Installing Bowtie
To get started:- Install Bowtie from http://bowtie-bio.sourceforge.net/index.shtml. We assume that Bowtie is installed in
/usr/local/bowtiebut you can just update the paths if it is placed elsewhere. - Download the scripts and configuration files made by CLC bio from http://www.clcbio.com/external-applications/bowtie.zip
- Place the
clcbiofolder and contents in the Bowtie installation directory. This is the script used to wrap the Bowtie functionality. - Make sure execute permissions are set on the scripts and the executable files in the Bowtie installation directory. Note that the user executing the files will be the user who started the Server process (if you are using the default start-up script, this will be root).
- Use the
bowtie.xmlfile as a new configuration on the server: Log into the server via the web interface and go to the External applications (
) tab under Admin (
) and click Import Configuration.
The bowtie.xml file contains configurations for three tools associated with Bowtie: CLC Bowtie build index, CLC Bowtie list indices and Bowtie Map. If you already have a set of indices you wish to use and the location of these is known to the system via the BOWTIE_INDEXES, then you can just use the Bowtie Map tool via the Workbench and specify the index to use by name.
Otherwise, you can build the index to use using the CLC Bowtie build index tool. Here, unless you edit the wrapper scripts in the files you download from CLC bio, the indices will be written to the directory indicated by the BOWTIE_INDEXES environmental variable. If you have not specified anything for this, indices will likely be written into the folder called indexes in the installation area of Bowtie. Please ensure that your users have appropriate write access to the area indices should be written to.
From ftp://ftp.cbcb.umd.edu/pub/data/bowtie_indexes/ you can download pre-built index files of many model organisms. Download the index files relevant for you and extract them into the indexes folder in the Bowtie installation directory.
The rest of this section focusses on understanding the integration of the Bowtie Map tool in particular.