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This verifies that GotCloud was installed correctly.
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:
To run the test case automatically, change your current directory to GotCloud's root directory, and type in the following command:
/bin/gen_biopipeline.pl --test OUTPUT_DIR
/bin/gen_biopipeline.pl --test OUTPUT_DIR
If you want to run this example from a different directory, make sure the FASTQ1 and FASTQ2 paths are correct. That is, each of the FASTQ1 and FASTQ2 entry in the index file should look like the following:
If you want to run this example from a different directory, make sure the FASTQ1 and FASTQ2 paths are correct. That is, each of the FASTQ1 and FASTQ2 entry in the index file should look like the following:
{gotcloud_base_dir}/test/align/fastq/Sample_1/File1_R1.fastq.gz
{ROOT_DIR}/test/align/fastq/Sample_1/File1_R1.fastq.gz
where {gotcloud_base_dir} is the base directory of your GotCloud installation.
where {ROOT_DIR} is the root directory of your GotCloud installation.
===3.2 Configuration file===
===3.2 Configuration file===
If you are in the test/align directory, you can use this file as-is. If you are using a different index file, make sure your index file is named correctly in the first line.
If you are in the test/align directory, you can use this file as-is. If you are using a different index file, make sure your index file is named correctly in the first line.
===3.3 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.
====3.3.1 Generating the Makefiles====
Enter the following command:
{ROOT_DIR}/bin/gen_biopipeline.pl --conf test.conf --out_dir {OUT_DIR}
where {ROOT_DIR} is the root directory of your GotCloud installation, and {OUT_DIR} is the directory in which you wish to store the resulting BAM files.
If everything went well, you will see the following messages:
Finished creating makefile {OUTDIR}/Makefiles/biopipe_Sample2.Makefile
Finished creating makefile {OUTDIR}/Makefiles/biopipe_Sample1.Makefile
--------------------------------------------------------------------
Run the following commands:
make -f {OUTDIR}/Makefiles/biopipe_Sample2.Makefile > {OUTDIR}/Makefiles/biopipe_Sample2.Makefile.log
make -f {OUTDIR}/Makefiles/biopipe_Sample1.Makefile > {OUTDIR}/Makefiles/biopipe_Sample1.Makefile.log
where {OUTDIR} will be replaced with the directory you entered above.
====3.3.2 Running the Makefiles====
To run a Makefile, simply enter one-by-one the commands generated in the previous step. 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.
