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CloudAligner_1_8.jar 2013-02-27 123.3 kB
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CloudAligner_1_9.jar 2012-11-02 121.4 kB
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Readme.txt 2012-11-02 1.8 kB
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CloudAligner.jar 2010-09-23 62.7 kB
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Assuming your read file is 1k.fa (read length = 36) and your reference genome is s_suis.fa

1/Convert the inputs to the "Writable" format to be processed in Cloud
	#java -cp .:sam-1.32.jar:cloudaligner.jar:$CLASSPATH utils.ConvertFastaReadFile s_suis.fa s_suis.ca
	#java -cp .:sam-1.32.jar:cloudaligner.jar:$CLASSPATH utils.ConvertFastaReadFile 1k.fa 1k.ca

2/Upload the converted files to HDFS (Assuming under folder /user/ubuntu/input). Note that we use the user ubuntu in this example, If you have other, please change it accordingly
	#hadoop fs -put 1k.ca /user/ubuntu/input
	#hadoop fs -put s_suis.ca /user/ubuntu/input
3/Make sure your CLASSPATH contains all libraries of Hadoop and "sam-1.32.jar" (samtools to generate SAM files)
 #export CLASSPATH=/usr/lib/hadoop/*:/usr/lib/hadoop/lib/*:/usr/lib/hadoop-mapreduce/*:./sam-1.32.jar
4/Run the alignment. 
Usage: CloudAligner refpath qrypath outpath readwidth maxmismatches seed_num seed_weight inputformat mapmode outputformat readPerRound chromename
/*******************
 * inputformat == 0: INPUT_MODE.FASTA_FILE
 * inputformat == 1: INPUT_MODE.FASTQ_FILE
 * mapmode == 0: MAP_MODE.MAP
 * mapmode == 1: MAP_MODE.BISULFITE
 * mapmode == 2: MAP_MODE.PAIR_END
 * outputformat == 0: OUTPUT_FORMAT.BED
 * outputformat == 1: OUTPUT_FORMAT.SAM
 * **/
 *NOTE: Currently, the "readPerRound" parameter is not used so you can put any number there.
 
 To run the tool:
 #hadoop jar cloudaligner.jar mappers.CloudAligner /user/ubuntu/input/s_suis.ca input/1k.ca output1 36 3 3 11 0 0 0 1000 s_suis
 
 (hadoop jar CloudAligner_1_9.jar input/s_suis.ca input/1k.ca output2 36 3 3 11 0 0 0 1000 s_suis)
 
5/Get the result back
 #java -cp cloudaligner.jar:$CLASSPATH utils.PrintAlignmentsInBED output2 output2.bed
Source: Readme.txt, updated 2012-11-02