-
Add an extra section about how to run workflows on HPC:
- Can run from login node - the workflow software will submit jobs for us automatically
- Need to run it from a persistent session using `tm…
-
I tried to run
https://github.com/PyPSA/pypsa-eur/blob/master/scripts/prepare_sector_network.py
as python script to debug and learn about it.
I got an error due to non-existing config file
…
-
After checking DRAKE, I think we could first try Snakemake to automate the benchmark. Both DRAKE and Snakemake use Make and they both appear simple to use and set up. I'd start with Snakemake just bec…
-
## Purpose
To get consensus on what the Vulcan config should look like.
Context:
Typically a snakemake pipeline is just:
- a Snakefile
- a config
- some scripts.
A vulcan pipeline …
-
**Snakemake version**
Tested with v8.18.1
Works with v7.30.2
**Describe the bug**
A collect rule that aggregates files from two sequential checkpoints fails to output all files in the …
-
After developing the initial workflow for the `dnadiff` method #12, we need to ensure that we can reproduce the `AlignedBases` value provided by `dnadiff`.
To achieve this, we should:
- Write a mo…
-
The generation of lp file can take quite some time for larger models. Hence it would be good to parallelize this part as well.
Do you think this would be very complicated @trevorb1?
I think in the o…
-
Hi,
Does someone know if it is possible to read a Snakefile in Python and load all the rules into variables?
For example, given the following Snakefile
```
WDIR="test"
rule all:
input:…
-
It seems like when I use the http storage plugin with the kubernetes executer, it submits the job but with an added argument `--storage-http-allow-redirects`.
Snakefile:
```python
storage HTTP…
-
Hi everyone
I am not very familiar with snakemake but its part of a pipeline I am trying to execute (align.smk in https://bitbucket.org/bucklerlab/msa_pipeline/src/master/workflow/rules/) . I have…