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 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@geniecms.org

Running from Command Line¶

If you want to use PHP’s built-in server (not recommended), just use following lines to install GenIE-Sys. This is only for the initial test installation, in order to make a full functional website you have to install Webbserver package 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.

Subfolder permissions¶

Web server 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 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 file shown below.

RedirectMatch 403 ^.*/genie_files/
ErrorDocument 403 &nbsp;
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 the 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 latest ZIP file from GitHub. 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 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