Remove Anaconda packages from defaults channel

[gq1]

Hi there.

We can't use any packages installed from Anaconda defaults channels in our institute due to the license.

Both the Docker images from BioConContainer and your own Docker hub are polluted.

• https://quay.io/repository/biocontainers/mikado?tab=tags
• https://hub.docker.com/r/gemygk/mikado/tags

I tried to install it from BioConda directly, which lots of packages missing.

And then I follow your instruction in README to build my own Docker container or conda env, which go much further but still failed with your test. Here is the Docker file:

FROM condaforge/miniforge3:24.11.3-0

RUN apt-get -y update && \
    apt-get install -y build-essential

RUN git clone https://github.com/EI-CoreBioinformatics/mikado.git && \
    cd mikado && \
    sed -i '/- defaults/d' environment.yml && \
    sed -i '/- anaconda/d' environment.yml && \
    conda env create -f environment.yml && \
    echo "source activate mikado2" > ~/.bashrc

WORKDIR /mikado

RUN /bin/bash -c "source activate mikado2 && \
    pip3 install wheel && \
    pip3 install -r requirements.txt && \
    pip3 install Cython && \
    python3 setup.py bdist_wheel && \
    pip3 install dist/*.whl && \
    conda clean -afy"

ENV PATH /opt/conda/envs/mikado2/bin:$PATH

And then the command help page works:

mikado -h
usage: Mikado [-h] [--version] {configure,prepare,serialise,pick,compare,util} ...

Mikado is a program to analyse RNA-Seq data and determine the best transcript for each locus in accordance to user-specified criteria.

optional arguments:
  -h, --help            show this help message and exit
  --version             Print Mikado current version and exit.

Components:
  {configure,prepare,serialise,pick,compare,util}
                        These are the various components of Mikado:
    configure           This utility guides the user through the process of creating a configuration file for Mikado.
    prepare             Mikado prepare analyses an input GTF file and prepares it for the picking analysis by sorting its transcripts and performing
                        some simple consistency checks.
    serialise           Mikado serialise creates the database used by the pick program. It handles Junction and ORF BED12 files as well as BLAST XML
                        results.
    pick                Mikado pick analyses a sorted GTF/GFF files in order to identify its loci and choose the best transcripts according to user-
                        specified criteria. It is dependent on files produced by the "prepare" and "serialise" components.
    compare             Mikado compare produces a detailed comparison of reference and prediction files. It has been directly inspired by
                        Cufflinks's cuffcompare and ParsEval.
    util                Miscellaneous utilities

But failed using your test:

python -c "import Mikado; Mikado.test(); Mikado.test(label='slow')"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/mikado/Mikado/__init__.py", line 29, in <module>
    from .utilities.log_utils import create_default_logger
  File "/mikado/Mikado/utilities/__init__.py", line 19, in <module>
    from .overlap import overlap
ModuleNotFoundError: No module named 'Mikado.utilities.overlap'

Any suggestion or you can put a fix?

Thanks.

[gemygk]

Hi @gq1

Thanks for getting in touch.

I will look into removing the Anaconda channel. We have other pipelines under development that use Mikado under the hood, so I need to ensure that I can install all the required packages from other channels.

Regarding the failed Mikado test, you can ignore it for now—Mikado should work fine otherwise. I still need to update the tests, and it was supposed to be removed from the README (I’ve done that now).

Thanks,
Gemy