Orthofinder installation in conflict with python3

[pavlo888]

Hi,

I am currently trying to install all the dependencies for Progenomics to run smoothly; however, I cannot successfully install Orthofinder since it comes in conflict with the already installed python=3.6.7.

How did you manage to install both Orthofinder and python=3.6.7?

Cheers, Pablo

[JDOUBLE-U]

Hi Pablo,

I used python version 3.7 and Orthofinder works like a charm. Hope it will also work for you.

Jan

[pavlo888]

Hi Jan,

I uninstalled Python 3.6.7 and installed Python 3.7 and then proceeded to try installing Orthofinder. However, it seems that Orthofinder only works with Python 2.3. This is the output I got on the terminal:

(progenomics) sam@BioInf2:~/Downloads/geneparser$ conda install orthofinder Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: \ Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. Examining python: 13%|█████▊ | 21/163 [00:00<00:00, 13124.78it/s] Comparing specs that have this dependency: 0%| | 0/2 [00:00<?, ?it/s] F- ding shortest conflict path for python[version='>=3.7,<3.8.0a0']: 50%|▌| 1/2 [00:00<00:00, 4424.37|

failed UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

• orthofinder -> python=2.7
• orthofinder -> python[version='>=2.7,<2.8.0a0']

Your python: python=3.7

If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that.

The following specifications were found to be incompatible with each other:

Package pip conflicts for: orthofinder -> python=2.7 -> pip python=3.7 -> pip Package wheel conflicts for: python=3.7 -> pip -> wheel orthofinder -> python=2.7 -> pip -> wheel Package ca-certificates conflicts for: python=3.7 -> openssl[version='>=1.0.2p,<1.0.3a'] -> ca-certificates orthofinder -> python=2.7 -> ca-certificates Package certifi conflicts for: python=3.7 -> pip -> setuptools -> certifi[version='>=2016.09'] orthofinder -> python=2.7 -> pip -> setuptools -> certifi[version='>=2016.09'] Package setuptools conflicts for: orthofinder -> python=2.7 -> pip -> setuptools python=3.7 -> pip -> setuptools

Is there anything I could do to fix this issue?

Cheers, Pablo

On Tue, Oct 8, 2019 at 1:13 PM Jan Willem Wijnands notifications@github.com wrote:

Hi Pablo,

I used python version 3.7 and Orthofinder works like a charm. Hope it will also work for you.

Jan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/SWittouck/progenomics/issues/4?email_source=notifications&email_token=AK4VSEV7QFZPFT36MPSCALLQNRTMDA5CNFSM4I4JQTWKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEATZPOI#issuecomment-539465657, or mute the thread https://github.com/notifications/unsubscribe-auth/AK4VSET3USRCFCGBINWQPGDQNRTMDANCNFSM4I4JQTWA .

[JDOUBLE-U]

You can try: conda install -c bioconda orthofinder instead of conda install orthofinder Hope that this works.

[SWittouck]

Hi Pablo,

My apologies for the late reply, it seems that my notifications were not turned on for this repository.

Have you been able to install OrthoFinder in the meantime? Otherwise, you can try to follow these instructions; they might circumvent the problem that you are experiencing with conda.

Let me know if it still doesn't work.

Best regards, Stijn

[pavlo888]

Hi Sander,

I have tried installing but alas I have no success

This is the log of what I get when I try to install it

Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: | Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. Examining python: 13%|█████▋ | 21/165 [00:00<00:00, 30257.78it/s] Comparing specs that have this dependency: 0%| | 0/2 [00:00<?, ?it/s] Finding shortest conflict path for python[version='>=3.7,<3.8.0a0']: 50%|▌| 1/2 [00:00<00:00, 12633.4- \ failed UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

• orthofinder -> python=2.7
• orthofinder -> python[version='<3|>=2.7,<2.8.0a0']

Your python: python=3.7

If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that.

The following specifications were found to be incompatible with each other:

Package pip conflicts for: orthofinder -> python=2.7 -> pip python=3.7 -> pip Package wheel conflicts for: python=3.7 -> pip -> wheel orthofinder -> python=2.7 -> pip -> wheel Package ca-certificates conflicts for: python=3.7 -> openssl[version='>=1.0.2p,<1.0.3a'] -> ca-certificates orthofinder -> python=2.7 -> ca-certificates Package certifi conflicts for: python=3.7 -> pip -> setuptools -> certifi[version='>=2016.09|>=2016.9.26'] orthofinder -> python=2.7 -> pip -> setuptools -> certifi[version='>=2016.09|>=2016.9.26'] Package setuptools conflicts for: orthofinder -> python=2.7 -> pip -> setuptools python=3.7 -> pip -> setuptools

Should I downgrade my python? But then there will be other incompatibilities with other packages I have installed in the same environment.

cheers, Pablo

On Tue, Oct 15, 2019 at 10:18 AM Stijn Wittouck notifications@github.com wrote:

Hi Pablo,

My apologies for the late reply, it seems that my notifications were not turned on for this repository.

Have you been able to install OrthoFinder in the meantime? Otherwise, you can try to follow these instructions https://github.com/davidemms/OrthoFinder#installing-orthofinder; they might circumvent the problem that you are experiencing with conda.

Let me know if it still doesn't work.

Best regards, Stijn

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/SWittouck/progenomics/issues/4?email_source=notifications&email_token=AK4VSEV57ZTF6JJPZ4XD7TDQOV4GRA5CNFSM4I4JQTWKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBH3ZCY#issuecomment-542096523, or unsubscribe https://github.com/notifications/unsubscribe-auth/AK4VSERLRMOULGO52JYQAHLQOV4GRANCNFSM4I4JQTWA .

[SWittouck]

Hi Pablo,

Your issue seems like a rather complicated one to solve. As an alternative, you could try the following:

1) Download OrthoFinder manually from here and untar it by running tar -xzf OrthoFinder.tar.gz. 2) Before you run progenomics, make sure that the command orthofinder refers to the right executable by running export progenomics=OrthoFinder-2.3.7/orthofinder. 3) Test progenomics again.

I hope this helps. If not, let me know.

Best, Stijn

[JessicaBrown11]

Hello, Pablo, I have met the same question with you before. But now I solve the problem. https://github.com/davidemms/OrthoFinder/releases/tag/2.3.8 Remember to download the third one. 1.tar the file tar -xzf OrthoFinder-2.3.8.tar.gz 2.enter into the file cd OrthoFinder-2.3.8 3.install python setup.py install

And then you can use orthofinder, hope everything is fine.