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Analysis with the Discovery Environment

learning-objectives

• Objective 1

• Objective 2

• Objective n

Description:

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Input Data:

Input	Description	Example
A fasta file containing DNA sequences to align.	We will use the previously uploaded file from the Data Management II section.	View the example MUSCLE input folder.

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Descriptive Steps

1. If necessary, log into the CyVerse Discovery Environment.

2. Click (Apps icon) from the DE workspace; search for MUSCLE- 3.8.31

3. Under “Analysis Info”, you can leave the defaults or make any desired notes.

4. Under “Select Input Data” click Browse, then navigate the uploaded file (DE_sample_plants.fas); then click OK.

5. Under “Sequence Type”, select DNA.

6. Under the optional “Advanced Settings”, leave the default settings. If required, some analyses may be launched with requests for more minimum Resource Requirements, but this may cause those analyses to sit longer in the submission queue until a node matching those minimum requirements becomes available.

7. Click Launch Analysis

8. You will receive a notification and be redirected to the Analyses Listing page.

Output/Results

Output	Description	Example
A folder of logs clstalw.aln fasta.aln phylip_interleaved.aln phylip_sequential.aln	The logs folder are log files returned with every Discovery Environment analyses. These can be useful for diagnosing failed analyses. All other files are outputs of the Muscle software and contain multiple sequence alignments in a variety of common formats.	View the example MUSCLE output folder.

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Description of output and results

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Self Assessment Questions

Question

Q1. Which of the following are true about Docker containers?

1. They share the host OS

2. They have process-level isolation.

3. They are are heavyweight.

4. They have a startup time in the minutes range.

Answer

Correct answer is A and B

Question

Q2. Which of the following are incorrect about Docker containers?

1. Dockerfiles are a recipe for creating Docker images.

2. Docker containers are a collection of Dockerfiles.

3. Docker images get built by running a Docker command which uses the Dockerfile.

4. Docker containers are running instances of a Docker image.

Answer

The incorrect statement is B

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