Line 8: |
Line 8: |
| 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 |
Line 37: |
Line 37: |
| 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=== |
Line 55: |
Line 55: |
| | | |
| 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. |