How to get started building GslCore, relationship to Gslc

[dionjwa]

Hi!

I'm taking over the Autodesk integration of GSL into the Genetic Constructor. I'm a little confused on the relationship between https://github.com/AmyrisInc/GslCore/ and https://github.com/AmyrisInc/Gslc. I can build the Gslc locally, but not the GslCore. The GslCore appears to contain features needed for primer generation.

Dion

[chrismacklin]

GslCore is released as a library, Gslc is the thin wrapper that bundles up the compiler as a command line application. You shouldn't need to build GslCore unless you are hacking on the core compiler internals. Building Gslc will pull in GslCore as a dependency from nuget.

[dionjwa]

Ok great. I am able to build Gslc without problems, I'm not able to get primers to generate correctly. It seemed to work in a previous version we had (that someone else compiled), but I don't have a record of which version they used. Is the current version expected to work correctly with primers? Here's my command:

mono /gslc/bin/Gslc.exe --lib /gslc/gslc_lib --flat /outputs/gslOutFlat.txt --json /outputs/gslOut.json --primers /outputs/gslOut.primers.txt --ape /outputs gslOut --cm /outputs gslOut /inputs/simple_promoter_gene_locus.gsl

With simple_promoter_gene_locus.gsl:

#refgenome S288C
#name NewGSLConstruct
#stitch
uHO; pTDH3 ; mERG10 ; dHO

The primers file produced does not have meaningful data in it (the rest of the outputs look fine).

Any ideas?

[chrismacklin]

@daz10000 has been working on primer output; Darren, what do we need to do to make primers work again in public version? This is without the thumper plugin, of course.

[daz10000]

Hey - sorry for delay. I have studied this just long enough to work out that primer emission still works with caveat that you need to turn on the thumper output (even if you don't want it). If you use --thumper . foo as well as --primers it will emit a primer file. This isn't ideal because --thumper implies other kinds of constraints and there's no fundamental reason why you need the rabit packaging to get primers. When I get a chance I will investigate further (conference time this coming week so maybe then), but in mean time, try using --thumper so you can see the primer output. Would like feedback on that output format as well. We can change columns names, clean up etc. If you're game, maybe you can find out where the restriction is coming in. I couldn't see a logical reason why it wasn't emitting without --thumper

[chrismacklin]

--thumper is gone from the public version

On Thu, May 4, 2017 at 7:47 PM, daz10000 [email protected] wrote:

Hey - sorry for delay. I have studied this just long enough to work out that primer emission still works with caveat that you need to turn on the thumper output (even if you don't want it). If you use --thumper . foo as well as --primers it will emit a primer file. This isn't ideal because --thumper implies other kinds of constraints and there's no fundamental reason why you need the rabit packaging to get primers. When I get a chance I will investigate further (conference time this coming week so maybe then), but in mean time, try using --thumper so you can see the primer output. Would like feedback on that output format as well. We can change columns names, clean up etc. If you're game, maybe you can find out where the restriction is coming in. I couldn't see a logical reason why it wasn't emitting without --thumper

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[daz10000]

Ok - reality check, I can't see it there either. Not sure how I got primers out last time, but I know the basic functionality is in there, so will re-instate, thanks for your patience