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Course_Server
README.md
add_database.yml
ansible.cfg
ansible_hosts
featuredetection.yml
ftp.yml
init.expect
msgfplus.yml
proteios-ansible.yml
swestore.yml
tandem.yml
tandem_apache.conf
update.expect

README.md

Ansible scripts for installing Proteios SE on Ubuntu 16.04 server

The scripts in this folder can be used to install the latest version of Proteios Software Environment on a fresh Ubuntu server. Note that you'll need all files in the folder. It is recommended to change the Proteios root password when you are done with the installation.

##Instructions First test ssh login to server (Ubuntu 16.04 LTS) using your certificate to check that you can access the server. Make sure that TCP ports 8080 (for http access to Proteios), and 8080 and 35000-36000 (for accessing the Proteios FTP server) are not blocked by any external firewall if you have trouble accessing the server at a later stage. Then:

  1. Edit ansible_hosts so that [proteios] points to the IP number of your new server. For local installation it should instead read localhost ansible_connection=local
  2. Edit ansible.cfg:
  • Edit inventory path so that it points to your ansible_hosts file: inventory = ...
  • Set the path to your private key file: private_key_file = .... The path is often /home/USER/.ssh/id_rsa
  • Set the remote user account to use: remote_user = .... For local installation it should be your username.
  1. Run: ansible-playbook proteios-ansible.yml
  • Note: If your installation requires password on sudo, you should add this ansible-playbook command line option at the end: --ask-become-pass. This also applies to the following steps.
  1. Check that you can log into proteios server as root (http://SERVER:8080/proteios/app) using a web browser.
  2. Run: ansible-playbook tandem.yml
  3. Run: ansible-playbook featuredetection.yml
  4. Run: ansible-playbook msgfplus.yml
  5. Log into you new proteios server (http://SERVER:8080/proteios/app) using a web browser.
  • List plugins to activate them (View->Plugins).
  • Create users

Done!

If you want to install a Proteios course server, proceed with the instructions and scripts in the Course_Server subfolder.

FTP server

If you want to start the Proteios FTP server, run ansible-playbook ftp.yml. Rerun the same script after server updates (see below) or if the FTP server has become inaccessible. The ftp server can be reached using passive FTP at port 8021.

Custom search database

If you want to add a custom database to the Proteios server:

  1. First ensure that the database fasta file contains an equal amount of decoy entries which have an r prefix. Target entries should thus not have accessions starting with r.
  2. Place the database fasta file in the same folder as the scripts.
  3. Edit add_database.yml with the fasta file name, and a short name (without whitespace) to appear in the database selection interface. For example:
database_file_name: swissprot_human_rev_20160606.fasta
database_name: sp_human_rev
  1. Run ansible-playbook add_database.yml.

Update server

If you want to update your Proteios server with the latest patches and latest version of Proteios, just rerun ansible-playbook proteios-ansible.yml anytime.