Difference between revisions of "Tutorial: GotCloud"

From Genome Analysis Wiki
Jump to: navigation, search
m
Line 10: Line 10:
 
To run the test case automatically, change your current directory to gotcloud's base directory, and type in the following command:
 
To run the test case automatically, change your current directory to gotcloud's base directory, and type in the following command:
  
/bin/gen_biopipeline.pl --test OUTPUT_DIR
+
/bin/gen_biopipeline.pl --test OUTPUT_DIR
  
where OUTPUT_DIR is the directory where you want to store the results.
+
where OUTPUT_DIR is the directory where you want to store the results.
  
 +
If you see "Test Passed", then you are ready to run a sample.
  
==3. Running a Sample==
 
  
Now that you have verified that GotCloud has been installed correctly, you are ready to analyze a sample.
+
==3. Running an Example Sample==
 +
 
 +
As an example, we can analyze the sample files used in the automatic test.
 +
 
 +
To make this easier, change to the test/align directory.  It contains an index file and a configuration file that can be used directly.
 +
 
 +
===3.1 Index file===
 +
 
 +
There are four fastq files in test/align/fastq/Sample_1 and four fastq files in test/align/fastq/Sample_2, both in paired-end format.  Normally, we would need to build an index file for these files. Conveniently, an index file has already been created for the automatic test samples in indexFile.txt.  It contains the following information in tab-delimted format:
 +
 
 +
MERGE_NAME FASTQ1                          FASTQ2                          RGID  SAMPLE    LIBRARY CENTER PLATFORM
 +
Sample1    fastq/Sample_1/File1_R1.fastq.gz fastq/Sample_1/File1_R2.fastq.gz RGID1  SampleID1 Lib1    UM    ILLUMINA
 +
Sample1    fastq/Sample_1/File2_R1.fastq.gz fastq/Sample_1/File2_R2.fastq.gz RGID1a SampleID1 Lib1    UM    ILLUMINA
 +
Sample2    fastq/Sample_2/File1_R1.fastq.gz fastq/Sample_2/File1_R2.fastq.gz RGID2  SampleID2 Lib2    UM    ILLUMINA
 +
Sample2    fastq/Sample_2/File2_R1.fastq.gz fastq/Sample_2/File2_R2.fastq.gz RGID2  SampleID2 Lib2    UM    ILLUMINA

Revision as of 23:54, 7 January 2013

1. Installation

First, make sure GotCloud is installed on your system. Installation instructions here.


2. Running the Automatic Test

This verifies that GotCloud was installed correctly.

To run the test case automatically, change your current directory to gotcloud's base directory, and type in the following command:

/bin/gen_biopipeline.pl --test OUTPUT_DIR

where OUTPUT_DIR is the directory where you want to store the results.

If you see "Test Passed", then you are ready to run a sample.


3. Running an Example Sample

As an example, we can analyze the sample files used in the automatic test.

To make this easier, change to the test/align directory. It contains an index file and a configuration file that can be used directly.

3.1 Index file

There are four fastq files in test/align/fastq/Sample_1 and four fastq files in test/align/fastq/Sample_2, both in paired-end format. Normally, we would need to build an index file for these files. Conveniently, an index file has already been created for the automatic test samples in indexFile.txt. It contains the following information in tab-delimted format:

MERGE_NAME FASTQ1                           FASTQ2                           RGID   SAMPLE    LIBRARY CENTER PLATFORM
Sample1    fastq/Sample_1/File1_R1.fastq.gz fastq/Sample_1/File1_R2.fastq.gz RGID1  SampleID1 Lib1    UM     ILLUMINA
Sample1    fastq/Sample_1/File2_R1.fastq.gz fastq/Sample_1/File2_R2.fastq.gz RGID1a SampleID1 Lib1    UM     ILLUMINA
Sample2    fastq/Sample_2/File1_R1.fastq.gz fastq/Sample_2/File1_R2.fastq.gz RGID2  SampleID2 Lib2    UM     ILLUMINA
Sample2    fastq/Sample_2/File2_R1.fastq.gz fastq/Sample_2/File2_R2.fastq.gz RGID2  SampleID2 Lib2    UM     ILLUMINA