pjvandehaar
commented
3 years ago What command did you run to try to install pheweb? Did you follow the instructions in https://github.com/statgen/pheweb#1-install-pheweb ?
Closed Mohammad-Vahed closed 3 years ago
pjvandehaar
commented
3 years ago What command did you run to try to install pheweb? Did you follow the instructions in https://github.com/statgen/pheweb#1-install-pheweb ?
Mohammad-Vahed
commented
3 years ago Hi Peter,
I followed your instructions:
python3 -m pip install -U cython wheel pip setuptools python3 -m pip install pheweb pheweb --help (Note: In most cases this is equivalent to pip3 install pheweb, but if you have a bad version of pip3 on your $PATH, using python3 -m pip will avoid it.)
If you get the error Segmentation fault (core dumped), try running python3 -m pip install --no-binary=cffi,cryptography,pyopenssl pheweb instead. (more info)
If you get an error related to pysam, run python3 -m pip install -U cython; python3 -m pip install https://github.com/pysam-developers/pysam/archive/master.zip and try again.
And I tested into two different Mac systems, both had the same error!
pjvandehaar
commented
3 years ago Do you have XCode developer tools installed? Try sudo xcode-select --install.
If you scroll down a bit on that page you'll see instructions for installing with miniconda3, and those should work for you.
Mohammad-Vahed
commented
3 years ago Hi,
Thanks a lot for your contributions to the Pheweb project. It's amazing to see the results displayed on a website. I am quite new to web development. I am exploring deploying the website built locally to the public. Now I have followed all the steps in your instructions and served the Pheweb and I can access it using my own computer (PC). However, I would like to make it public and allow everyone to access it. Could you guide me on how I can deploy Pheweb App? What are you recommend to the best way to publish/deploy the Pheweb App?
Thanks!
pjvandehaar
commented
3 years ago Great, I’m glad it works for you!
What command are you using to serve the pheweb on your computer?
The README has instructions for running a pheweb on a server accessible to the internet. They’re not great and I’ll improve them sometime, so thanks for reminding me of them.
I always serve phewebs using systemd and with a reverse proxy (like apache2). If you don’t have a server already, any of the big VPS providers are good (AWS, GCE, DigitalOcean, etc). You can just rsync the directory from your computer to the server.
Mohammad-Vahed
commented
3 years ago Hi,
Thank you, I used "pheweb serve --open" to open "localhost:5000" (on Ubuntu). I would people can access Pheweb by specific domain or IP. (for the first test on our samples) Before using the AWS, we rather test in a PC as a server and get results and show them on the website. I always deploy web tools by VS, but for an installed App and using the command for a run ""pheweb serve --open"" I do know!!! Please guide me.
I appreciate you.
pjvandehaar
commented
3 years ago I can't help you get a computer with an externally-accessible IP address. Once you find or rent one, you can run pheweb the same way as on your computer.
Mohammad-Vahed
commented
3 years ago Hi, Sorry, I mean how can set up Pheweb to access in public domain? for example as your web site: https://pheweb.org/UKB-TOPMed/ Or: http://67.205.180.40:443/
pjvandehaar
commented
3 years ago Have you never worked on a server before? It's a great skill to learn and I hope you enjoy it. A server is just a computer with an unchanging IP address that can be reached from the internet. It sounds like you don't have one, so you'll need to ask a sysadmin at your school/job or rent a VPS.
It's probably easier to experiment using python3 -m http.server 5000 or something like that instead of pheweb.
If you want to rent a VPS, you can follow this tutorial: https://www.digitalocean.com/community/tutorials/how-to-set-up-an-ubuntu-20-04-server-on-a-digitalocean-droplet . After that you can just try things or follow https://www.digitalocean.com/community/tutorials/how-to-serve-flask-applications-with-gunicorn-and-nginx-on-ubuntu-20-04 . And google a lot!
Please include:
pheweb -h. If you're not on the latest version, consider upgrading withpip3 install --upgradeand trying again.Hello. I several times tried to install the pheweb to the different desktops but every time got the same error, Could you help me to solve it? Thank you.
ERROR: Command errored out with exit status 1: command: /Library/Developer/CommandLineTools/usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/fs/05kbflqd1xz6pc5fqj7t7z840000gn/T/pip-install-d8_f0gk5/pysam_30e290a207234bf1a494c0a8d71ed110/setup.py'"'"'; file='"'"'/private/var/folders/fs/05kbflqd1xz6pc5fqj7t7z840000gn/T/pip-install-d8_f0gk5/pysam_30e290a207234bf1a494c0a8d71ed110/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/fs/05kbflqd1xz6pc5fqj7t7z840000gn/T/pip-record-vtlo95bi/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /Users/mohammad/Library/Python/3.8/include/python3.8/pysam cwd: /private/var/folders/fs/05kbflqd1xz6pc5fqj7t7z840000gn/T/pip-install-d8_f0gk5/pysam_30e290a207234bf1a494c0a8d71ed110/ Complete output (279 lines):
pysam: cython is available - using cythonize if necessary
ERROR: Command errored out with exit status 1: /Library/Developer/CommandLineTools/usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/fs/05kbflqd1xz6pc5fqj7t7z840000gn/T/pip-install-d8_f0gk5/pysam_30e290a207234bf1a494c0a8d71ed110/setup.py'"'"'; file='"'"'/private/var/folders/fs/05kbflqd1xz6pc5fqj7t7z840000gn/T/pip-install-d8_f0gk5/pysam_30e290a207234bf1a494c0a8d71ed110/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/fs/05kbflqd1xz6pc5fqj7t7z840000gn/T/pip-record-vtlo95bi/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /Users/mohammad/Library/Python/3.8/include/python3.8/pysam Check the logs for full command output.