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vpc-ccg / tksm

Very modular, very cool long-read transcriptomic simulator
MIT License
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Provided examples fail #26

Open rickbeeloo opened 4 months ago

rickbeeloo commented 4 months ago

Hey!

We would love to use the tool but have quite some trouble getting it to work.

There were quite some versions that are not compatible (anymore) in the mamba install -c bioconda tksm. So I had to install it from source which may contribute to the issues below.

After installing, then following the example:

snakemake --configfile config-test.yaml -j32

KeyError in file .../tksm/Snakefile, line 21:
'models'
  File ".../tksm/Snakefile", line 21, in <module>

This seems to make sense as config-test.yaml does not have models like for example this yaml in the repo. I then thought I will just use the default config.yaml to at least see if it runs further: snakemake --configfile config.yaml -j32 This brings another error:

NameError in file .../tksm/Snakefile, line 285:
name 'exprmnt' is not defined
  File ".../tksm/Snakefile", line 285, in <module>

Not sure why this happens, exprmnt seems defined in the wildcards but looking at the snakemake docs the strings should just use the wildcards directly instead of using the string formatting (but maybe your code does require this to be formatted later on?). To try, instead of f"..." with {{x}} I just used {x}. This got me further but then I get:

NameError in file .../tksm/Snakefile, line 633:
name 'ref_names' is not defined
  File ".../tksm/Snakefile", line 633, in <module>

Seems to be the same with the formatting. After changing that it does run:

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 32
Rules claiming more threads will be scaled down.
Job stats:
job      count
-----  -------
all          1
total        1

Select jobs to execute...

[Fri Jul 12 09:55:43 2024]
localrule all:
    jobid: 0
    reason: Rules with neither input nor output files are always executed.
    resources: tmpdir=/tmp

[Fri Jul 12 09:55:43 2024]
Finished job 0.
1 of 1 steps (100%) done

but nothing seems to have happened, nor any errors.

I'm a bit clueless of how to get it to work properly?

f0t1h commented 2 months ago

Sorry for the delayed answer. We've revised the method since we uploaded the example. We are working on a new version of example dataset.