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phac-nml / ncov-dehoster

Removal of human reads from ncov nanopore sequencing data
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pysam update causes issues #34

Open lynettios opened 1 year ago

lynettios commented 1 year ago

Hi,

I'm using the nanopore dehosting nextflow/conda pipeline. Cmd below: nextflow run phac-nml/ncov-dehoster -profile conda --nanopore --minimap2 --fastq_directory $1 --human_ref $2 --human_minimap2_index $3 --cov2019_ref $4 --composite_minimap2_index $5 --run_name $6 --min_length $7 --max_length $8

Unfortunately looks like the most recent update to pysam causes mamba to be unable to create the environment (error below). It is possible to restrict the pysam to previous version 0.20.0 in nanopore.yml?

Caused by: Failed to create Conda environment command: mamba env create --prefix /ces/docker-outdir/work/conda/nanopore-adfdf55de82ec4caa3e5e04d4bf3ca55 --file /ces/docker-outdir/.nextflow/assets/phac-nml/ncov-dehoster/environments/nanopore.yml status : 1 message: warning libmamba Could not parse mod/etag header warning libmamba Could not parse mod/etag header warning libmamba Could not parse mod/etag header warning libmamba Could not parse mod/etag header Pip subprocess error: error: subprocess-exited-with-error

  × Building wheel for pysam (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [5394 lines of output]
      <string>:435: SyntaxWarning: invalid escape sequence '\S'
      # pysam: cython is available - using cythonize if necessary
      # pysam: htslib mode is shared
      # pysam: HTSLIB_CONFIGURE_OPTIONS=None
     <removed middle part lots of errors>
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for pysam
ERROR: Could not build wheels for pysam, which is required to install pyproject.toml-based projects

CondaEnvException: Pip failed

Thanks - any help would be greatly appreciated!!! Lynette

DarianHole commented 1 year ago

Hi Lynette,

Yes it is definitely possible to restrict the pysam version! I'll get to work on addressing this!

DarianHole commented 1 year ago

Originally, installing pip with pysam worked better but it appears that the conda install is working without issue so switching to that!

For changes specific to this issue, I've pinned specific tool versions so now the environments should be more stable. In the future adding in Docker/Singularity containers would also likely be a solid addition but for now this should be ok.

For testing, the CI test is using mamba 1.5.1 with conda 23.5.2 and nextflow 23.04.3

lynettios commented 1 year ago

Amazing!!! Thank you so much DarianHole!