make test problem

[Noah603]

Hey!

I've installed the Katuali pipeline and installed the requiered packages as well, mostly with conda. I needed to install pomoxis into a virtual env. becouse the server has python 3.7 and 3.6 was requierd. When i do the make test following problem comes up:

Using /home/hflatau/katuali/venv/lib/python3.6/site-packages Finished processing dependencies for katuali==0.3.2

15x Wildcard constraints in inputs are ignored. Building DAG of jobs... MissingInputException in line 30 of /home/hflatau/katuali/katuali/data/basecalling.snake: Missing input files for rule basecall_guppy: /home/hflatau/git/pomoxis/venv/bin/activate Makefile:56: recipe for target 'test_basecall' failed make: *** [test_basecall] Error 1

Pomoxis is in the /home/hflatau directory, but it had no venv folder, /bin/activate were just in the /home/hflatau/pomoxis. I figuerd that creating the venv folder and putting the bin folder into it would help resolve the problem but it did not.

In the config.yaml file I changed the directory for pomoxis from line 119 IN_POMOXIS: "~/git/pomoxis/venv/bin/activate" to IN_POMOXIS: "~/hflatau/git/pomoxis/venv/bin/activate". It did not resolve the problem as well.

Thanks for taking your time :)

[cjw85]

Hi @Noah603

Its not clear to me from the above what you have done to install pomoxis. Could you confirm how this was done? Katuali expects that it is installed into a virtual environment, we haven't had the development time to make it support conda environments.

[Noah603]

Thanks for your fast reply. I indeed installed pomoxis in a conda activated environment. Can i fix it, by activating the katuali virtual environment and installing it there?

[Noah603]

Okay, i am gernally confused. I tryed to reinstall pomoxis while being in the katuali environment (wich has python 3.6.9) with conda, but it says that the wrong python version is activated (python3.8) and does not finish the installation. Do i need to activate another, non conda, environment?

[cjw85]

As above, katuali expects pomoxis to be installed into a virtual environment (not a conda environment). If you are on Linux, possibly the easiest thing to do is:

cd pomoxis
make install

This will install pomoxis and the third party programs that it uses.

pomoxis supports Python >= 3.5.2 and <3.7. I don't recall why there is the restriction to <3.7; this might simply be because we haven't tested it with anything after Python 3.6.

I apologise for the inconvenience of this; we haven't had the development opportunity to support alternative methods of installation.