dammit install on bioconda

[desmondramirez]

Hi,

I'm trying to install dammit using bioconda but conda hangs on solving the environment-- I left it overnight and it hadn't progressed. I tried to install dammit with pip but got an error about not being able to load module log.

Any ideas?

Thanks,
Des

[johnsolk]

Hi @desmondramirez,

This happens to me too sometimes. It's probably because there are A LOT of dependencies underneath. To get around, install several dependencies individually from the conda recipe for dammit, then try installing dammit with bioconda again.

conda install parallel
conda install last
conda install transdecoder
conda install shmlast=1.2.1
conda install pytest
conda install infernal
conda install pandas
conda install numpy
conda install matplotlib

Then:

conda install dammit

Hope this helps!

[desmondramirez]

Thanks for the tip! I'm trying it right now-- still solving the environment for dammit, fingers crossed. I have never been able to get BUSCO installed through bioconda, I wonder if that's what's causing the biggest issue on my end.

[johnsolk]

Hmm, interesting. Perhaps try installing the specific version of BUSCO separately?

conda install -c bioconda busco=3.0.2

[desmondramirez]

Hi,

An update-- BUSCO indeed caused the long delay. I think if you install BUSCO first and then dammit that you might not even have to install the other packages by hand. In any case, I did get it install, and will try it out soon. Thanks so much for your help!

[Gurlaz]

Hi,

I tried all the suggestions here getting all dependencies individually. But it was running for hours in the solving environment. Then I tried installing specific version of BUSCO separately and it also was running overnight only in the solving environment step.

Any more ideas that I can try? @ljcohen @desmondramirez

Thank you,

Gurlaz

[desmondramirez]

@Gurlaz, can you install other packages with conda in general? I had to leave BUSCO solving the environment at least overnight. For most of the others that @ljcohen listed to install individually, they all took less than an hour, except dammit itself, which also took a good bit of time. If you have the luxury of just letting BUSCO try to solve the environment for even longer, it might just need a little bit more time than overnight. If you can get everything else besides BUSCO, you might be able to install BUSCO yourself (not using conda) in the same directory that all the other databases get installed to.

[Gurlaz]

I also tried pip installation. It seemed that installation ran fine but when I tried to test if dammit works I got following error:

Traceback (most recent call last):
  File "/home/gurlazk/miniconda3/bin/dammit", line 4, in <module>
    import dammit
  File "/home/gurlazk/miniconda3/lib/python3.6/site-packages/dammit/__init__.py", line 4, in <module>
    import log
ModuleNotFoundError: No module named 'log'

[Gurlaz]

@Gurlaz, can you install other packages with conda in general? I had to leave BUSCO solving the environment at least overnight. For most of the others that @ljcohen listed to install individually, they all took less than an hour, except dammit itself, which also took a good bit of time. If you have the luxury of just letting BUSCO try to solve the environment for even longer, it might just need a little bit more time than overnight. If you can get everything else besides BUSCO, you might be able to install BUSCO yourself (not using conda) in the same directory that all the other databases get installed to.

Conda is working for me in general. I will try BUSCO again now.
Thanks!

[desmondramirez]

I also tried pip installation. It seemed that installation ran fine but when I tried to test if dammit works I got following error:

Traceback (most recent call last):
  File "/home/gurlazk/miniconda3/bin/dammit", line 4, in <module>
    import dammit
  File "/home/gurlazk/miniconda3/lib/python3.6/site-packages/dammit/__init__.py", line 4, in <module>
    import log
ModuleNotFoundError: No module named 'log'

I struggled with this error for a while as well and of course I forgot to write down how I solved it. I think getting all of the packages installed resolved the issue. If I remember what I did or find a record, I'll let you know.

[Gurlaz]

Hi,

Conda did not work for me for dammit or the BUSCO. However, following version specific pip installation worked and I can use dammit now.

pip install dammit==1.0rc2

Thanks!

Gurlaz

[camillescott]

Hi all. Sorry for the long delay! Updates to bioconda over the summer, and some fixes to dammit pinnings, should make the install go a lot faster now. Current version on bioconda is v1.2.