Mascot Server Installation and Setup © 2021 Matrix Science Ltd. All rights reserved. The information contained in this publication is for reference purposes only and is subject to change at any time. Every effort has been made to supply complete and accurate information. However, Matrix Science Ltd. accepts no responsibility and will not be liable for any consequential loss or damages that might result from the use of this manual or from any errors or omissions in the information contained herein. No part of this document may be reproduced or transmitted in any form or by any means, electronic or mechanical, for any purpose, without the express written permission of Matrix Science Ltd. Mascot is a trademark of Matrix Science Ltd. All third party trademarks and service marks referred to in this publication are hereby acknowledged. Address: Matrix Science Ltd. 64 Baker Street London W1U 7GB UK Phone: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 Email: [email protected] WWW: https://www.matrixscience.com July 2021, Revision 2.8.0 Contents 1. Introduction................................................................................................... 1 Overview ................................................................................................................................... 1 Mascot Components ................................................................................................................. 2 2. Installation: Linux ........................................................................................ 5 Release Notes............................................................................................................................ 5 Cluster Mode ............................................................................................................................ 5 System Requirements .............................................................................................................. 5 Mascot Directory Structure ..................................................................................................... 7 Installation ............................................................................................................................... 8 Miscellaneous ......................................................................................................................... 14 3. Installation: Windows ................................................................................. 19 Web Server .............................................................................................................................. 19 Release Notes.......................................................................................................................... 19 Cluster Mode .......................................................................................................................... 19 Overview ................................................................................................................................. 20 System Requirements ............................................................................................................ 20 Mascot Installation ................................................................................................................ 28 Miscellaneous ......................................................................................................................... 35 Troubleshooting ...................................................................................................................... 36 4. Validation .................................................................................................... 39 CGI Operation ........................................................................................................................ 39 Monitor Test ........................................................................................................................... 39 5. Sequence Database Setup .......................................................................... 43 6. Configuration & Log Files .......................................................................... 49 Configuration Files................................................................................................................. 49 Log files ................................................................................................................................... 85 7. Program Reference ...................................................................................... 89 Mascot Search Engine ............................................................................................................ 89 Monitor .................................................................................................................................... 91 GetSeq ..................................................................................................................................... 93 Status ...................................................................................................................................... 98 Review ................................................................................................................................... 101 GetTaxonomy ........................................................................................................................ 102 SearchControl ....................................................................................................................... 109 CreatePIP.............................................................................................................................. 115 Miscellaneous Utilities ......................................................................................................... 120 8. I/O File Formats ........................................................................................ 123 Search Input File .................................................................................................................. 124 Results File ........................................................................................................................... 126 9. Taxonomy .................................................................................................. 141 Modifying the “Taxonomy lineage’ link .............................................................................. 143 Common Questions .............................................................................................................. 145 Taxonomy data files ............................................................................................................. 146 How Mascot gets a taxonomy ID for a database entry ...................................................... 148 Taxonomy in Database Manager......................................................................................... 154 10. Mascot Daemon ....................................................................................... 159 Overview ............................................................................................................................... 159 11. Cluster Mode ........................................................................................... 161 Introduction .......................................................................................................................... 161 Installation of Mascot .......................................................................................................... 163 Reference ............................................................................................................................... 172 Very large Mascot clusters .................................................................................................. 179 12. Mascot Security ....................................................................................... 183 A. Basic Regular Expressions ....................................................................... 191 B. Error Messages ......................................................................................... 195 C. System Limits ........................................................................................... 197 D. Web Server Configuration ....................................................................... 199 Mascot Directory Structure ................................................................................................. 199 Microsoft Internet Information Services ............................................................................ 199 Apache ................................................................................................................................... 200 E. SELinux .................................................................................................... 205 F. End User Licence Agreements ................................................................. 209 Mascot Server ....................................................................................................................... 209 Xerces, C++ thread pool library........................................................................................... 212 Curl........................................................................................................................................ 215 gzip, ht://Dig, cksum, touch, libstdc++ ................................................................................ 216 bzip2 .....................................................................................................................................