Comments (3)
Sorry @scharch, this default behavior doesn't make too much sense. I will update the default but you are correct that setting one of the templates included in the repo will work.
Regarding:
SCons Error: --partis-yaml-file option requires an argument
and other cases where it you've specified an argument which looks like it isn't being recognized:
You for whatever reason need to specify using =
like this scons --run-linearham --partis-yaml-file=output/partis_run.yaml
(for example).
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Actually, I can't run it at all, since the default value for the template path is None
:
root@d4094c82cf56:/linearham# cp -R data/linearham/ output
root@d4094c82cf56:/linearham# scons --run-linearham
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
scripts/parse_cluster.py output/partis_run.yaml --indel-reversed-seqs --fasta-output-file output/cluster-0/cluster_seqs.fasta --yaml-output-file output/cluster-0/cluster.yaml
only one annotation in partis output file. Using it.
writing 53 sequences to output/cluster-0/cluster_seqs.fasta
scons: *** [output/cluster-0/mcmciter10000_mcmcthin10_tuneiter5000_tunethin100_numrates4_rngseed0/revbayes_run.rev] AttributeError : 'NoneType' object has no attribute 'get_ninfo'
scons: building terminated because of errors.
root@d4094c82cf56:/linearham# scons --run-linearham --template-path templates/revbayes_asr_template.rev
scons: Reading SConscript files ...
usage: scons [OPTION] [TARGET] ...
SCons Error: --template-path option requires an argument
I will edit the SConstruct to put templates/revbayes_asr_template.rev as the default, I guess.
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@scharch the template to use is actually templates/revbayes_template.rev
not templates/revbayes_asr_template.rev
. I will rename the latter to make this clear.
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Related Issues (20)
- remove dockerhub image HOT 1
- git describe crashes build HOT 1
- Do we really want to use scons? HOT 3
- NodeList object where it expected a string HOT 1
- change actions to positional argument
- make default tag on quay.io HOT 1
- Use new partis fcn add_seqs_to_line() HOT 4
- Cause of huge number of low-probability nodes HOT 6
- update readme with newer (?) output files HOT 2
- update partis + maybe add --min-cluster-size arg HOT 1
- Docker container doesn't build HOT 2
- light chain crash HOT 3
- Github Actions & Quay Container building HOT 2
- Update Master -> Main
- crash in asr/ess script HOT 7
- Inferred ancestral sequences have mutations in ambiguous regions
- Branch lengths almost all much larger than hamming distance
- Add option for less verbose output dir HOT 1
- Failed Quay build from trigger
- How to handle paired h/l data
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