- 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 from http://www.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.xmlfile as a new configuration on the server by going to the External applications () tab under Admin () in the web administrative interface and clicking on the button labeled Import Configuration.
bowtie-pp2.xml file contains configurations for three tools associated with 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 12.4.3 for details. 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.