Integrate bowtie to Galaxy

1. Download
>wget http://sourceforge.net/projects/bowtie-bio/files/bowtie/0.12.5/bowtie-0.12.5-linux-x86_64.zip/download

2. unzip
>unzip bowtie-0.12.5-linux-x86_64.zip

3. clean
>rm -fr bowtie-0.12.5-linux-x86_64.zip

4. test
>cd bowtie-0.12.5/
>./bowtie --version

5. download pre-build indexes (UCSC HG19)

>wget ftp://ftp.cbcb.umd.edu/pub/data/bowtie_indexes/hg19.ebwt.zip

>unzip hg19.ebwt.zip

>cd /home/ying/tools/bowtie-0.12.5

>mkdir -p data/UCSC

>mv *.ebwt /home/ying/tools/bowtie-0.12.5/data/UCSC

>ls /home/ying/tools/bowtie-0.12.5/data/UCSC

hg19.1.ebwt hg19.2.ebwt hg19.3.ebwt hg19.4.ebwt hg19.rev.1.ebwt hg19.rev.2.ebwt

6. Change the configuration file in galaxy

>vi /home/ying/galaxy/tool-data/bowtie_indices.loc

It should has this line:

#############################

hg19 /home/ying/tools/bowtie-0.12.5/data/UCSC/hg19

#############################

7. Restart the Galaxy

8. Make a online test

8.1 Upload a FASTQ file.

8.2 Apply FASTAQ Groomer

8.3 Run Bowtie