@@ -43,23 +43,29 @@ install your own from [their repository](https://github.com/lh3/minimap2).
Some python modules are required (will be automatically installed by the commands above):
flask==0.12.*
Flask-Mail==0.9.*
Jinja2==2.9.*
peewee==2.10.2
docopt==0.6.*
numpy
wget==3.2
requests==2.18.*
biopython==1.70
python-crontab==2.2.*
psutil==5.4.*
tendo==0.2.*
matplotlib==2.1.*
drmaa==0.7.*
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.
How to start
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@@ -82,6 +88,8 @@ Optional arguments:
### Webserver mode
*Note: this mode is only available for Unix systems and will NOT work on MS Windows.*
#### Recommended method
Flask webserver (which is used in standalone mode) is not recommended in production servers.
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@@ -285,6 +293,8 @@ The `dgenies` command can be used to do some maintenance staff.
Gallery
-------
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: