1. Start your mysqld server daemon.
   (For the sake of this example, we'll assume we're running on port 9999; you shouldn't actually use this port because only one daemon can run on any port number.)
2. Login to the server as root user, using the mysql client.
3. Create a database to store Elgg's tables. We'll call the database elggalpha.
   mysql> create database elggalpha;
4. Grant access to a user — for this example we'll call him/her elggalphauser.

   mysql> grant all privileges on elggalpha.* to 'elggalphauser'@'moxie'
       -> identified by 'secretpassword';
   

1. Type umask 022
2. Change into your public_html directory (aka folder).
   cd public_html
3. make a directory called elgg
   mkdir elgg
4. Change into the elgg subdirectory of public_html.
   cd elgg
5. download elgg into this directory
6. you'll end up with a file named
   /home/your-user-id/public_html/elgg/elgg-X.X.X.X.zip
   (It's not literally X.X.X.X, it might be elgg-1.8.0.1.zip, for example.)
7. unzip elgg
   unzip -q elgg-1.8.0.1.zip
8. you'll end up with a directory (folder) named
   /home/your-user-id/public_html/elgg/elgg-X.X.X.X
9. make a symbolic link (aka shortcut) to this
   ln -s elgg-X.X.X.X alpha
   (For example, ln -s elgg-1.8.0.1 alpha)
10. Give user nobody access to this directory
    /usr/misc/bin/acl.sh -r -u nobody elgg-1.8.0.1
11. create a data directory for elgg (get into your home directory first):

    cd
    mkdir -p elgg/alpha/data
    chmod -R 755 elgg/alpha/data
    

12. Change into the elgg/alpha directory.
    cd elgg/alpha
13. Give user nobody access to this subdirectory data
    /usr/misc/bin/acl.sh -u nobody data
14. In your browser, navigate to your elgg installation
    http://moxie.cs.oswego.edu/~your-user-id/elgg/alpha/
    You'll have a screen which includes this message:

    Welcome
    
    Installing Elgg has 6 simple steps and reading this welcome is the first one!
    
    If you haven't already, read through the installation instructions included with Elgg (or click the instructions link at the bottom of the page).
    
    If you are ready to proceed, click the Next button.
    

15. Follow configuration process:
    • The first screen probably will contain a success message in green and a failure message in pink:

      Requirements check
      
      Your server failed the requirements check. After you have fixed the below issues, refresh this
      page. Check the troubleshooting links at the bottom of this page if you need further assistance.
      PHP

      Your server's PHP satisfies all of Elgg's requirements.

      Web server

      We think your server is running the Apache web server. The rewrite test failed and the most likely cause is that AllowOverride is not set to All for Elgg's directory. This prevents Apache from processing the .htaccess file which contains the rewrite rules. A less likely cause is Apache is configured with an alias for your Elgg directory and you need to set the RewriteBase in your .htaccess. There are further instructions in the .htaccess file in your Elgg directory.

      Database

      The database requirements are checked when Elgg loads its database.
    • To correct this, replace the .htaccess file that Elgg created with one that you can edit:

      cp -ip .htaccess temp-htaccess
      rm .htaccess
      mv temp-htaccess .htaccess
      

    • Edit the .htaccess file: Go to approximately line 101 (where it says #RewriteBase /) and add the line:
      RewriteBase /~your-user-id/elgg/alpha/
    • Be sure to save the edited file.

       

       

    • Click the Refresh button.

       

       

    • If this hasn't fixed things, seek professional help.

       

       

    • Click the Next button.

       

       

    • Fill in the parameters appropriate to your MySQL installation.

      Database installation
      
      If you haven't already created a database for Elgg, do that now. Then fill in the values below to
      initialize the Elgg database.
      
      Database Username

      elggalphauser

      User that has full priviledges to the MySQL database that you created for Elgg
      
      Database Password

      secretpassword

      Password for the above database user account
      
      Database Name

      elggalpha

      Name of the Elgg database
      
      Database Host

      ^‡
      moxie:9999

      Hostname of the MySQL server (usually localhost)
      ‡You might need to use 127.0.0.1:9999 for the host
          if you haven't set up MySQL as we've done.
      
      
      
      Database Table Prefix

      elgg_

      The prefix given to all of Elgg's tables (usually elgg_)
      

      Next

       

       

    • Continue filling in forms as requested.

      Configure site

      Database has been installed.

      We need some information about the site as we configure Elgg. If you haven't created a data directory for Elgg, you need to do so now.
      
      Site Name

      My Elgg Site version Alpha

      The name of your new Elgg site
      
      Site Email Address

      your-user-id@oswego.edu

      Email address used by Elgg for communication with users
      
      Site URL

      http://moxie.cs.oswego.edu/~your-user-id/elgg/alpha/

      The address of the site (Elgg usually guesses this correctly)
      
      Elgg Install Directory

      /home/your-user-id/public_html/elgg/elgg.1.8.0.1/

      The directory where you put the Elgg code (Elgg usually guesses this correctly)
      
      Data Directory

      /home/your-user-id/elgg/alpha/data

      The directory that you created for Elgg to save files (the permissions on this directory are checked
      when you click Next)
      
      Default Site Access

      Public

      The default access level for new user created content
      

    • Create admin account

      Site settings have been saved.

      It is now time to create an administrator's account.
      
      Display Name

       

      The name that is displayed on the site for this account
      
      Email Address

       

      Username

       

      Account username used for logging in
      
      Password

       

      Account password must be at least 6 characters long
      
      Password Again

       

      Retype password to confirm

Motif Discovery

cosmo

The cosmo package allows to search a set of unaligned DNA sequences for a shared motif that may function as transcription factor binding site. The algorithm extends the popular motif discovery tool MEME (Bailey and Elkan, 1995) in that it allows the search to be supervised by specifying a set of constraints that the motif to be discovered must satisfy. Documentation

ShortRead

The ShortRead package provides input, quality control, filtering, parsing, and manipulation functionality for short read sequences produced by high throughput sequencing technologies. While support is provided for many sequencing technologies, this package is primairly focused on Solexa/Illumina reads. Documentation

Rsamtools

Rsamtools provides functions for parsing and inspecting samtools BAM formatted binary alignment data. SAM/BAM is quickly becoming a universal standard alignment format, and is now supported by a wide variety of alignment tools. Documentation

Samtools Website
BWA (Burrows-Wheeler Alignment) Website

Additional tools for SNP analysis: 

snpMatrix

BSgenome

BSgenome provides an object oriented infrastructure for interacting with a Biostring based genome sequence. BSgenome packages exist for many common genomes, and can be created to represent custom genomes. See the "How to forge a BSgenome data package" Vignette for instructions to create a new BSgenome package if a prebuilt package does not exist for your organism. Documentation

rtracklayer

rtracklayer provides an interface for exporting annotation feature data to various genome browsers and file formats (such as GFF). See the Small RNA Profiling exercise for an example of using rtracklayer to visualize alignment coverage. Documentation

biomaRt

The biomaRt package, provides an interface to a growing collection of databases implementing the BioMart software suite (http:// www.biomart.org). The package enables online retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas. This data is retrieved automatically via the Internet, so it's recommended that you cache the data locally, or check versions if your code will be adversely affected by updates to these data. Documentation

ChIP-Seq Analysis Packages

Bioconductor provides various packages for analyzing and visualizing ChIP-Seq data. Only a small selection of these packages is introduced here. Additional useful introductions to this topic are: BioC ChIP-seq Case Study and BioC ChIP-Seq.

chipseq

The chipseq package combines a variety of HT-Seq packages to a pipeline for ChIP-Seq data analysis. Documentation

BayesPeak

BayesPeak is a peak calling package for identifying DNA binding sites of proteins in ChIP-Seq experiments. Its algorithm uses hidden Markov models (HMM) and Bayesian statistical methods. The following sample code introduces the identification of peaks with the BayesPeak package as well as the incorporation of read coverage information obtained by the chipseq package. Documentation [ Publication ]

PICS

The PICS package applies probabilistic inference to aligned-read ChIP-Seq data in order to identify regions bound by transcription factors. PICS identifies enriched regions by modeling local concentrations of directional reads, and uses DNA fragment length prior information to discriminate closely adjacent binding events via a Bayesian hierarchical t-mixture model. The following sample code uses the test data set from the above BayesPeak package in order to compare the results from both methods by identifying their consensus peak set. Documentation [ Publication ]

ChIPpeakAnno

The ChIPpeakAnno package provides. batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. It includes functions to retrieve the sequences around peaks, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. The package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages. Documentation

Additional ChIP-Seq Packages

DiffBind: Documentation

MOSAICS: Documentation

iSeq: Documentation

ChIPseqR: Documentation

ChiPsim: Documentation

CSAR: Documentation

ChIP-Seq Pipeline: PICS, rGADEM and MotIV (developer web site)

SPP: ChIP-seq processing pipeline

SPP Tutorial

MACS

SIPeS

RNA-Seq Analysis

Counting Reads that Overlap with Annotation Ranges 

The GenomicRanges package provides support for importing into R short read alignment data in BAM format (via Rsamtools) and associating them with genomic feature ranges, such as exons or genes. This way one can quantify the number of reads aligning to annotated genomic regions. The package defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome. The two main functions for read counting provided by this infrastructure are countOverlaps and summarizeOverlaps. For their proper usage, it is important to read the corresponding PDF manual. Documentation

Differential Gene Expression Analysis with DESeq

The DESeq package contains functions to call differentially expressed genes (DEGs) in count tables based on a model using the negative binomial distribution. It expects as input a data frame with the raw read counts per region/gene of interest (rows) for each test sample (columns).  Such a count table can be imported into R or generated from BAM alignment files using the countOverlaps function as introduced above. Documentation

Differential Gene Expression Analysis with edgeR

The edgeR package uses empirical Bayes estimation and exact tests based on the negative binomial distribution to call differentially expressed genes (DEGs) in count data. 

Documentation

A variety of additional R packages are available for normalizing RNA-Seq read count data and identifying differentially expressed genes (DEG):

easyRNASeq (simplifies read counting per genome feature)

DEXSeq (Inference of differential exon usage); parathyroidSE explains how to generate exon read counts in R

DEGseq

baySeq (also see: segmentSeq)

Genominator (Bullard et al. 2010)

HT-Seq Data Visualization

ggbio: ggplot2 extension for genomics data (online manual) Gviz: Plotting data and annotation information along genomic coordinates HilbertVis: Hilbert genome plots

GenomeGraphs: Plotting genomic information from Ensembl

TileQC: Flow Cell Quality Visualization

rtracklayer: R interface to genome browsers

genoPlotR: Plotting maps of genes and genomes

Genominator: Tools for storing, accessing, analyzing and visualizing genomic data.

To install all packages

source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite(c("ShortRead", "Biostrings", "IRanges", "BSgenome", "rtracklayer", "biomaRt", "chipseq", "ChIPpeakAnno", "Rsamtools", "BayesPeak", "PICS", "GenomicRanges", "DESeq", "edgeR", "leeBamViews", "GenomicFeatures", "BSgenome.Celegans.UCSC.ce2"))