[BioTools] FTP upload to Galaxy using ProFTPD and MySQL Backend on CentOS7

1. Install Galaxy

# groupadd galaxy -g 500

# useradd galaxy -u 500 -g 500

# yum -y install mercurial

# su - galaxy

  $ git clone -b release_17.09 https://github.com/galaxyproject/galaxy.git

$ hg clone https://bitbucket.org/galaxy/galaxy-central

$ cd galaxy-central/config

$ cp galaxy.ini.sample galaxy.ini

$ vi galaxy.ini

[server:main]

#port = 8080

port = 9090

#host = 127.0.0.1

host = 0.0.0.0

[app:main]

use_pbkdf2 = False

#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE

database_connection = mysql://galaxyftp:galaxy123@localhost/galaxyprod?unix_socket=/var/lib/mysql/mysql.sock

#debug = False

debug = False

#use_interactive = True

use_interactive = False

admin_users = isbyeon@kribb.re.kr

#ftp_upload_dir = None

ftp_upload_dir = /home/galaxy/galaxy-central/galaxy-ftp-upload

#ftp_upload_site = None

ftp_upload_site = localhost:21

$ mkdir -p /home/galaxy/galaxy-central/galaxy-ftp-upload

$ exit

2. Install MariaDB

# yum -y install epel-release

# yum -y install mariadb-server mariadb-devel python-devel

# systemctl start mariadb

# systemctl enable mariadb

# mysql_secure_installation

# mysql -u root -p

MariaDB [mysql]> use mysql;

MariaDB [mysql]> insert into mysql.user(User,Host,Password) VALUES('galaxyftp', 'localhost', PASSWORD('galaxy123'));

MariaDB [mysql]> flush privileges;

MariaDB [mysql]> CREATE DATABASE galaxyprod;

MariaDB [mysql]> GRANT ALL PRIVILEGES ON galaxyprod.* to galaxyftp@localhost;

MariaDB [mysql]> flush privileges;

MariaDB [mysql]> exit

3. Install Proftpd

# yum -y install proftpd proftpd-mysql

# cp /etc/proftpd.conf /etc/proftpd.conf.BAK

# vi /etc/proftpd.conf

ServerName                      "Galaxy FTP File Upload - KOBIC"

AuthOrder                          mod_sql.c mod_auth_unix.c

LoadModule                      mod_sql.c

LoadModule                      mod_sql_passwd.c

LoadModule                      mod_sql_mysql.c

User                                   galaxy

Group                                galaxy

<Global>

  CreateHome                    on 775 dirmode 700

~~~

</Global>

~~~

~~~

AuthPAM                           off

SQLPasswordEngine        on

SQLPasswordEncoding    hex

SQLEngine                        on

SQLLogFile                       /var/log/proftpd/proftpd.log

SQLBackend                    mysql

SQLConnectInfo              galaxyprod@localhost galaxyftp galaxy123

SQLAuthTypes                 SHA1

SQLAuthenticate             users

SQLDefaultHomedir        /home/galaxy/galaxy/galaxy-ftp-upload

SQLMinID                       500

SQLUserInfo                   custom:/LookupGalaxyUser

SQLNamedQuery           LookupGalaxyUser SELECT "email,password,500,500,'/home/galaxy/galaxy/galaxy-ftp-upload/%U','/bin/bash' FROM galaxy_user WHERE email='%U'"

4. Start Galaxy

# su - galaxy

$ cd galaxy-central

$ sh run.sh

5. Galaxy 웹페이지에서 사용자 가입 후 데이터베이스에서 확인

# mysql -ugalaxyftp -p galaxyprod

MariaDB [galaxyprod]> select email from galaxy_user where email='isbyeon@kribb.re.kr';

+---------------------+

| email               |

+---------------------+

| isbyeon@kribb.re.kr |

+---------------------+

6. Start Proftpd

# systemctl start proftpd.service

# systemctl enable proftpd.service

7. Check...

# ftp localhost

Trying ::1...

Connected to localhost (::1).

220 FTP Server ready.

Name (localhost:root): isbyeon@kribb.re.kr

331 Password required for isbyeon@kribb.re.kr

Password:

230 User isbyeon@kribb.re.kr logged in

Remote system type is UNIX.

Using binary mode to transfer files.

ftp> mkdir Data

257 "/Data" - Directory successfully created

ftp> ls

229 Entering Extended Passive Mode (|||3709|)

150 Opening ASCII mode data connection for file list

drwxr-xr-x   2 isbyeon@kribb.re.kr galaxy          6 Jan 16 01:21 Data

226 Transfer complete

#ls -l /home/galaxy/galaxy-central/galaxy-ftp-upload/isbyeon\@kribb.re.kr/

total 0

drwxr-xr-x 2 galaxy galaxy 6 Jan 16 10:21 Data

8. Step by Step