Testing conda installation

gputzel commented 6 years ago

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 commented 6 years ago

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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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 ...

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bhillmann commented 3 years ago

@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 commented 3 years ago

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

GabeAl commented 3 years ago

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

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 https://github.com/knights-lab/SHOGUN/issues/19#issuecomment-841511546, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5NOBTC7JMVKCIXQ6MRYFLTNWIMBANCNFSM4FDHCR2A .

mortonjt commented 3 years ago

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

knights-lab / SHOGUN

Testing conda installation #19