This project intends to be a contrib around BioMAJ3 (https://github.com/genouest/biomaj). It is a kind of swiss knife extending BioMAJ3 by adding some methods helping you to have extra information about your banks like pending bank(s), information about a bank, history of a banks (updated releases) plus some more.
- Install required packages
pip install -r requirements.txt- Now go to the biomaj-manager directory and type
python setup.py install
A configuration file is required to work. This file called manager.properties must be located
in the same location as global.properties from BioMAJ3.
It must start with a section called [MANAGER] and at least have the following properties defined to work.
[MANAGER]
root.dir=/path/to/config/directory
template.dir=%(root.dir)s/templates
news.dir=%(root.dir)s/news
production.dir=%(root.dir)s/production
plugins.dir=%(root.dir)s/plugins
usage: biomaj-manager.py [-h] [-A [Max release]] [-D] [-H] [-i] [-I] [-J] [-l]
[-L] [-N] [-n] [-P] [-R] [-s] [-X] [-U] [-v]
[-V] [--test] [-Z] [-b BANK] [-B [path to check]]
[-C [path to clean]] [-c CONFIG] [--db_type DB_TYPE]
[-E [session id]] [-o OUT] [-F OFORMAT] [-r RELEASE]
[-S [blast2|golden]] [-T TEMPLATE_DIR]
[--vdbs [blast2|golden]]
[--visibility all|public|private] [-w file:seq_num]
BioMAJ Manager adds some functionality around BioMAJ.
optional arguments:
-h, --help show this help message and exit
-A [Max release], --check_prod_release [Max release]
Look for bank having stored releases greater than [Max
release, default to 'keep.old.version']. [-b
available]
-D, --save_versions Prints info about all banks into version file.
(Requires permissions)
-H, --history Prints banks releases history. [-b] available.
-i, --info Print info about a bank. [-b REQUIRED]
-I, --remote-info Print remote info for a bank remote connection. [-b
REQUIRED]
-J, --check_links Check if the bank required symlinks to be created
(Permissions required). [-b REQUIRED]
-l, --links Just (re)create symlink, don't do any bank switch.
(Permissions required). [-b REQUIRED]
-L, --bank_formats List supported formats and index for each banks. [-b]
available.
-N, --news Create news to display at BiomajWatcher. [Default
output txt]
-n, --simulate Simulate action, don't do it really.
-P, --show_pending Show pending release(s). [-b] available
-R, --rss Create RSS feed. [-o available]
-s, --switch Switch a bank to its new version. [-b REQUIRED]
-X, --synchronize_db Synchronize database and bank data on disk
-U, --show_update If -b passed prints if bank needs to be updated.
Otherwise, prints all bank that need to be updated.
[-b and --visibility] available.
-v, --version Show version
-V, --verbose Activate verbose mode
--test Test method. [-b REQUIRED]
-Z, --clean_sessions Clean dead sessions from the database. [-b REQUIRED]
-b BANK, --bank BANK Bank name
-B [path to check], --broken_links [path to check]
Check for broken symlinks in production directory.
-C [path to clean], --clean_links [path to clean]
Remove old/broken links (Permissions required)
-c CONFIG, --config CONFIG
BioMAJ global.properties configuration file
-E [session id], --failed-process [session id]
Get failed process(es) for a bank. Session id can be
used. [-b REQUIRED]
-o OUT, --out OUT Output file
-F OFORMAT, --format OFORMAT
Output format. Supported [csv, html, json]
-S [blast2|golden], --section [blast2|golden]
Prints [blast2|golden] section(s) for a bank. [-b
REQUIRED]
-T TEMPLATE_DIR, --templates TEMPLATE_DIR
Template directory. Overwrites template_dir
--vdbs [blast2|golden]
Create virtual database HTML pages for tool. [-b
available]
--visibility all|public|private
Banks visibility. Use with --show_update.
Biomaj Manager is able to work plugins. To do so, a plugins directory is here to put your own developed
plugins. Plugins support is based on Yapsy (http://yapsy.sourceforge.net/) package. In order to plug you
plugin into Biomaj Manager, create a python package youplugin.py and a description file yourplugin.yapsy-plugin
in the plugins directory. To describe your plugin, see http://yapsy.sourceforge.net/PluginManager.html for
more information.
Once this is done, fill file manager.properties within the [PLUGINS] section as follow:
...
plugins.dir=/path/to/biomaj-manager/plugins
[PLUGINS]
plugins.list=yourplugin
[YouPlugin]
yourplugin.var=value
yourplugin.anothervar=anothervalue
...
The way the plugin system is working, it requires that the plugin class you created in yourplugin.py
must match the [YouPlugin] and must inherit from BMPlugin (biomajmanager.plugin) section to work.
For example yourplugin.py:
import os
import sys
from biomajmanager.plugins import BMPlugin
class YouPlugin(BMPlugin):
"""
My first Biomaj Manager plugin
"""
def __init__(self, ...)
You can run tests by typing nosetests
It is also possible to clone this repo into gitlab and run tests using gitlab-ci. There's a .gitlab-ci.yml available for
this as well as a Dockerfile to run gitlab tests inside Docker.
