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This will verify whether GotCloud was installed correctly.
This will verify whether GotCloud was installed correctly.
*To run the test case for the alignment pipeline automatically, change your current directory to GotCloud's root directory, and type in the following command:
*To run the test case for the alignment pipeline automatically, type in the following command:
bin/gen_biopipeline.pl --test OUTPUT_DIR
{ROOT_DIR}/bin/gen_biopipeline.pl -test OUTPUT_DIR
where OUTPUT_DIR is the directory where you want to store the test results.
where OUTPUT_DIR is the directory where you want to store the test results. (We will call the directory in which GotCloud is installed "{ROOT_DIR}".)
If you see "Test Passed", then you are ready to align samples.
If you see "Test Passed", then you are ready to align samples.
*To run the test case for the variant-calling pipeline (UMAKE), change your current directory to GotCloud's root directory, and type in the following command:
*To run the test case for the variant-calling pipeline (UMAKE), change your current directory to GotCloud's root directory, and type in the following command:
bin/umake.pl --test OUTPUT_DIR
{ROOT_DIR}bin/umake.pl -test OUTPUT_DIR
where OUTPUT_DIR is the directory where you want to store the test results.
where OUTPUT_DIR is the directory where you want to store the test results.
==Aligning a Sample==
==Aligning a Sample==
As an example, we can align the sample fastq files used in the automatic test. They belong to two different samples, which we will call "Sample1" and "Sample2". They are found in {ROOT_DIR}/test/align/fastq. (We will call the directory in which GotCloud is installed "{ROOT_DIR}".)
As an example, we can align the sample fastq files used in the automatic test. They belong to two different samples, which we will call "Sample1" and "Sample2". They are found in {ROOT_DIR}/test/align/fastq.
To make this easier, change to the {ROOT_DIR}/test/align directory. It contains an index file and a configuration file that can be used directly.
To make this easier, change to the {ROOT_DIR}/test/align directory. It contains an index file and a configuration file that can be used directly.
{ROOT_DIR}/test/align/fastq/Sample_1/File1_R1.fastq.gz
{ROOT_DIR}/test/align/fastq/Sample_1/File1_R1.fastq.gz
Alternately, if you want to run this example from a different directory, but do not want to edit the index file, you can copy all the fastq files to a new directory with the relative path listed in the index file:
Alternately, if you want to run this example from a different directory, but do not want to edit the index file, you can create a relative path to the test fastq files so their path agrees with that listed in the index file:
ln -s {ROOT_DIR}/test/align/fastq fastq
ln -s {ROOT_DIR}/test/align/fastq fastq
===Running the alignment pipeline===
===Running the alignment pipeline===
You are now ready to run the alignment pipeline. This requires two steps: first, generating the Makefiles; and second, running those Makefiles.
You are now ready to run the alignment pipeline.
To run the alignment pipeline, enter the following command:
{ROOT_DIR}/bin/gen_biopipeline.pl --conf test.conf --out_dir {OUT_DIR}
{ROOT_DIR}/bin/gen_biopipeline.pl -conf test.conf -out_dir {OUT_DIR}
where {OUT_DIR} is the directory in which you wish to store the resulting BAM files (for example, ~/out).
where {OUT_DIR} is the directory in which you wish to store the resulting BAM files (for example, ~/out).
If everything went well, you will see the following messages:
If everything went well, you will see the following messages:
Created {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile
Created {OUT_DIR}/Makefiles/biopipe_Sample1.Makefile
--------------------------------------------------------------------
---------------------------------------------------------------------
Submitted 2 commands
Waiting for commands to complete... . . Commands finished in 33 secs with no errors reported
The log files for the runs will be found in the Makefiles directory, while the BAM files will be found in the {OUT_DIR}/alignment.recal directory. If you see two BAM files, one for each sample, then you have successfully aligned the fastq files.
The aligned BAM files are found in {OUT_DIR}/alignment.recal/
