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==1. Installation==
==Installation==
First, make sure GotCloud is installed on your system. Installation instructions [[GotCloud#Setup|here]].
First, make sure GotCloud is installed on your system. Installation instructions [[GotCloud#Setup|here]].
==2. Running the Automatic Test==
==Running the Automatic Test==
This verifies that GotCloud was installed correctly.
This verifies that GotCloud was installed correctly.
==3. Running an Example Sample==
==Running an Example Sample==
As an example, we can analyze the sample files used in the automatic test.
As an example, we can analyze the sample files used in the automatic test.
To make this easier, change to the test/align directory. It contains an index file and a configuration file that can be used directly.
To make this easier, change to the test/align directory. It contains an index file and a configuration file that can be used directly.
===3.1 Index file===
===Index file===
There are four fastq files in test/align/fastq/Sample_1 and four fastq files in test/align/fastq/Sample_2, both in paired-end format. Normally, we would need to build an index file for these files. Conveniently, an index file (indexFile.txt) already exists for the automatic test samples. It contains the following information in tab-delimted format:
There are four fastq files in test/align/fastq/Sample_1 and four fastq files in test/align/fastq/Sample_2, both in paired-end format. Normally, we would need to build an index file for these files. Conveniently, an index file (indexFile.txt) already exists for the automatic test samples. It contains the following information in tab-delimted format:
where {ROOT_DIR} is the root directory of your GotCloud installation.
where {ROOT_DIR} is the root directory of your GotCloud installation.
===3.2 Configuration file===
===Configuration file===
Similar to the index file, a configuration file (test.conf) already exists for the automatic test samples. It contains the following information:
Similar to the index file, a configuration file (test.conf) already exists for the automatic test samples. It contains the following information:
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===
===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.
====3.3.1 Generating the Makefiles====
====Generating the Makefiles====
Enter the following command:
Enter the following command:
where {OUTDIR} will be replaced with the directory you entered above.
where {OUTDIR} will be replaced with the directory you entered above.
====3.3.2 Running the Makefiles====
====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.
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.
