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alaesahbou / BuscoPhylo

BuscoPhylo : Easy Busco-based phylogenomic analysis tool
MIT License
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Script never starts #3

Open rubenluz opened 1 year ago

rubenluz commented 1 year ago

Hello, I was able to set up the server. As requested I created the database with host: localhost, and user: root. However it only created the databse busco_laravel, I nedeed to import it anyway from /opt/lampp/htdocs/BuscoPhylo/db.

Side not: the /etc/php5/cli/php.ini full location is /opt/lampp/etc/php.inifor those using xampp, these should be included in the readme page.

Now i set up everything, but it never runs, it always stays like this:

http://localhost/BuscoPhylo/item/1692667581/cyanoFinalTest image

I checked and the data is being imported correctly to /opt/lampp/htdocs/BuscoPhylo/admin/core/data/cyanoFinalTest, it seems the script is simply not running, it never starts...

Any suggestions?

after some debug try, it looks like on busco.php the problems starts on $output = shell_exec('mkdir '.$path.'/'.$data["posts"][0]['input'].'outBusco'); this never happens

So the problem was the permissions, moving from /opt/ to /home/ solved one part. The script still do not run. however if I run it myself after submitting the data it starts. just: ~/htdocs/BuscoPhylo/admin/core$ php busco.php

Anything i can do to put it running directly from the gui?

alaesahbou commented 12 months ago

Thank you for reaching out with the details of the issue you're facing. It's great that you were able to set up the server and create the database.

Regarding the issue you're experiencing, it seems that the script might not be running due to permission issues. You mentioned that you moved the directory from /opt/ to /home/ and that solved part of the problem. However, it still doesn't run directly from the GUI.

I'd like to ensure that you've followed the setup instructions correctly. Please double-check if you've completed the following steps:

  1. Give BuscoPhylo root privileges:

    sudo chown -R daemon /BuscoPhylo_directory
sudo visudo

    Then insert the following lines after the User privilege specification comment:

    [USER] ALL=(ALL:ALL) ALL
[USER] ALL=(ALL) NOPASSWD: ALL

    Please replace [USER] with the actual username (daemon for xampp or ampps for ampps).

  2. Regarding the PHP configuration file: The full location for the php.ini file is /opt/lampp/etc/php.ini for those using xampp. Thank you for bringing this to our attention, and I'll make sure to include this in the README for future reference.

  3. Ensure that all the required dependencies are installed:

    • Python3
    • Busco
    • Biopython
    • MUSCLE
    • trimAl
    • IQ-TREE
    • ETE3

Additionally, please make sure that you have uploaded at least 4 genome sequence files in FASTA format as input.

If you've checked all of the above and are still facing issues, you can try running the script manually after submitting the data using the command:

~/htdocs/BuscoPhylo/admin/core$ php busco.php

If this solves the problem, it indicates there might be an issue with how the script is triggered from the GUI.

Remember, you can also use the online version at https://buscophylo.inra.org.ma/ or utilize the API.

Let me know if you have any further questions or need additional assistance.``