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USDA-ARS-GBRU / itsxpress

Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis
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Conda install not compatible with QIIME2 2019.10 #16

Closed ppericard closed 5 months ago

ppericard commented 4 years ago

Hi, Right now it seems that ITSxpress (1.7.2 and 1.8.0) is not compatible with QIIME2 2019.10 when installing both through conda (https://data.qiime2.org/distro/core/qiime2-2019.10-py36-linux-conda.yml). The incompatibility rises from HMMER version specification between ITSxpress and SEPP (qiime2 2019.10 dependancy):

UnsatisfiableError: The following specifications were found to be in conflict:
  - itsxpress=1.7.2 -> hmmer[version='>=3.1']
  - sepp=4.3.10 -> hmmer==3.1b2

In conda versioning, v3.1b is strictly inferior to v3.1 which leads to a conflict. Would it be possible to lower ITSxpress bioconda specification of HMMER version to >=3.1b in order to make it compatible with QIIME2 latest version?

Thanks in advance, Pierre

arivers commented 4 years ago

There should be no issue with downgrading it other than I just released the new 1.8.0 this morning on conda :(

I see you contacted SEPP too. Should I hold off until we see what they say?

ppericard commented 4 years ago

@arivers, yep just saw your update... Timing sucks... We definitely can wait a bit to see what the SEPP team response will be. It would make more sense for them to relax the HMMER version if they can. But then, we would need to make sure either the SEPP bioconda recipe is updated at the same version, or that qiime2-2019.10 update their dependencies to make ITSxpress compatible with them again...

arivers commented 4 years ago

my travicCI build uses 3.1b2 without issue. I could also change my dependencies to hmmer>= 3.1b2

Hmmer versioning is goes 3.0, 3.1b1, 3.2b2, 3.2, 3.2.1

ppericard commented 4 years ago

So, it seems that it is gonna be difficult to change the HMMER dependency of the SEPP bioconda recipe. I'm wondering if you can just change the recipe in bioconda without having to change the version of ITSxpress? Technically it doesnt impact your tool, just the way it is installed via bioconda.

arivers commented 4 years ago

I'll do that.

arivers commented 4 years ago

I submitted a pull request to update the itsxpress bioconda recipe:

https://github.com/bioconda/bioconda-recipes/pull/19282