Testing conda installation

[gputzel]

The README instructions for testing the installation say:

change directory into the root folder of the repository

But the installation instructions don't indicate any repository directory. Perhaps add something about where to find this directory for a conda installation?

[bhillmann]

Yeah, those instructions are clearly wrong. For testing the installation with conda I will have to think more about it. The shogun library does exist in your conda environment as a folder, but it isn't easy to find.

[ReneKat]

Hello!
I am eager to use shogun on my shallow shotgun metagenomics dataset. Currently, I am troubleshooting the
python -m unittest discover shogun

I have installed shogun via conda and cloned the git repository. I cd into the repository to run this test and I receive the following error:

FAIL: test_burst_pipeline (tests.test_pipeline.TestAligner)

Traceback (most recent call last):
File "/mnt/c/Users/Student/github/SHOGUN/shogun/tests/test_pipeline.py", line 93, in test_burst_pipeline
self.assertTrue(df_infile.shape[1] == 3)
AssertionError: False is not true

Ran 52 tests in 221.048s

FAILED (failures=1)

When I run conda uninstall shogun, it uninstalls dependencies as well. So that when I install via pip the test fails because it cannot find the dependencies.

Any help would be appreciate.
Many thanks,
Rene

[mortonjt]

Can't comment on the above error, but I am noticing machine-specific installation issues.
I'm able to install shogun on my local machine without problems. But I run into issues installing it on my cluster via

conda create -n shogun -c knights-lab shogun

I get the following error

conda create -n shogun -c knights-lab shogun
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: \ 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                                                     

UnsatisfiableError: 

Not exactly sure what is going on ...

[GabeAl]

What version of python is default on the cluster? Might need to create a new environment with the python version locked in! Does it list what's unsatisfied? If not it seems like a weird glitch in the default env's package config But I'm no conda expert so I'll let Ben weigh in!

…

On Fri, May 14, 2021, 3:03 PM Jamie Morton ***@***.***> wrote: Can't comment on the above error, but I am noticing machine-specific installation issues. I'm able to install shogun on my local machine without problems. But I run into issues installing it on my cluster via conda create -n shogun -c knights-lab shogun I get the following error conda create -n shogun -c knights-lab shogun Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: \ Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed UnsatisfiableError: Not exactly sure what is going on ... — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#19 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB5NOBQ67Q2R3QWAVWHIRV3TNVXYVANCNFSM4FDHCR2A> .

[bhillmann]

@mortonjt You are probably experiencing this issue because you aren't including the bioconda channel in your installation command.

conda install -c knights-lab -c bioconda -conda-forge shogun

[mortonjt]

yes, conda install -c knights-lab -c bioconda -c conda-forge shogun fixed this issue. Thanks!

[GabeAl]

Thanks Ben!! At least I was right about conda dependencies (but wrong about the python version thing!). Wonder if there's a way to implicitly add those repo dependencies into the recipe? Glad it works for you now, Jamie! I'm curious how/why the home installation worked with the minimal commandline. Maybe your repofile had those repos in it already? Cheerio, Gabe

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On Fri, May 14, 2021 at 5:25 PM Jamie Morton ***@***.***> wrote: yes, conda install -c knights-lab -c bioconda -c conda-forge shogun fixed this issue. Thanks! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#19 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB5NOBTC7JMVKCIXQ6MRYFLTNWIMBANCNFSM4FDHCR2A> .

[mortonjt]

I already had conda-forge in my .condarc so that may have been the reason.