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| This will verify whether GotCloud was installed correctly. | | This will verify whether GotCloud was installed correctly. |
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− | *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: |
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− | bin/gen_biopipeline.pl --test OUTPUT_DIR | + | {ROOT_DIR}/bin/gen_biopipeline.pl -test OUTPUT_DIR |
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− | 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}".) |
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| If you see "Test Passed", then you are ready to align samples. | | If you see "Test Passed", then you are ready to align samples. |
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| *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: |
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− | bin/umake.pl --test OUTPUT_DIR | + | {ROOT_DIR}bin/umake.pl -test OUTPUT_DIR |
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| 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. |
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| ==Aligning a Sample== | | ==Aligning a Sample== |
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− | 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. |
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| 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. |
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| {ROOT_DIR}/test/align/fastq/Sample_1/File1_R1.fastq.gz | | {ROOT_DIR}/test/align/fastq/Sample_1/File1_R1.fastq.gz |
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− | 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: |
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| ln -s {ROOT_DIR}/test/align/fastq fastq | | ln -s {ROOT_DIR}/test/align/fastq fastq |
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| ===Running the alignment pipeline=== | | ===Running the alignment pipeline=== |
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− | 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. |
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− | ====Generating the Makefiles====
| |
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− | Enter the following command:
| + | To run the alignment pipeline, enter the following command: |
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− | {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} |
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| 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). |
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| If everything went well, you will see the following messages: | | If everything went well, you will see the following messages: |
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− | Finished creating makefile {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile | + | Created {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile |
− | Finished creating makefile {OUT_DIR}/Makefiles/biopipe_Sample1.Makefile | + | Created {OUT_DIR}/Makefiles/biopipe_Sample1.Makefile |
− | -------------------------------------------------------------------- | + | --------------------------------------------------------------------- |
− | Run the following commands: | + | Submitted 2 commands |
− | | + | Waiting for commands to complete... . . Commands finished in 33 secs with no errors reported |
− | make -f {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile > {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile.log
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− | make -f {OUT_DIR}/Makefiles/biopipe_Sample1.Makefile > {OUT_DIR}/Makefiles/biopipe_Sample1.Makefile.log
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− | | |
− | where {OUT_DIR} will be replaced with the directory you entered above.
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− | | |
− | | |
− | ====Running the Makefiles====
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− | | |
− | To run a Makefile, simply enter one-by-one the commands generated in the previous step. If you wish to run the alignment in the background, add "&" after the make command, as follows:
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− | | |
− | make -f {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile > {OUT_DIR}/Makefiles/biopipe_Sample2.Makefile.log &
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− | 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/ |
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