Running BWA aligner problems

There was the following error when running bwa aln (bwa Version: 0.6.1-r104) in ubuntu
[bwa_aln_core] calculate SA coordinate… Segmentation fault (core dumped)

solution:
Use an older version of bwa, such as 0.5.9rc1

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Hadoop: Error: Java heap space

solution: increase memory size, such as hadoop jar XXX.jar -Dmapred.map.child.java.opts=”-Xmx3000m”

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How to download 1000genomes data from Amazon S3

1000genomes has a S3 bucket on Amazon located at s3://1000genomes
To access the data, we can either use s3 tools such as s3cmd (http://s3tools.org/s3cmd, commamd line tool), S3 browser (http://s3browser.com, GUI tool for windows) or
we can use linux wget, such as wget http://1000genomes.s3.amazonaws.com/alignment.index to download a specific file directly.
The later method is more straightforward.

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how to pass parameters to Hadoop mapper or reducer

In the main method class, set the parameters to be passed
Configuration conf = new Configuration();
conf.set("name1", "value1");
conf.set("name2", "value2");
Job job = new Job(conf,"job discription"); //this line must be after the above conf.set lines, otherwise the pamareters cannot be passed

In the mapper/reducer class, get the passed parameters
conf = context.getConfiguration();
String value1 = conf.get("name1");
String value2 = conf.get("name2");



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compiling samtools on fedora/ubuntu problems

if there is the error: zlib.h no such file or directory
$yum install zlib-devel.x86_64

if there is the error:  bam_tview.c:5:20: error: curses.h: No such file or directory
$yum install ncurses-devel ncurses
(on ubuntu sudo apt-get install libncurses-dev)

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