurus]

I guess theoretically it could happen. If it does, I can deal with it later on. Nothing critically important running right now.

[tatarsky]

OK. Proceeding.

[tatarsky]

Hmm. The grass module is failing for unclear reasons one of its test modules.

Type of arg 1 to push must be array (not private variable) at t/Transcript.t line 69, near "$Exon;"
Execution of t/Transcript.t aborted due to compilation errors.
# Looks like your test exited with 255 before it could output anything.
t/Transcript.t .............. 
Dubious, test returned 255 (wstat 65280, 0xff00)

No Git issues logged similar. Could ignore test I suppose.

[callosciurus]

$exons might be a list and not an array as required by push?

my $exons = []; push $exons, $Exon;

[callosciurus]

Would ignore for now

[tatarsky]

I tend to view requests for software installation as something that should build or its really a request for software development.

But ignored the make test. Onto BRASS.

[tatarsky]

BRASS is dependent on pstreams. So there will be a pause as I have to go to a meeting and then I will get that built as a module as well as it is not an RPM item.

http://pstreams.sourceforge.net/

[callosciurus]

Ok, thanks! This is also not so urgent, so whenever is a good time.

[tatarsky]

Its just a header file it turns out. But will get it going shortly.

[tatarsky]

So BRASS has a similar sort of fail of one of its tests. Install anyway?

[tatarsky]

The test failure BTW was quite non-clear:

t/2_pl_compile.t     (Wstat: 256 Tests: 6 Failed: 1)
  Failed test:  6
  Non-zero exit status: 1

So for now I've commented that test as well.

So over to you to tell me if this script actually works:

brass.pl 

ERROR: Option must be defined.

Usage:
    brass.pl [options]

      Required parameters:

(science!)

Same module as battenberg...

[callosciurus]

Thank you very much! I'll take a closer look at this and report back.

[tatarsky]

How we doing here? Just checking on you. No rush if you haven't had time.

[callosciurus]

Haven't managed to evaluate properly yet. Looks good at first glance. More coming today/tomorrow

[callosciurus]

I am missing this tool for preprocessing: https://github.com/cancerit/VAGrENT

[tatarsky]

Hmm. I built that and I thought it installed. Checking.

[tatarsky]

Rebuilt. Setup log for that package appears to feel its installed. Whats the error message? Seems to be partly some scripts in bin and a pile of perl modules.

VAGrENT-2.1.2]$  ./setup.sh  /cbio/cslab/share/cgpBattenberg
Max compilation CPUs set to 64
Installing build prerequisite File::ShareDir... done.
Installing build prerequisite File::ShareDir::Install... done.
Building tabix ... done.
Building vcftools ... done.
Building samtools ... done.
Installing Perl prerequisites ... done.
Installing vagrent ...done.

[callosciurus]

Ok, thanks. I will look at the scripts.

[tatarsky]

It looks like it feels it was happy in its install, but the ways of the setup.sh are a bit opaque. All I've been doing is git cloning the items you ask for and running:

./setup.sh  /cbio/cslab/share/cgpBattenberg

Which when combined with the environment from the module of the same name should pull all that perl into play.

Got any error output?

[callosciurus]

It's running for now. Was looking for it in the wrong place.

[tatarsky]

Cool! Something I need to mod in the module/perl pile or all good?

[callosciurus]

I don't think so. The tool runs though, but doesn't produce the output I am expecting, yet. Most likely I am not passing the right input. I will need a while to check out what's going on. Thanks!

[tatarsky]

I do note that some of the modules have some updates recently. We may want to consider a "prod/dev" tree and module for all this code from these folks.

[tatarsky]

Just a check back on this. If all set advise or fine to say "not had time to check"

[callosciurus]

Yep, installed software works fine. I wasn't able to immediately resolve issues relating to data formatting. Closing for now, will revisit at a later stage and reopen if needed. Thanks very much!