Releasing Unicycler v0.5.0 on conda as a package?

[wanyuac]

Hi Ryan,

Would it be possible to have a conda package of Unicycler v0.5.0? I failed to install Unicycler through pip3 install git+https://github.com/rrwick/Unicycler.git on the HPC that I am using for compatibility issues.

Thanks

[hoelzer]

Hi, I finally managed to install unicycler 0.5.0 (with focus on a Docker container) via basically

# update some basics
apt --allow-releaseinfo-change update && apt install -y procps pigz bzip2 wget make cmake g++ libz-dev libbz2-dev && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# configure conda channels
conda config --add channels defaults && \
	conda config --add channels bioconda && \
	conda config --add channels anaconda && \
	conda config --add channels conda-forge

# we like mamba more
conda install -y mamba

# install unicycler which needs python 3.10 but this will install SPAdes 3.15.3
mamba install -y -c bioconda python=3.10 unicycler=0.5.0

# remove SPAdes v3.15.3 which interferes w/ python 3.10 needed by unicycler v0.5.0
# SPAdes v3.15.4 can not be directly installed with the above mamba command bc/ python must be <=3.9 according to the current conda SPAdes recipe
# we use conda again bc/ mamba does not support (yet) removing a single package w/ removing all of its dependencies 
# see https://stackoverflow.com/questions/38459186/conda-uninstall-one-package-and-one-package-only
conda uninstall --force spades

# now install SPAdes v3.15.4 using the pre-build binary and that fixes an error w/ python 3.10
wget http://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4-Linux.tar.gz
tar -xzf SPAdes-3.15.4-Linux.tar.gz
export PATH=$PATH:/SPAdes-3.15.4-Linux/bin/

conda clean --all

# finally we have Unicycler v0.5.0 w/ SPAdes v3.15.4 and python 3.10

I had to do some tricks tp get

• unicycler v0.5.0
• SPAdes v3.15.4
• python 3.10

all together installed. My main problem was, that the Unicycler conda recipe installs SPAdes v3.15.3 which has then subsequently issues with python 3.10 that is required by Unicycler v0.5.0. Thus, I hacked a way to get SPAdes updated to hopefully fix that issue w/ Python 3.10.

The container is also publicly available if this helps:

docker pull nanozoo/unicycler:0.5.0--b2d57cb

[meono]

I see the linux version is already there. would be great to have the osx version updated too (or a noarch version if that's reasonable).

[wanyuac]

The conda package of Unicycler 0.5.0 is available: https://anaconda.org/bioconda/unicycler. Therefore, this issue is closed.

[JustdukeP]

When I try conda install -c bioconda unicycler the version 0.48 is installed

But with conda install unicycler the latest version, 0.5 is installed (https://bioconda.github.io/recipes/unicycler/README.html)