BUG: Changed installation instructions in README to install unreleased qiime2 version 2024.5

[VinzentRisch]

temporary fix for #69

Set up an environment for apple silicone

CONDA_SUBDIR=osx-64 mamba create -yn q2-amr \
  -c conda-forge -c bioconda -c defaults \
  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ -c qiime2 \
  qiime2 q2cli q2templates q2-types rgi

conda activate q2-amr
conda config --env --set subdir osx-64

pip install --no-deps --force-reinstall \
  git+https://github.com/misialq/rgi.git@py38-fix \

pip install git+https://github.com/qiime2/qiime2.git  

Run it locally

1. First, clone the repo and checkout the PR branch:

git clone https://github.com/bokulich-lab/q2-amr.git
cd q2-amr
git fetch origin pull/70/head:pr-70
git checkout pr-70
pip install -e .

2. Download test files
   PR_56.zip

3. Test it out!
   Run all this command from the PR_56 directory.

qiime amr collate-reads-allele-annotations --i-annotations partition_reads_allele/sample1.qza partition_reads_allele/sample2.qza --o-collated-annotations partition_reads_allele/collate.qza

[VinzentRisch]

Hi @Sann5
Could you try this out?
Its a temporary fix for a problem that will be solved when the new qiime2 version is released, until then it needs this additional step in the installation instructions.
There are no code changes, only a small addition in the README

[Sann5]

@VinzentRisch sure thing. Ill try it out rn.

[Sann5]

Disclaimer: I don't have an apple silicon so I followed the instructions on the README.md rather than the one in the PR message

So I ran into an error basically because the conda q2-types from is version 2023.7 and you rely on a newer one. So I simply pip installed q2-types from GitHub also and then it worked.

[VinzentRisch]

a sorry no that was because i had an error with my installation instructions.
If you try again now the correct types should be installed with the instructions in the PR

[Sann5]

@VinzentRisch should I also try the CONDA_SUBDIR=osx-64 and conda config --env --set sub dir osx-64 lines or is that only for the Apple Silicon Installation?

[VinzentRisch]

That is only for an apple silicone installation.
I forgot that you have an intel mac.
I just read your disclaimer, so that means you used the installation instructions in the readme with the additional
pip install git+https://github.com/qiime2/qiime2.git ? And this led to q2-types 2023.7 getting installed?

[Sann5]

Rather I think when you conda/mamba install q2-types in the first command the 2023.7 gets installed. I looked at the Anaconda repo and that is the latest version there. But maybe it's looking in the wrong channel if you know there is already a newer one available in conda.

Because i think pip install git+https://github.com/qiime2/qiime2.git should not install any dependencies.

[Sann5]

Actually I just checked and it is indeed the channel that you removed now, e.g. -c qiime2 that was present before.

[VinzentRisch]

Yes I understand that.
But It does not happen for me if i do

CONDA_SUBDIR=osx-64 mamba create -yn q2-amr_testtypes \
  -c conda-forge -c bioconda -c defaults \
  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ -c qiime2 \
  qiime2 q2cli q2templates q2-types rgi

conda activate q2-amr_testtypes
conda config --env --set subdir osx-64

pip install --no-deps --force-reinstall \
  git+https://github.com/misialq/rgi.git@py38-fix \
  git+https://github.com/bokulich-lab/q2-amr.git

it installs q2-types 2024.2

maybe there is a difference because of the different processors

can you please try again with this and see if it happens again?

mamba create -yn q2-amr_testtypes \
  -c conda-forge -c bioconda -c defaults \
  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ -c qiime2 \
  qiime2 q2cli q2templates q2-types rgi

conda activate q2-amr_testtypes

pip install --no-deps --force-reinstall \
  git+https://github.com/misialq/rgi.git@py38-fix \
  git+https://github.com/bokulich-lab/q2-amr.git

And if it happens again can you try with this where the order of the channels is different

mamba create -yn q2-amr_testorder \
  -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ -c qiime2 \
  -c conda-forge -c bioconda -c defaults \
  qiime2 q2cli q2templates q2-types rgi

conda activate q2-amr_testorder

pip install --no-deps --force-reinstall \
  git+https://github.com/misialq/rgi.git@py38-fix \
  git+https://github.com/bokulich-lab/q2-amr.git

[Sann5]

Ok so setting up the q2-amr-testorder env from above and then runing the example in the PR message will throw the follwoing error:

ValueError: Cannot place Tuple[SampleData[CARDAlleleAnnotation % Properties('kma', 'bowtie2')]] and Tuple[SampleData[CARDAlleleAnnotation % Properties('kma', 'bwa')]] in the same type variable.

Then because I was curious I pip install git+https://github.com/qiime2/qiime2.git. This updates the version from 2024.2.0 to 2024.5.0. Then the action works ✨

[VinzentRisch]

Yes Okay perfect, thanks for the testing :)

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.53%. Comparing base (6cb68a5) to head (3fc1427).

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #70   +/-   ##
=======================================
  Coverage   93.53%   93.53%           
=======================================
  Files          20       20           
  Lines        1314     1314           
=======================================
  Hits         1229     1229           
  Misses         85       85           

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