Galaxy Tutorial 2012 Extras

Jump to: navigation, search
Items shown on this page were part of earlier drafts of the 2012 Summer School Galaxy workshop. They were moved here either in the interests of time, or because they no longer fit well with other content. However, these sections are still informative.

Defining Genomes to Trackster

From the Learn/Visualization wiki page

Trackster needs chrom/contig length information for builds to be able to be visualized, either in the form of .len files or custom user builds. The former option allows all users to be able to use the build. Trackster looks for the .len files in the tool-data/shared/ucsc/chrom/ directory by default, but this location can be configured in the universe_wsgi.ini file:

# Directory where chrom len files are kept, currently mainly used by trackster
#len_file_path = tool-data/shared/ucsc/chrom

For example, to enable visualization of hg18, a file called hg18.len must exist in the previously specified folder. The contents of the .len file is tab-delimited and specifies the length of each chrom/contig of that build, each on a separate line, eg:

chr1    27473282
chr2    38882233
chrX    28883322

To populate this directory with common UCSC builds, run the following commands:

mkdir ./tool-data/shared/ucsc/chrom/
python ./cron/ ./tool-data/shared/ucsc/chrom/

To display a build's genome data (i.e. bases/nucleotides) when sufficiently zoomed in: (a) create a 2bit file from the genome's fasta file using faToTwoBit, which is available from UCSC's tools (source, executables and (b) add an entry to the tool-data/twobit.loc file to indicate that where the build's twobit file is located.

Finally, you will need to make sure your datatypes_conf.xml file contains the necessary datatype converters that GTB uses, such as bam_to_bai.xml, bed_to_tabix.xml, etc. If you have not made local changes to datatypes_conf.xml, then simply copy everything from datatypes_conf.xml.sample into datatypes_conf.xml to make sure you have the latest copy.

Note: the above script will run for almost an hour

After restarting Galaxy, Trackster will now know about the size of all chromosomes for many genome builds.

Adding a new tool

Note: This was the "create a tool" example used in previous years. This year I switched the time to cover the Galaxy Tool Shed instead. However, this is such a nice example that I couldn't delete it altogether. Dave C.

The SAM format contains 12 required fields representing the read and the position it maps to, followed by a variable number of optional fields of the form CODE:TYPE:VALUE. Suppose we want to filter by these optional fields. We can whip up a quick command line tool in Python (or perl, or awk, or...) to do this.

Let's first create a directory for our new tool:

$ mkdir tools/gmod_2012

The tool command (script)

And then using a text editor, create tools/gmod_2012/ containing:

#!/usr/bin/env python
Usage: input_file output_file flag value
import sys
out = open( sys.argv[2], "w" )
for line in open( sys.argv[1] ):
    # Strip end of line and split on tabs
    fields = line.rstrip( "\r\n" ).split( "\t" )
    # Look only at optional fields
    write_line = False
    for field in fields[12:]:
        flag, type, value = field.split( ":" )
        if flag == sys.argv[3] and value == sys.argv[4]:
            write_line = True
    # If any optional field matched, keep the read
    if write_line:
        out.write( line )

The tool wrapper

Next, we need to create the tool configuration. Edit the file tools/gmod_2012/sam_filter.xml and start with the following skeleton:

<tool id="sam_filter_1" name="SAM Filter">
    <command interpreter="python">

First, let's define the output. This tool has a single output, of type sam, so we modify the configuration to contain:

<tool id="sam_filter_1" name="SAM Filter">
    <command interpreter="python">
        <data name="output1" format="sam" />

The name can be anything, but it will be used later to identify the output file in the command line. Second, let's define the following inputs

  • An input dataset of type sam
  • An input flag, which is selected from a predefined set
  • An input value, which can be any text

The resulting configuration:

<tool id="sam_filter_1" name="SAM Filter">
    <command interpreter="python">
        <param type="data" format="sam" name="input1" label="File to filter"/>
        <param type="select" name="flag" label="Optional field to filter on">
            <option value="NM">Edit Distance</option>
            <option value="MD">Mismatching positions / bases</option>
	    <option value="AS">Alignment score</option>
	<param type="text" name="value" label="Value to require for flag"/>
        <data name="output1" format="sam" />

Finally, we define how to construct our command line based on values for the inputs. The command line is a template, where we can substitute in the value of each input (filenames in the case of datasets). Thus our final tool configuration is:

<tool id="sam_filter_1" name="SAM Filter">
    <command interpreter="python"> $input1 $output1 $flag $value
        <param type="data" format="sam" name="input1" label="File to filter"/>
        <param type="select" name="flag" label="Optional field to filter on">
            <option value="NM">Edit Distance</option>
            <option value="MD">Mismatching positions / bases</option>
	    <option value="AS">Alignment score</option>
	<param type="text" name="value" label="Value to require for flag"/>
        <data name="output1" format="sam" />

We now need to modify tool_conf.xml to register our new tool and run Galaxy. Modify the top of tool_conf.xml to look like:

<?xml version="1.0"?>
  <section name="GMOD 2012 Course Tools" id="gmod_2012">
    <tool file="gmod_2012/sam_filter.xml"/>

and run Galaxy using

$ sh --reload

Running the new tool

Return to the Galaxy web interface and from the Tools panel and select GMOD 2012 Course Tools → SAM Filter.

The dataset 3: Map with BWA... should already be selected. Because we defined the type of data the tool can accept, Galaxy knows this is the only dataset in our history that is valid.

Select Edit distance for the flag, enter 0 for the value, and click Execute.

GalaxyExtras SamFilter 1.png

We know have a new dataset 4: Sam Filter on data 3 which contains only reads that mapped exactly to the reference.

GalaxyExtras SamFilter 2.png

Configuring Galaxy (2)

Tool dependencies

In the example above, we added a new tool to the default Galaxy installation. This included, adding the new tool to the Tools panel. However, many of the tools that are listed in the default Tools panel need additional software installed before they will work (we are currently working on an enhanced dependency management system to make this easier).

Suppose we'd like to analyze some Illumina datasets. We see that the Map with BWA tool requires us to install BWA (surprise!). To save time, BWA is already compiled on the AMI, so let's copy it to a location on the PATH:

$ sudo cp /home/ubuntu/Galaxy/BWA/bwa-0.6.2/bwa /usr/local/bin

Now bwa can be run from the command line:

$ bwa
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.6.2-r126
Contact: Heng Li <>

The Galaxy tool also requires a loc file which contains the locations of indexes for locally stored genome builds. We don't have any, so we can just use the empty sample:

$ cp tool-data/bwa_index.loc.sample tool-data/bwa_index.loc

and then start Galaxy

$ sh --reload

A second example with NGS data

Having made these changes and restarted Galaxy, access it at Template:YourUrlGalaxy.

You will notice that your history has been lost. This is the result of moving to Postgres. On startup, Galaxy will again have created a new database from scratch.

1. Upload datasets

We will again use the Get Data → Upload File tool to upload data into Galaxy. You can enter multiple URLs into the URL / Text box. Enter:

and click Execute:

GalaxyExtras SecondAnalysis 1.png

After uploading the datasets, expand them in the History. We can see that Galaxy has successfully detected the file formats of both files.

GalaxyExtras SecondAnalysis 2.png

However, we need to make one modification. The FASTQ format is ill-defined, and Galaxy needs to know how the quality scores are scaled. Click the pencil icon for dataset 2, and change the datatype from fastq to fastqsanger (be careful, there are many similar choices here). Finally, click Save.

2. Run BWA to map reads

In the Tools panel, select NGS: Mapping → Map with BWA for Illumina.

Change the value of the first parameter to Use one from the history and make sure that 1: ftp: // ftp.gmod.or...4_genome.fa is selected.

Make sure that for parameter FASTQ file that 2: ftp: // ftp.gmod.or...fastqsanger is selected.

Click Execute.

GalaxyExtras SecondAnalysis BWASettings.png

A new dataset is generated containing the mapped reads in SAM format.

GalaxyExtras SecondAnalysis 3.png

Making genome / alignment data available to Galaxy

Note: We probably won't do this section during class, due to time constraints. The process for loading genome builds into Galaxy will also be changing shortly.

Galaxy is designed so that a single Galaxy instance can work with many genomes simultaneously. To use certain tools, Galaxy needs to be configured to know where to find data for those genomes. As an example, let's create a new fake genome and configure some data for it.

Every genome in Galaxy needs to have a unique identifier (called the build identifier or dbkey). For our example, the identifier will be a_example_1.

Python package management tools

DO NOT DO THIS NOW: This has already been done on the AMI.

First, install a few packages that will allow us to index our data. At the terminal, enter:

  $ sudo apt-get install python-dev python-setuptools python-pip


Do not do this now either. This has already been done on your image.

This would install some support files needed by Python. Next type

  $ sudo pip install bx-python

This would install the bx-python package, a collection of scripts and Python libraries for working with genomic and comparative genomic data.

Get datasets for our genome

Now, we will download the datasets for our example genome:

$ mkdir tool-data/a_example_1
$ cd tool-data/a_example_1
$ wget
$ wget
Note: These files are also available on the image in /home/ubuntu/Galaxy/Data/.

Next, we will use the script (put in /usr/local/bin/ when bx-python was installed) to create a binary index that allows fast selection of alignments from a MAF file:

$ a_example_1.maf
$ ls
a_example_1.2bit  a_example_1.maf  a_example_1.maf.index
$ cd ~/Galaxy/galaxy-dist

Edit configuration files

We now need to edit several configuration files to inform Galaxy of the existence of our genome, and of these associated datasets.

NOTE: these are TAB separated files, and it is important that the tabs are in the right places. If you have trouble cutting and pasting from the wiki, you can cut and paste from this text file instead:

Add this line to tool-data/shared/ucsc/builds.txt

a_example_1	Example genome

Add this to tool-data/alignseq.loc

seq	a_example_1	/home/ubuntu/Galaxy/galaxy-dist/tool-data/a_example_1/a_example_1.2bit

Add this to tool-data/maf_index.loc

a_example_1 with 3 other species	a_example_1_3way	a_example_1	a_example_1,apiMel2,n_vitripennis_20100409,dm3	/home/ubuntu/Galaxy/galaxy-dist/tool-data/a_example_1/a_example_1.maf

Now, stop and start your running Galaxy with

$ sh --reload

Create dataset using new genome build

Now let's see if our new data is available in Galaxy. Click Get Data → Upload File.

Paste the following into the URL/Text box:

scaffold0	450	650
scaffold0	2000	3000

Set the File Format to bed, make sure Convert spaces to tabs is selected, and click in the Genome: box. You should be able to find your genome by typing example.

Extract sequence corresponding to these intervals

In the Tools menu, click Fetch Sequences → Extract Genomic DNA.

GalaxyExtras Fetch 1.png

The tool interface should open in the main panel. The default values are probably fine (make sure the dataset you just created is selected). Click Execute. A new dataset will be created containing the DNA for your regions of interest.

GalaxyExtras Fetch ExtractedDNA.png

Extract multiple alignments corresponding to these intervals

In the Tools menu, click Fetch Alignments → Extract MAF Blocks.

GalaxyExtras Fetch 2.png

The tool interface will open in the main panel. Again, the defaults should be reasonable, but click Select All to do alignments to all other species. Click Execute. A new dataset will be created containing alignments corresponding to your intervals of interest.

GalaxyExtras Fetch 3.png