BWA TOOL FOR MAC TERMINAL INSTALL
BWA TOOL FOR MAC TERMINAL SOFTWARE

Create BWA indexes for the reference genome.Get the reference genome in the FASTA format.Add a new built-in reference dataset, we will be using the sacCer1 genome build.

Note the choices available under 'Select a reference genome:' hint: this list is empty.When the BWA tool is installed, Click 'Analyze Data' menu item and select the BWA tool.When uploading these datasets set the datatype to 'fastqsanger'.These are paired end datasets created using Illumina technology, obtained from EBI SRA, and decreased to ~10,000 reads.There should be a tool-data/bwa_index.loc file (copied from 'bwa_' if not already created).View shed_tool_data_table_conf.xml should have the bwa tool_data_table_ table entries added.View shed_tool_conf.xml it should now contain a bwa_wrapper entry.From the Galaxy admin page: Click 'Search and browse tool sheds'.

BWA TOOL FOR MAC TERMINAL INSTALL

Then restart galaxy.Īdmin_users = Install the BWA Galaxy tool If the issue persists: adjust universe_wsgi.ini by adding an admin_user email you will register with when you first log in - use commas ONLY - no spaces - to separate admin email addresses. If you don't have an admin menu item on your tool bar, refresh your browser.You can also use the preconfigured username: password: galaxy.In your VM web browser, visit Register your admin email address if you haven't already done so and log in. Check that your galaxy instance is running.Stop Galaxy if it's running sh run.sh -stop-daemon Open a terminal/shell and go to galaxy dirĬd /home/galaxy/Desktop/Data_Managers/galaxy/galaxy-central #phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa #then the bwa_index.loc entry would look like this: #So, for example, if you had phiX indexed stored in #file has this format (longer white space characters are TAB characters): #the directories in which those files are stored. #similar to this one (store it in this directory) that points to #to create these data files and then create a bwa_index.loc file

#to use a directory of BWA indexed sequences data files. #This is a sample file distributed with Galaxy that enables tools Find and click on 'tool_data_table_' which defines the mapping to the 'tool-data/bwa_index.loc' fileĤ.

Find and click on 'bwa_wrapper.xml' and note the section that uses indexed data:ģ.

Click 'Repository Actions' and select 'Browse repository tip files'.

search toolshed for bwa tool that uses reference data.

The Tool Data Tables abstraction layer should be used.Įxample of typical use of reference data in a Galaxy tool

Should not be accessed directly in a tool.

Tab delimited flat files, where each row is an entry in the table.

Need not end in the suffix of '.loc', although they commonly do by convention.

Often used to store the path (location on disk) of reference data and indexes, along with appropriate metadata (display names, dbkeys/genome builds).

Colloquially referred to as 'loc' or 'location' files.

Used as a way to provide additional configuration details to a tool, without having to manually edit the actual tool XML file.

Graphical Overview of Interplay between Built-in Data and Galaxy Tools

Introduce presenters and circulating tutorsġ5:40-16:00 Using Reference Data in Galaxy Tools.

BWA TOOL FOR MAC TERMINAL SOFTWARE

Secure Shell (SSH) client software such as PuTTY for Windows, or the Terminal Application that comes with Mac OS.

If you don't know what cd, mv, rm, mkdir, chmod, grep and so on can do then you will struggle in this workshop.

Knowledge and comfort with the Unix/Linux command line interface and a text editor.

Google Chrome, Firefox and Safari will work best.

A wi-fi enabled laptop with a modern web browser.

The virtual machine image for this workshop should be installed before you arrive.

For a video overview on Data Managers, see this presentation from GCC2013.

This session covers the tool and ToolShed requirements for using reference data within galaxy tools, and the design and development of tool data managers to install reference data on a Galaxy server. For example, Bowtie requires prebuilt indexes in order to efficiently map sequences to a genome.ĭata Managers enable a Galaxy administrator to add reference data to a Galaxy server via the admin webpage or through the Galaxy API. Galaxy tools can require installed reference data in order to be used effectively. Presenters: Dan Blankenberg and Jim Johnson Summary This workshop is offered on June 30, from 3:30 through 6pm, in Room 304 of Charles Commons. This is the workshop page for the Tool Development from bright idea to toolshed - Data Managers Training Day session at GCC2014.

Bwa tool for mac terminal