- Go to the Import tab
- Press the Prepare Download
- Wait while the file builds (can take several minutes if a lot of data has been uploaded)
- When the button says Download File, click the button and a FASTA file with the uploaded data will be downloaded to your local computer
- Keep this file safe. You will be able to use it to upload the data to your new installation
- Go to the root directory of the installation. It is usually something like
abYsis Distribution
This page allows you to download and install abYis and its data files. You may also wish to visit the abYsis Installation Manual page
abYsys V4.0.6 - Release: 20230616 (June 2023)
Please follow these instructions precisely.
Previous Installation
The new installation will build a brand new database. This means that any sequences added to an existing database using the Import facility will not be ported to the new installation. If you wish to transfer over any imported sequences follow the steps below.
If you are installing the new version of abYsis on to the same server as your existing installation then please follow these steps to deactivate it.
cd /home/abysis/abysis_x.y.z
cd database_server sudo -u abysis ./stop.sh
sudo mv /var/www/html/abysis /var/www/html/abysis.orig
Your existing abYsis installation will still be intact, but switched off.
Setup
1. Log in to your server as root user and go to the root home directory
cd
2. Download the Installation package from our distribution site (InstallScripts.tar), substituting USERNAME and PASSWORD for the username and password you were provided for downloading abYsis.
curl -O http://USERNAME:PASSWORD@download.abysis.org/distribution/InstallScripts.tar
3. Unpack the installation package to your home directory.
tar xf InstallScripts.tar
4. Enter the installation directory.
cd InstallScripts
Configure
5. Edit the configuration file (abysis.config) to set options appropriate to your installation. You will need to either
- Set DOWNLOAD_USERNAME and DOWNLOAD_PASSWORD with your abYsis username and password for downloading the abYsis code and database.
- Download the abYsis code (abysis.tar.bz2) and database (abysis_data.tar.bz2) independently to the server from http://USERNAME:PASSWORD@download.abysis.org/distribution
- Set SOFTWARE_DOWNLOAD and DATA_DOWNLOAD with the full path to the files on the server.
For a normal install, no other changes should be needed in the abysis.config file. For more information please refer to the installation guides that can be found in the InstallScripts directory.
Installation
6. Start the install. This is run in the background in case your connection to your server times out.
./install_abysis.sh &
7. The install process can take up to 2 hours and the screen may appear inactive at times.
During the installation the server will be checked for compatibility, required operating system packages will be updated or installed. The software will then be downloaded and installed followed by the database files. Third party software such as PostgreSQL will be installed and will generate a lot of messages to the screen. The database will then be populated and finally, the web server will be configured.
8. During the installation a directory for logs and backups will be created.
/root/InstallScripts/install_abysis_4.x.x
This directory will contain the logs from the installation and backups of files that may have been changed on your system such as:
- abysis_install.log – a log file of the installation process
- httpd.orig – the original /etc/httpd/conf/httpd.conf (if modified)
- iptables.orig – the original /etc/sysconfig/iptables (if modified)
9. On completion, you will be given the machine's MAC address that will look something like this
01:23:45:67:89:AB
To obtain a licence key to activate your installation (instructions), please send this MAC address to licence@abysis.org. Your licence will be sent to you with instructions on how to activate your installation.
When you have received a licence key activate it on the Licence & Info page of your abYsis installation.
Tools > Licence & Info10. You will also be presented with the public and private/local URL of your server and whether your website is accessible or not. Example below.
Public visibility of the installation Public web site : http://nnn.nnn.nnn.nnn/abysis/ is visible Local network location of the installation Private web site : http://nnn.nnn.nnn.nnn/abysis/ is up
If you have any questions or concerns please contact us at licence@abysis.org. If the installation fails it is best to email us and include a copy of the abysis_install.log (Section 7 above) so that we can help you through the process.
Obtaining a licence file
From V2.2, abYsis provides a licensing system to remind you to
renew your licence. Please read the
Changes in this version...
- 20230616 V4.0.6Improved germline gap display and improved database status detection.
- 20230306 V4.0.5 Improved Excel export and sequence import process. Allowed for insert double-letter numbering, germline organism menu and improved error-handling.
- 20230130 V4.0.4 Fixed licence page bug.
- 20221202 V4.0.3 Fixed some install and licence page bugs.
- 20220927 V4.0.2 Fixed Blast Bomb and colour by Frequency/None bugs.
- 20220907 V4.0.1 Improvements to the install process. Bugfixing Excel output.
- 20220803 V4.0.0 This version introduces a brand new UI, paired analysis, triage filtering, full global settings, database schema change, germline matching on annotation, added licence/info page and masses of user experience/code improvements
- 20201109 V3.6.0 Removed unused colours. Improvements to Excel and CSV downloads. 'Add humanized sub-group annotation' no longer the default. New Germline data table. New button that annotates a modified humanized sequence.
- 20200702 V3.5.2 Using latest version of abnum. Improved reliability for low resource servers and improved installing for hardened OS releases.
- 20200610 V3.5.1 Loading of the Annotation tabs have been speeded up and JSAV data table columns are controlled with drop- down menus.
- 20200325 V3.5.0 Improved Blast interface using multiple sequence alignment display. Improved germline alignment. View different numbering schemes simultaneously. Standardisation of data tables over Search, Annotate and Blast.
- 20200213 V3.4.3 Refined germline alignment gap penalty, stopped browser caching, added NGlyc PTMS and renamed MET_OXIDIDATION_EXTRA PTMS as MET_OXIDIDATION.
- 20191005 V3.4.2 Bugfix to remove warnings from web server log files and a Red Hat installation fix.
- 20190905 V3.4.1 This release provides faster searches, user interface improvements, simpler installation, Aho and IMGT numbering, support for scFvs, and the upload now has delete and backup options.
- 20190120 V3.1.2 This release provides a number of enhancements to the install procedure, support for CentOS7, fixes for perl 5.26, replacement of most HTML forms with CGI scripts, update to font awesome 5.3.1, improvements to the data uploads and bug fixes for the Humanize tab.
- 20180417 V3.1 This is the first public release of the V3.x series. This provides a completely new interface, Additional PTM annotations and parallelised loading of FASTA sequences.
- 20170904 V2.7.4.6 Primarily a bug-fix release with some small documentation enhancements and additional PTM annotations. Updated quick install manual and example FASTA input; Update to warnings when parsing of EMBL file; Fixes bug when running perl 5.10.1; Fix for upload of filenames with spaces; Added additional PTM annotations
- 20170712 V2.7.4.5 Internal release
- 20170608 V2.7.4.4 Internal release
- 20170522 V2.7.4.3 Internal release
- 20170101 V2.7.4.2 Skipped
- 20160818 V2.7.4.1 The help buttons have been overhauled with a little more information next to some search boxes; Some visual improvements; CSV download buttons for distributions; Documentation improvements.
- 20160613 V2.7.3.2 Some internal fixes for Perl version portability. Added new frontpage image. Updated to JSAV V1.10 for sequence alignment display. Bug fix when changing numbering scheme in numbering and regions tab.
- 20160328 V2.7.2 Autogenerates an online manual; Fixed problem with installation script on recent Mac OS/X versions; Some fixes to highlighting CDRs when some sequences not numbered.
- 20160229 V2.7 Added display of sequence alignments with results from database searches; Changes to annotation columns displayed by search; Added link to online manual; Updated install documentation; Minor bug fixes and cosmetic changes.
- 20160124 V2.6.2 Internal update to annotation code.
- 20160111 V2.6.1 Improved import and residue numbering for alignment; Improved import including option to rebuild statistics; Added residue labels to alignment for bulk annotation.
- 20151229 V2.6 Key annotation now supports multiple sequences.
- 20150623 V2.5.2 Some minor corrections to the Quick Install manual. No end-user code changes.
- 20150501 V2.5.1 Some minor cosmetic fixes. New Quick Install manual. Improvements to installation to ensure it will install on CentOS6.6-minimal. Bug fixes to address: (i) missing features in earlier versions of Perl and Perl-DBI; (ii) mis-handling of cut-and-paste from Macs; (iii) improved handling of user-input sequences in humanization tab; (iv) allow numbers in uploaded dataset identifiers.
- 20150203 V2.5 This version adds the ability to upload sequences to the database from the web interface (commercial version only). There are also some cosmetic enhancements.
- 20141222 V2.4 New features include lots more PTM sites annotated in sequences, a new 'humanization' tab and use of JSMol rather than JMol. Also lots of internal changes to the code.
- 20140328 V2.3.3 Some minor new features and code reorganization. Various minor bug fixes including species assignment from PDB files.
- 20131024 V2.2 This version adds a licencing file to avoid using abYsis beyond the licenced period.
- 20130701 V2.1 This version fixes a few minor bugs and implements a much improved PDB filter, rejecting a large number of false postives (i.e. things that were not antibodies) and finding a large number of antibodies - including Llama and Camel antibodies - that were previously missed.
- 20130613 V2.0.1 This release simply changes the sort order in results returned from a search to push uinclassified sequences to the end of the list.
- 20130601 V2.0 This is the first release of abYsis2. This is a complete rewrite of abYsis with a new enhanced interface.
- 20120721 V1.12
- 20120503 V1.11
- 20120116 V1.10
- 20111111 V1.9
- 20111031 V1.8
- 20110504 V1.6
- 20100802 V1.4
- 20090915 V1.3
Archive versions
