- perl
- R version 3.1.1
- bwa
- bowtie2
- picard-tools
- samtools
- DBD [http://search.cpan.org/CPAN/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.031.tar.gz]
- Exporter-Tiny [http://search.cpan.org/CPAN/authors/id/T/TO/TOBYINK/Exporter-Tiny-0.042.tar.gz]
- DBI [http://search.cpan.org/CPAN/authors/id/T/TI/TIMB/DBI-1.633.tar.gz]
- List::MoreUtils [http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/List-MoreUtils-0.413.tar.gz]
- MASS [http://cran.r-project.org/src/contrib/MASS_7.3-40.tar.gz]
- calibrate [http://cran.r-project.org/src/contrib/calibrate_1.7.2.tar.gz]
- getopt [http://cran.r-project.org/src/contrib/getopt_1.20.0.tar.gz]
- optparse [http://cran.r-project.org/src/contrib/optparse_1.3.0.tar.gz]
- plotrix [http://cran.r-project.org/src/contrib/plotrix_3.5-11.tar.gz]
- DBI [http://cran.r-project.org/src/contrib/DBI_0.3.1.tar.gz]
- RMySQL [http://cran.r-project.org/src/contrib/RMySQL_0.10.3.tar.gz]
- zoo [http://cran.r-project.org/src/contrib/zoo_1.7-12.tar.gz]
- diptest [http://cran.r-project.org/src/contrib/diptest_0.75-6.tar.gz]
- randomForest [http://cran.r-project.org/src/contrib/randomForest_4.6-10.tar.gz]
Step 1: Download source from GitHub
> git clone https://github.com/getiria-onsongo/tso_cnv.git tso_cnv
Step 2: Navigate to parent directory
> cd tso_cnv
Step 3: Download generic MySQL source code
> wget https://s3.msi.umn.edu/CNVMySQL/mysql-5.6.24-linux-glibc2.5-x86_64.tar.gz
*Original mysql source from here
Selected options for Linux - Generic, compressed TAR archive.*
Step 4: Navigate to directory that will contain base MySQL tables
> mkdir tso_tables
> cd tso_tables
Step 5: Download and uncompress MySQL base tables
> wget https://s3.msi.umn.edu/CNVMySQL/mysql_tables.tar.gz
> tar xzvf mysql_tables.tar.gz
Step 6:
Edit my.cnf to specify MySQL configurations appropriate for your system. Default setting assume a machine with at least 64GB of RAM. The file my-small.cnf contains example values for a smaller machine (at least 5GB of RAM). For more details on editing MySQL option file see
Step 7:
Edit configuration file (config_template.ini) to specify expected input values. Note, The program assumes your data was sequenced on two lanes and expects four fastq files for both sample and its matched control.
Step 8: Generate PBS script to run program on cluster.
> cd ..
> sh launcher.sh config_template.ini
NOTE: The template PBS script is in "template/run_sample.pbs". Edit this template to conform to your clusters settings
Step 9: Submit job to cluster
> cd sample_name
> qsub run_cnv_sample_name.pbs
NOTE: sample_name is the name of the sample being analyzed which is specified in the configuration file (config_template.ini)