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First, make sure you are running a Linux computer with the following:
* C++ compiler * a python interpreter * R
From an organisational perspective you need:
* You also need a webserver with apache installed and php working. * End-users must fill the form for their given run * You need an administrator to oversee the process
Also, make sure you have installed the following dependencies:
- bamtools (works fine with 2.2.2)
- libgab (http://github.com/grenaud/libgab)
- freeIbis (http://github.com/grenaud/freeIbis)
- fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
* biohazard (http://github.com/udo-stenzel/biohazard/) * network-aware-bwa (http://github.com/udo-stenzel/network-aware-bwa/)
To compile and link, the C++ compiler needs bamtools and libgab. Please put the full path for each in makefile.defs. Once this is done, you can just type make.
The workflow can be described as follows:
- The read directory from where your sequencer(s) will write their sequencing data (basecalls and intensities in /Data/Intensities/)
- The write directory is where aLib will produce the usable data
YYMMDD_SEQUENCERID_RUN#_COMMENTS
The main configuration file is confix.xml
| Field | Meaning |
| alibdir | The base directory where aLib is installed. |
| fastqcdir | Directory containing fastqc |
| illuminareaddir | The directory where the sequencer writes the sequencing data (basecalls and intensities) |
| illuminawritedir | This is the directory where aLib will write the processed data |
| sequencers | Enter the id and type of the sequencer for your sequencing center |
| runstodisplay | The number of runs to display |
| emailAddrToSend | Email of the administrator |
| genomedirectory | Directory that contains the BWA genomic databases. |
| tempdirectory | Directory used by aLib to write temp files |
| freeibispath | Path to freeIbis |
| controlindex | 7 bp index for reads used a phiX control spike-in |
| phixref | Path to the phiX reference |
| chimeras | For various protocols, define the name of the protocol, the sequence of the adapters and putative chimeric sequences |
| Indices | Define as the high level the indexing scheme and the id to sequence data for the indices used |
Create a directory that is web accessible and copy the contents of webForm/ in there. Let the URL defined by this directory as http://internal.webserver.com/aLib/
Direct the users to the address for the webserver described above to http://internal.webserver.com/aLib/form.php. Ask the user to select their run and click launch.
Users will fill the form and an email will be sent each time a run is processed. Once this is done, makefiles will be created in the write directory for the given run. In general, it suffices to cd to that directory, cd to build and type:
make -k -j 8