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cjneely10 / EukMetaSanity

Structural and functional annotation of eukaryotic metagenome-assembled genomes
GNU General Public License v3.0
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Installation issue with conda #7

Closed JSSaini closed 3 years ago

JSSaini commented 3 years ago

Installation freezes during conda environment creation. Tried to install it twice, first left it overnight and then left it for 12 hours at least but no success in installing the tool.

cjneely10 commented 3 years ago

Hi @JSSaini, thank you for trying out EukMetaSanity.

There have been a couple reported issues with long installation times, so we are currently brainstorming solutions.

Meanwhile, you can try allotting more time (>16 hours). Additionally, a clean conda installation can also decrease EukMetaSanity install times (~8 hours on my system)

Sorry for the inconvenience, Chris

akrinos commented 3 years ago

If I could provide input - we've been having the same problems recently with EUKulele and long installation times. Using mamba rather than conda appears to resolve the issue. I just attempted to install EukMetaSanity's conda-based dependencies with mamba and it took under a half an hour, though I recognize this is just one leg of the overall installation process. Maybe you've already tried this!

cjneely10 commented 3 years ago

@akrinos That is an awesome find, thank you! Let me add in mamba to the installation process and see how it functions.

cjneely10 commented 3 years ago

The EukMetaSanity installation now proceeds using mamba and is far faster!

@JSSaini Please attempt a re-install at your convenience. You may wish to remove existing conda environments, if any:

conda remove -y --name EukMS_run --all
conda remove -y --name EukMS_report --all
conda remove -y --name EukMS_refine --all

And then follow the installation steps in the installation README. Be sure to use pull the latest version of this repo prior to running the installation script.

Let me know if you have any further issues installing EukMS, Chris

JSSaini commented 3 years ago

Tried the new installation after removing the old stuff. The new installation still running for at least 9 hours. Mamba installation is integrated into the new installation steps? Thank you.

cjneely10 commented 3 years ago

@JSSaini Sorry, can you please confirm that you are running that latest version of this repo (your INSTALL.sh file should have conda install mamba -n base -c conda-forge as line 9 of the file)?

If so, I'll need to double check why there is still the slow installation issue on outside systems.

If not, please pull the latest version of the repo prior to running the installation.

Thanks,

JSSaini commented 3 years ago

It worked after getting the updated repo from git. Took less than an hour for mamba installation. Plus additional 8-10 hours for Dfam. Thanks.