Sunday, May 20, 2012

YoLinux LDAP Tutorial: Deploying OpenLDAP 2.x/1.2

YoLinux LDAP Tutorial: Deploying OpenLDAP 2.x/1.2

LDAP Directory Server Installation and configuration

http://www.yolinux.com/

Description: Lightweight Directory Access Protocol (LDAP) is a means of serving data on individuals, system users, network devices and systems over the network for e-mail clients, applications requiring authentication or information. The LDAP server is a means of providing a single directory source (with a redundant backup optional) for system information look-up and authentication. Using the LDAP server configuration example on this page will enable you to create an LDAP server to support email clients, web authentication, etc. We have many useful links for other LDAP deployments. LDAP can also be distributed in a hierarchical fashion but my examples refer to a single LDAP server. This tutorial will cover the setup and configuration of an LDAP server on Linux, the loading of data and use. Once configured, I recommend "gq" as an admin tool. (Note: Red Hat no longer ship with gq but it can still be downloaded and compiled manually.)
Simply put, this tutorial will enable you to create an LDAP server to which your e-mail clients (Outlook, Mozilla, Netscape, etc) can connect with their address books. It will allow one to search the LDAP database for people's e-mail addresses which are then pulled into the address list. Try it out with Thunderbird, Mozilla, Netscape or Outlook on our LDAP site ldap.yolinux.com for a demo. Cool eh! You can also try out authentication by pointing your application to authenticate at ldap.yolinux.com.

LDAP Server Tutorial Table of Contents:

# LDAP e-Mail Clients: configuration etc
# OpenLDAP Tutorial: Server Installation, Configuration, slapd, Loading LDIF data, Usage - (Creating a web accessible address book directory server.)
# LDAP Manual pages
# Berkeley BDB database
# Links to other YoLinux LDAP tutorials
# LDAP Links
# LDAP Books

Securing and Optimizing Linux

RedHat Edition -A Hands on Guide

http://www.faqs.org/docs/securing/index.html

Gerhard Mourani

Open Network Architecture www.openna.com

             gmourani@openna.com
             gmourani@netscape.net

Madhu "Maddy"

Table of Contents

Preface

1. Why did i write this book?
2. Why fiddle?
3. DocBook !
4. DocBook/XML

1. Getting Started

1. Introduction

2. Installation

2. Overview of OS Linux
3. Installation of your Linux Server
4. Post-Install

3. Security, Optimization and Upgrade

5. General System Security
6. Linux General Optimization
7. Configuring and Building a Secure, Optimized Kernel

4. Networking -Management, Firewall, Masquerading and Forwarding

8. TCP/IP -Network Management
9. Files -Networking Functionality
10. Networking -Firewall
11. The firewall scripts files
12. Networking Firewall -Masquerading and Forwarding

5. Software -Security

13. Linux -The Compiler functionality
14. Software -Security/Monitoring

6. Software -Networking

15. Software -Securities
16. Software -Securties(commercial)
17. Software -Securities/System Integrity
18. Linux Tripwire ASR 1.3.1
19. Software -Securities/Management & Limitation
20. Set Limits using Qouta
21. Software -Networking
22. Software -Server/Mail Network
23. Linux IMAP & POP Server
24. Software -Networking/Encryption
25. Linux FreeS/WAN VPN
26. Linux OpenLDAP Server
27. Linux PostgreSQL Database Server
28. Software -Server/Proxy Network
29. Software -Network Server, web/Apache
30. Optional component to install with Apache
31. Software -Server/File Sharing-Network
32. Linux FTP Server

7. Backup and Restore

33. Why's and When's of Backup and Restore

I. Appendixes

A. Resources
B. Tweaks, Tips and Administration tasks
C. Obtaining Requests for Comments (RFCs)

List of Tables
3-1. Sample representaion of partitions
33-1. Dump scheme

List of Examples
3-1. Starting and Stopping various Daemon's
5-1. Export file systems using NFS
5-2. Disable console-equivalent access
5-3. Print log reports
5-4. Use man pages
5-5. Use find to find
6-1. For 128 MB of RAM
7-1. SMP support
8-1. Two ISA ethernet cards
12-1. rc.firewall.blocked
13-1. Using tar
15-1. Remote login using ssh
15-2. scp Secure Copy utility
15-3. local to remote
16-1. login to a remote using ssh2
16-2. sftp2, Secure File Transfer
18-1. Usage of Tripwire
19-1. Importing using gpg
19-2. Signing key
19-3. Encrypting
19-4. Decrypting
20-1. usrquota
20-2. grpquota
21-1. dnsquery
21-2. Look up host names
21-3. Using host
21-4. List a complete domain
22-1. Overriding RBL
22-2. Alternative names
22-3. sendmail.cf
26-1. my-data-file
26-2. LDMB backend
26-3. modifyentry
26-4. Address Book
30-1. Using Netscape browser
33-1. Backup directory of a week
33-2. scp SSH command
33-3. scp SSH command

Thursday, May 3, 2012

solid2fastq convertors

A plethora of solid2fastq or csfasta convertors to fastq

I hadn't realised that there's an accumulation of prog/scripts to do the same task. Last count is 4 of these in my tool closet.

The C binary from bfast

solid2fastq 0.6.4a

Usage: solid2fastq [options]
        -c              produce no output.
        -n      INT     number of reads per file.
        -o      STRING output prefix.
        -j              input files are bzip2 compressed.
        -z              input files are gzip compressed.
        -J              output files are bzip2 compressed.
        -Z              output files are gzip compressed.
        -t      INT     trim INT bases from the 3' end of the reads.
        -h              print this help message.

send bugs to bfast-help@lists

solid2fastq.pl from bfast-0.6.4a
with notes in the script to refer to the above
# Author: Nils Homer
# Please see the C implementation of this script.

EDIT: THANKS to iceman for his reminder in the comments
"Make sure that you use the BWA's solid2fastq.pl if you are going to use BWA as it "double-encodes" the reads."

solid2fastq.pl from bwa-0.5.7
Usage: solid2fastq.pl

Note: is the string showed in the `# Title:' line of a
      ".csfasta" read file. Then F3.csfasta is read sequence
      file and F3_QV.qual is the quality file. If
      R3.csfasta is present, this script assumes reads are
      paired; otherwise reads will be regarded as single-end.

      The read name will be :panel_x_y/[12] with `1' for R3
      tag and `2' for F3. Usually you may want to use short
      to save diskspace. Long also causes troubles to maq.

# Author: lh3
# Note: Ideally, this script should be written in C. It is a bit slow at present.
# Also note that this script is different from the one contained in MAQ.

maq-0.7.1/scripts/solid2fastq.pl

Usage: solid2fastq.pl

Note: is the string showed in the `# Title:' line of a
      ".csfasta" read file. Then F3.csfasta is read sequence
      file and F3_QV.qual is the quality file. If
      R3.csfasta is present, this script assumes reads are
      paired; otherwise reads will be regarded as single-end.

      The read name will be :panel_x_y/[12] with `1' for F3
      tag and `2' for R3. Usually you may want to use short
      to save diskspace. Long also causes troubles to maq.

# Author: lh3
# Note: Ideally, this script should be written in C. It is a bit slow at present.