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statgen / pheweb

A tool to build a website to browse hundreds or thousands of GWAS.
MIT License
154 stars 65 forks source link

"pip3 install pheweb" failed #169

Closed jielab closed 5 months ago

jielab commented 2 years ago

Dear Peter:

Please see the error message below. I tried to run "pip3 install pheweb" on a remote server, which has python2 as default (it does have python3 installed).

111

Can you please let me know how to address this issue?

Thank you & best regards, Jie

hyunminkang commented 2 years ago

If you use conda to make python3 as default, wouldn't it solve the problem?

Hyun.

On Sun, Aug 15, 2021 at 5:01 PM Jie Huang @.***> wrote:

Dear Peter:

Please see the error message below. I tried to run "pip3 install pheweb" on a remote server, which has python2 as default (it does have python3 installed).

[image: 111] https://user-images.githubusercontent.com/26947455/129492777-332ca267-194d-4923-9db8-a81b864293f7.png

Can you please let me know how to address this issue?

Thank you & best regards, Jie

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pjvandehaar commented 2 years ago

I think your screenshot missed part of the error on the right side.

jielab commented 2 years ago

Dear Hyun:

I now used "alias" to make python3 as the default. However, the error message still persists, shown as below. 11

Can you please let me know what is the cause of this error?

You said to "use conda to make python3 as default". Exactly how to do that? I thought that "conda" is not involved. We simply used "pip3 install pheweb".

Best regards, Jie

pjvandehaar commented 2 years ago

  1. What kind of machine are you running on?

  2. Please post the results of lsb_release -a and uname -a and free -m.

  3. Can you find that .so file, or get pip to leave it behind after the failure? Maybe pip3 install --no-clean pheweb? I'd like to see ls -l of that .so file.

If these results don't show anything obvious, you should just install miniconda and use that instead.

jielab commented 2 years ago

Dear Peter:

Below is the log, based on your instruction

image

Best regards, Jie

pjvandehaar commented 2 years ago

You should try to install miniconda and use that to install pheweb. There are instructions at https://github.com/statgen/pheweb/blob/master/etc/detailed-install-instructions.md#installing-on-linux-or-mac-with-miniconda3

jielab commented 2 years ago

Dear Peter:

Yes, sure. Let's ignore the above error message for now. I ask my programmer to work on the add_rsids.py python script so that it does not require the REF/ALT alleles. Instead, A1/A2, or EA/NEA, as long as there are two alleles, it should work. I will keep you posted and let you try it out once it is ready.

I am still not quite sure how "cache=" behaviors in pheweb. I think the correct syntax is "cache=" instead of "cache_dir=".

Please see the screenshot below. After I run pheweb once and it already put the huge file rsids-v154-hg19.tsv.gz into the cache directory. Why it downloads the file again when I run pheweb the second time?

image

Please let me know the right configuration to write into config.py so that I don't need to download the huge hg19.tsv.gz file again and again?

Best regards, jie