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To make this easier, change to the {ROOT_DIR}/test/align directory. (We will call the directory in which GotCloud is installed "{ROOT_DIR}".) 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. (We will call the directory in which GotCloud is installed "{ROOT_DIR}".) It contains an index file and a configuration file that can be used directly.
===Index file===
===Index file===
This will create a symbolic link to the test fastq directory from your current directory.
This will create a symbolic link to the test fastq directory from your current directory.
===Configuration file===
===Configuration file===
If you are in the {ROOT_DIR}/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 not running this from {ROOT_DIR}/test/align, make sure your configuration and index files are in the same directory.
If you are in the {ROOT_DIR}/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 not running this from {ROOT_DIR}/test/align, make sure your configuration and index files are in the same directory.
===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. This requires two steps: first, generating the Makefiles; and second, running those Makefiles.
====Generating the Makefiles====
====Generating the Makefiles====
where {OUT_DIR} will be replaced with the directory you entered above.
where {OUT_DIR} will be replaced with the directory you entered above.
====Running the Makefiles====
====Running the Makefiles====
Using umake, you can analyze the BAM files generated in the previous step and generate a VCF file. Once again, we can analyze BAM files used in the automatic test. You will need three files for this: index, configuration, and bed.
Using umake, you can analyze the BAM files generated in the previous step and generate a VCF file. Once again, we can analyze BAM files used in the automatic test. You will need three files for this: index, configuration, and bed.
===Index file===
===Index file===
ln -s {ROOT_DIR}/test/umake/bams bams
ln -s {ROOT_DIR}/test/umake/bams bams
===BED file===
===BED file===
You can copy this to the current directory and use it as-is.
You can copy this to the current directory and use it as-is.
===Configuration file===
===Configuration file===
where {OUT_DIR} is the name of directory in which you want the output to be stored. If you do not specify this in the configuration file, you will need to add an extra parameter when you run UMAKE in the next step.
where {OUT_DIR} is the name of directory in which you want the output to be stored. If you do not specify this in the configuration file, you will need to add an extra parameter when you run UMAKE in the next step.
===Running UMAKE===
===Running UMAKE===
