# Troubleshooting GenIE-Sys can easily be installed without an effort. Unfortunately, there is always space for problems due to multiple server setups and PHP versions. In this section, we try to answer the most frequent issues in order to install GenIE-Sys as effortless as possible. Please send us an email if you still get trouble with installation or updates: `contact@geniesys.org` ### Running from Command Line If you want to use PHP’s built-in server (**not recommended**), just use the following lines to install GenIE-Sys. This is only for the initial test installation, in order to make a fully functional website you have to install Webserver packages such as MAMP or LAMP. ``` git clone --recursive https://github.com/irusri/geniesys.git cd geniesys php -S localhost:3000 ``` You should now be able to access GenIE-Sys at: `http://localhost:3000` in your browser. ### Sub-folder permissions The Webserver runs in a different group than your user account on most servers. Following subfolder permissions will necessary to grant write access from GenIE-Sys.: ``` chgrp -R www-data geniesys chmod -R 775 geniesys/genie_files ``` Please make sure that the root folder is also readable by the webserver. ### Broken subpages Whenever you have problems(can not open or a server error) with subpages, you can try the following steps. * Make sure that the .htaccess file is present inside GenIE-Sys folder. * mod\_rewrite should be enabled on your server. * You need to check the .htaccess. You can test this by adding some extra characters into your .htaccess. If this cause an “Internal Server Error”, the file gets loaded. Otherwise, you need to enable AllowOverride all in your Web server configuration file. An example of `GenIE-Sys/.htaccess` the file is shown below. ``` RedirectMatch 403 ^.*/genie_files/ ErrorDocument 403   RewriteEngine on Options -Indexes ServerSignature Off RewriteCond %{REQUEST_FILENAME} !-f RewriteCond %{REQUEST_FILENAME} !-d RewriteCond $1#%{REQUEST_URI} ([^#]*)#(.*)\1$ RewriteRule ^([^\.]+)$ %2?page=$1 [QSA,L] ErrorDocument 404 /notfound.html ``` Please make sure that you are using PHP 5.4 or higher. ### Example input files `head input/example.gff3` ``` Potra000001 leafV2 gene 9066 10255 . - . ID=Potra000001g00001;Name=Potra000001g00001;potri=Potri.004G180000,Potri.004G180200 Potra000001 leafV2 mRNA 9066 10255 . - . ID=Potra000001g00001.1;Parent=Potra000001g00001;Name=Potra000001g00001;cdsMD5=71c5f03f2dd2ad2e0e00b15ebe21b14c;primary=TRUE Potra000001 leafV2 three_prime_UTR 9066 9291 . - . ID=Potra000001g00001.1.3pUTR1;Parent=Potra000001g00001.1;Name=Potra000001g00001.1 Potra000001 leafV2 exon 9066 9845 . - . ID=Potra000001g00001.1.exon2;Parent=Potra000001g00001.1;Name=Potra000001g00001.1 Potra000001 leafV2 CDS 9292 9845 . - 2 ID=Potra000001g00001.1.cds2;Parent=Potra000001g00001.1;Name=Potra000001g00001.1 Potra000001 leafV2 CDS 10113 10236 . - 0 ID=Potra000001g00001.1.cds1;Parent=Potra000001g00001.1;Name=Potra000001g00001.1 Potra000001 leafV2 exon 10113 10255 . - . ID=Potra000001g00001.1.exon1;Parent=Potra000001g00001.1;Name=Potra000001g00001.1 Potra000001 leafV2 five_prime_UTR 10237 10255 . - . ID=Potra000001g00001.1.5pUTR1;Parent=Potra000001g00001.1;Name=Potra000001g00001.1 Potra000001 leafV2 gene 13567 14931 . + . ID=Potra000001g00002;Name=Potra000001g00002;potri=Potri.004G179800,Potri.004G179900,Potri.004G180100 Potra000001 leafV2 mRNA 13567 14931 . + . ID=Potra000001g00002.1;Parent=Potra000001g00002;Name=Potra000001g00002;cdsMD5=df49ed7856591c4a62d602fef61c7e37;primary=TRUE ``` `head annotation_file.txt` ``` Potra000001g00001.1 Germin-like protein subfamily 1 member Potra000001g00002.1 Germin-like protein Potra000002g00003.1 uncharacterized protein LOC105113244 Potra000002g35060.1 Pyruvate, phosphate dikinase regulatory Potra000002g00005.3 Gibberellin 2-beta-dioxygenase Potra000002g00005.2 Gibberellin 2-beta-dioxygenase Potra000002g00005.1 Gibberellin 2-beta-dioxygenase Potra000002g00005.5 Gibberellin 2-beta-dioxygenase Potra000002g00005.4 Gibberellin 2-beta-dioxygenase Potra000002g00006.5 DnaJ homolog subfamily ``` ### Updates **Manual updates** GenIE-Sys can be updated manually using the latest ZIP file from [GitHub](https://github.com/irusri/geniesys/archive/master.zip). Please backup your older version of `geniesys/plugins/settings.php` and `geniesys/genie_files` before you do the latest update. First, unzip the genie.zip file from your download folder and move into the Web Server server. Finally copy the `geniesys/plugins/settings.php` and `geniesys/genie_files` into the latest version of GenIE-Sys. **Updates using Git** Here is the easy way to update GenIE-Sys using git submodules: ``` cd geniesys git checkout master git pull git submodule foreach --recursive git checkout master git submodule foreach --recursive git pull ``` ### Browse extentions There are some browser extentions which can cause problems to the GenIE-Sys and plugins. We suggest you to test the GenIE-Sys with private mode browser (incognito mode) without any extentions or plugins installed. ### **Enable read/write for MySQL installed via MAMP (on Mac):** 1. open "MAMP" use spotlight 2. click "Stop Servers" 3. edit \~/.my.cnf (using vi or your favourite editor) and add the following lines: $ vi \~/.my.cnf > ``` > [mysqld_safe] > [mysqld] > secure_file_priv="/Users/username/" > ``` 1. click "Start Servers" (in MAMP window) ### More problems? Please contact us:`contact@geniecms.org` --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://geniesys.gitbook.io/geniesys/for-administrators/troubleshooting.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.