suyanan / vioser

VIOS repository's docker deployment version. Refer to the result on DockerHub.

VIOS

Virus Identification On Site

[TOC]

INTRODUCTION

**1.0/directory** includes some ngs softwares, supported with ubuntu16.04. *The image is too fat ,so not recommended.*；

**2.0/derectory** is through ubuntu17.10 repository list including some ngs softwares. *The image is so simple , so recommended.*；

VIOS function is to identify **virus** and confirm its classitication.
From ngs **FASTQ** data, VIOS can achieve that the viruses category 、proportion 、coverage , and so on.

method1：link(useful, not recommend)

1. set DATABASE variable in settings.py:

   DATABASES = {
       'default': {
           'ENGINE': 'django.db.backends.mysql',
           'NAME': 'vios_db',
           'HOST':'mysqler',  #mysql_container_hostname(--hostname=mysqler)
           'PORT':'3306',
           'USER':'root',
           'PASSWORD':'1234aaaa',
       }
   }
   

2. start myslq container, and appoint the hostname para same with the HOST element of DATABASE variable:

   docker run -it --hostname=mysqler --name mysql -e MYSQL_ROOT_PASSWORD=1234aaaa -e MYSQL_DATABASE=vios_db mysql:5.7
   

3. start vios container, and appoint the link para which can connect to MySQL: create image, first：

   docker image build -t suyanan/vios:1.0 . docker pull suyanan/vios:1.0

   docker container run -it --name vios --hostname vioser -v `pwd`/VIOS:/vios/VIOS -v `pwd`/database:/vios/database --link mysql:db suyanan/vios:1.0
   docker inspect -f '{{.NetworkSettings.IPAddress}}' vios
   #add IP manually, IF IP is not included int *ALLOWED_HOSTS* variable.
   ALLOWED_HOSTS = [
   u'127.0.0.1',
   u'localhost',
   u'172.17.0.3',
   ]
   

   FIANLLY, access IP:8000 in browser.

   CAUTION：

   link para is useful but not recommended in current Docker version(1.17).

method2 : network（useful, recommed）

1. generate network

   docker network create neter
   

2. start mysql container, and appoint the network

   docker run -it --hostname=mysqler --network neter --name mysql -e MYSQL_ROOT_PASSWORD=1234aaaa -e MYSQL_DATABASE=vios_db mysql:5.7
   

3. start vios container，and make its network same with that of mysql container(both network is neter)，achieve the access to MySQL create image, first：

   docker image build -t suyanan/vios:1.0 . docker pull suyanan/vios:1.0

   docker container run -it --name vios --hostname vioser --network neter -v `pwd`/VIOS:/vios/VIOS -v `pwd`/database:/vios/database suyanan/vios:1.0
   

   docker inspect mysql
   docker inspect vios
   

4. set the HOST elemen of DATABASE variable and ALLOWED_HOSTS variable in settings.py:

   DATABASES = {
       'default': {
           'ENGINE': 'django.db.backends.mysql',
           'NAME': 'vios_db',
           'HOST': ##mysql_container_ip
           'PORT':'3306',
           'USER':'root',
           'PASSWORD':'1234aaaa',
       }
   }
   ALLOWED_HOSTS = [
   u'127.0.0.1',
   u'localhost',
   #vios_container_ip
   ]
   

   CAUTION：

   • Just RESTART the vios container if you can't find sample_list or sample_se_list AFTER you upload your raw FASTQ datas.
   • start container with two commands:

     dockecontainer run -it --name vios --hostname vioser --network neter -v `pwd`/VIOS:/vios/VIOS -v `pwd`/database:/vios/database vios_pipeliner sh -c "python /vios/VIOS/manage.py migrate && python /vios/VIOS/manage.py runserver 0.0.0.0:8000"
     

   • start container with /bin/bash to test internally(cover the CMD in Dockerfile):

     dockecontainer run -it --name vios --hostname vioser --network neter -v `pwd`/VIOS:/vios/VIOS -v `pwd`/database:/vios/database vios_pipeliner /bin/bash
     

method3 : compose manages the two containers（optimal, at present）

```
docker tag suyanan/vios：1.0 vioser_pipeliner
OR:
docker-compose up  #create and start containers
docker-compose down -v   #shutdown and remove containers
```

**CAUTION**：
  - There are still problems with using compose to manage the two containers(pipelinre——same as vios, and mysql)：
    *pipeliner_1  | django.db.utils.OperationalError: (2003, "Can't connect to MySQL server on 'mysqler' (111)")*

---

CAUTION!!!：

1. local images：

   docker image save suyanan/vios:x.0 -o suyanan_vios_x.0.tar
   docker image load -i suyanan_vios_x.tar
   

2. warning messages while building Dckerfile：

   WARNING: apt does not have a stable CLI interface. Use with caution in scripts. debconf: delaying package configuration, since apt-utils is not installe

3. NO supporting window interface WITH Docker deployment SO：Force matplotlib to not use any Xwindows backend. add codes below in file config_para.py：

   import matplotlib
   matplotlib.use('Agg')
   

   The visualization results is located in corresponding directories.

4. softwares downloaded postion：

   1.0/directory : JAVA and ngs softwares is necessary，and you can download from BaiduYun;

   2.0/directory : velvet is necessary，but you need to decompress and rename with "velvet_1.2.10.tgz", and recompress it.

--- **COPY RIGHT**

201712.11

The End