BUG: action `generate-reads` is missing the `pysam` dependency

[misialq]

BUG: action `generate-reads` is missing the `pysam` dependency

[mikerobeson]

I received the same error this morning within qiime2-shotgun-2023.9. I also received this error:

Plugin error from assembly:
An error was encountered while running InSilicoSeq, (return code 1), please inspect stdout and stderr to learn more.
See above for debug info.

I assume the InSilicoSeq depends on pysam? I saw the pysam issue too.

• System information:
  • SPAdes version: 3.15.2
  • Python version: 3.8.15
  • OS: Linux-3.10.0-693.el7.x86_64-x86_64-with-glibc2.10

[misialq]

Thanks for confirming @mikerobeson! Yes, it does depend on pysam but it also has it in the list of dependencies in its bioconda recipe so it should be included in the environment I guess... It used to be the case at least when I was installing it before, not using the distro route 😞

[ebolyen]

Looks like we need to add pysam to the recipe. I have no idea why the original tool isn't pulling that in, but I expect it's a particularly convoluted solve to get the rest of the distro working...