mosdepth not found due to dependency issue

[ashrosewood]

I recently tried your workflow, and found mosdepth was crashing due to a dependency issue. I was able to fix it by providing the versions that you have listed on the Structural variation analysis page on the Nanopore Community page:

channels:
    - bioconda
    - conda-forge
    - r
dependencies:
    - snakemake-minimal
    - minimap2=2.17
    - sniffles=1.0.11
    - samtools=1.9
    - nanofilt
    - nanoplot
    - pybedtools=0.8.0
    - bedtools=2.29.0
    - bcftools=1.9
    - pysam
    - scipy
    - tqdm
    - vcftools=0.1.16
    - vcflib
    - make
    - mosdepth=0.2.5
    - pyfaidx
    - pyvcf=0.6.8
    - progressbar2
    - python-Levenshtein
    - intervaltree=2.1.0
    - rtg-tools
    - r
    - r-nanopore
    - imagemagick
    - graphviz
    - pandoc
    - igv
    - bioconductor-rsamtools=2.0.0 

And exported my environment for exact packages and dependancies. You may want to add the above versions to insure the environment does not have any dependency issues. It is quite a hefty amount of packages to install for this workflow.

Thanks,
Ashley

name: ont_tutorial_sv
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
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  - bedtools=2.29.2=hc088bd4_0
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  - jpeg=9c=h14c3975_1001
  - jsonschema=3.2.0=py36_0
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  - lcms2=2.9=hbd6801e_1
  - ld_impl_linux-64=2.33.1=h53a641e_7
  - libblas=3.8.0=14_openblas
  - libcblas=3.8.0=14_openblas
  - libclang=9.0.1=default_hde54327_0
  - libcroco=0.6.13=h8d621e5_0
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  - libgomp=9.2.0=h24d8f2e_2
  - libiconv=1.15=h516909a_1005
  - liblapack=3.8.0=14_openblas
  - libllvm9=9.0.1=hc9558a2_0
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  - libstdcxx-ng=9.2.0=hdf63c60_2
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  - minimap2=2.17=h8b12597_1
  - more-itertools=8.1.0=py_0
  - mosdepth=0.2.7=hbeb723e_0
  - nanofilt=2.6.0=py_0
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  - tqdm=4.7.2=py36_0
  - urllib3=1.25.7=py36_0
  - vcflib=1.0.0_rc2=h56106d0_2
  - vcftools=0.1.16=he860b03_3
  - wcwidth=0.1.8=py_0
  - wheel=0.33.6=py36_0
  - wrapt=1.11.2=py36h516909a_0
  - xorg-fixesproto=5.0=h14c3975_1002
  - xorg-inputproto=2.3.2=h14c3975_1002
  - xorg-kbproto=1.0.7=h14c3975_1002
  - xorg-libice=1.0.10=h516909a_0
  - xorg-libsm=1.2.3=h84519dc_1000
  - xorg-libx11=1.6.9=h516909a_0
  - xorg-libxau=1.0.9=h14c3975_0
  - xorg-libxdmcp=1.1.3=h516909a_0
  - xorg-libxext=1.3.4=h516909a_0
  - xorg-libxfixes=5.0.3=h516909a_1004
  - xorg-libxi=1.7.10=h516909a_0
  - xorg-libxpm=3.5.13=h516909a_0
  - xorg-libxrender=0.9.10=h516909a_1002
  - xorg-libxt=1.1.5=h516909a_1003
  - xorg-libxtst=1.2.3=h516909a_1002
  - xorg-recordproto=1.14.2=h516909a_1002
  - xorg-renderproto=0.11.1=h14c3975_1002
  - xorg-xextproto=7.3.0=h14c3975_1002
  - xorg-xproto=7.0.31=h14c3975_1007
  - xz=5.2.4=h14c3975_1001
  - yaml=0.2.2=h516909a_1
  - zipp=1.0.0=py_0
  - zlib=1.2.11=h516909a_1006
  - zstd=1.4.4=h3b9ef0a_1

[philres]

Thanks a lot, will do that.