Installing Bowtie
To get started:- Install Bowtie from https://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 from https://resources.qiagenbioinformatics.com/external-applications/bowtie-pp2.zip
- Place the
clcbiofolder and contents in the Bowtie installation directory. This folder contains the scripts used to wrap the Bowtie functionality. Those wrapper scripts are what is then configured via the External Applications folder. - Make sure execute permissions are set on these wrapper scripts and on the executable files located in the Bowtie installation directory. The user that will execute these files will be the user that started the CLC Server process.
- Import the
bowtie-pp2.xmlconfiguration file: Log into the server via the web administrative interface and go to the External applications (
) tab. Expand the "External applications configuration" section and click on the Import Configuration... button.
The bowtie-pp2.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.
When configuring Bowtie to run as an external application on master-node setups, the Environment configuration will need to be edited. See the Configuring the execution environment section below. In addition, Bowtie indices will have to be placed somewhere accessible to all nodes. One option could be areas configured as Import/Export areas on the CLC Server.
The rest of this section focuses on understanding the integration of the Bowtie Map tool in particular.