config.py template, and host on dreamhost.com

[jielab]

Hi, there:

The installation guide for pheweb is TOO simple. There is nothing for me to "git clone"? I only need to run "pip3 install pheweb" and then create a directory and write a config.py file and throw a GWAS file there, and then everything will run magically? Is there a template config.py file that I could use?

Also, I have been using dreamhost.com for unlimited hosting. Is there a guide on how to run pheweb from 3rd servers such as dreamhost.com? I think I would not be able to run "pheweb serve --open" from such a 3rd party server. I would deeply appreciate if someone coudl share some experience on this.

Thank you & best regards, Jie

[pjvandehaar]

You’re right, that’s a great point.

1. I think I’ll add a command pheweb init which makes config.py with some comments about settings you might want. What do you think?

2. Maybe I’ll add a sample directory to the repo that’s easy to run. There’s already something like that in the test directory but would it be helpful if I had a simple folder with a config.py and input data and a simple shell script to run everything?

3. The README has instructions for how to serve pheweb from a VPS like Dreamhost here: https://github.com/statgen/pheweb#6-serve-the-website

On Sat, Aug 14, 2021 at 06:31 Jie Huang @.***> wrote:

Hi, there:

The installation guide for pheweb is TOO simple. There is nothing for me to "git clone"? I only need to run "pip3 install pheweb" and then create a directory and write a config.py file and throw a GWAS file there, and then everything will run magically? Is there a template config.py file that I could use?

Also, I have been using dreamhost.com for unlimited hosting. Is there a guide on how to run pheweb from 3rd servers such as dreamhost.com? I think I would not be able to run "pheweb serve --open" from such a 3rd party server. I would deeply appreciate if someone coudl share some experience on this.

Thank you & best regards, Jie

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/statgen/pheweb/issues/168, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGSPCM23GD4VOAF6BDNS7TT4ZV4NANCNFSM5CFDHMSA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email .

[pjvandehaar]

I'm at a computer now and re-reading your post. What's the step that you're unsure about on Dreamhost? You have a real VPS or cloud server where you can run terminal commands, right? Or are you on a static-file-only hosting plan? You need to be on a server where you can pip3 install pheweb.

[jielab]

Dear Peter:

Thank you very much! It would be really helpful if I could use something like "git clone pheweb" to get all necessary files including config.py and an example.sh script to run an example.

I think this is quite standard for the Github community.

Best regards, Jie

[jielab]

Dear Peter:

I now created the confiy.py and two testing GWAS. However, please see the screenshot below, there is error.

Can you please let me know what is happening and how to fix this?

Best regadrs, Jie

[pjvandehaar]

What’s in “parse-failures.txt”?

2. Pheweb needs columns “chrom” and “pos”

On Sun, Aug 15, 2021 at 13:23 Jie Huang @.***> wrote:

Dear Peter:

I now created the confiy.py and two testing GWAS. However, please see the screenshot below, there is error.

Can you please let me know what is happening and how to fix this?

Best regadrs, Jie

[image: 11] https://user-images.githubusercontent.com/26947455/129491694-66834a68-b2b9-4287-a396-fe898b064f0b.png

— You are receiving this because you commented.

Reply to this email directly, view it on GitHub https://github.com/statgen/pheweb/issues/168#issuecomment-899105143, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGSPCIC6HOGABYSNRSNUDLT5AO5LANCNFSM5CFDHMSA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email .

[jielab]

Dear Peter:

My GWAS file has CHR and POS. I just checked the error message and found that it is due to some POS is not sorted. I fixed it and now it works.

So, I have no issue with installing PheWeb now. I will open a new ticket to ask some other questions.

Thank you very much & Best regards, Jie

[pjvandehaar]

Great, I'm glad this worked!