@@ -16,22 +16,22 @@ Alternatively, you can install it manually:
cd dgenies
pip3 install -r requirements.txt
python3 setup.py install
### Upgrade
#### Standalone mode
pip3 install dgenies --upgrade
#### Webserver mode
dgenies clear -c
pip3 install dgenies --upgrade
Then, you need to restart your webserver.
### Requirements
D-Genies requires python >= 3.5 to run.
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@@ -52,32 +52,32 @@ Some python modules are required (will be automatically installed by the command
intervaltree==2.1.*
argparse==1.4
Markdown==2.6.*
Additional modules for webserver mode:
Flask-Mail==0.9.*
peewee==2.10.2
python-crontab==2.2.*
And if you use a cluster (webserver mode):
drmaa==0.7.*
In webserver mode, you must install `mysqlclient` python module (will not be installed automatically) if you use mysql as RDBM.
Windows
-------
We provide an installer to install D-Genies. You can download it [here](https://github.com/genotoul-bioinfo/dgenies/releases/download/v1.0.1/dgenies-1.0.1_setup.exe).
We provide an installer to install D-Genies. You can download it [here](https://github.com/genotoul-bioinfo/dgenies/releases/download/v1.0.1/dgenies-1.0.1_setup.exe).
All requirements are present inside the package, so you don't have to do anything else.
### System requirements
You need Windows 7 or newer, 64 bits architecture.
How to start
-------------
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@@ -90,10 +90,10 @@ simultaneously or if you run it on a server, you must run it in webserver mode.
Unix: start with the command below:
dgenies run
Optional arguments:
`-p <port>` run in a specified port (default: 5000)
`-p <port>` run in a specified port (default: 5000)
`--no-browser` don't start the browser automatically
Windows: just click on the launcher in the desktop or into the install folder.
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@@ -104,7 +104,7 @@ Windows: just click on the launcher in the desktop or into the install folder.
#### Recommended method
Flask webserver (which is used in standalone mode) is not recommended in production servers.
Flask webserver (which is used in standalone mode) is not recommended in production servers.
So, we recommend using the WSGY module of Apache (or µWSGI + nginx, not documented here).
Once dgenies is installed, you just need to use the `/var/www/dgenies.wsgi` file into your apache
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@@ -117,7 +117,7 @@ Here is an example of configuration file for apache:
With `<dir>`: the folder into save the scripts (must be accessible by cluster nodes).
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@@ -178,7 +178,7 @@ To change this file, please copy it into `application.properties.local` (at the
### Global
Main parameters are stored into this section:
Main parameters are stored into this section:
*`config_dir`: where configuration file will be stored.
*`upload_folder`: where uploaded files will be stored.
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@@ -299,17 +299,17 @@ The `dgenies` command can be used to do some maintenance staff.
**Clear all jobs:**
dgenies clear -j [--max-age <age>]
`--max-age` (opt): set the max age of jobs to delete (default: 0, for all)
**Clear all log:**
dgenies clear -l
**Clear crons (webserver mode):**
dgenies clear -c
Gallery
-------
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@@ -318,22 +318,22 @@ Note: gallery is only available in webserver mode.
To add a job to the gallery, copy illustrating picture file into the *gallery* folder inside the data folder (*~/.dgenies/data/gallery* as default, create it if not exists). Then use the *dgenies* command:
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