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Installation of ncPRO-seq

You can download the source of ncPRO-seq and annotation files of different species from our project page in sourceforge (http://sourceforge.net/projects/ncproseq/files/).

To build the ncPRO-seq pipeline, extract the source and species annotation file you choose, move the whole folder of species annotation files to annotation/ in the sources folder.
Edit the config-system.txt file in the sources folder and change the paths of the required softwares.

1whitegray!20
Table 1: Set Paths in the config-system.txt file before installation.
gray Options Description Example
INSTALL_WWW 0/1. If 1, the web interface of ncPRO-seq is installed in WWW_DIR and CGI_DIR 1
APPLI_DIR Absolute path of installation folder /home/ncPROseq/
WWW_DIR HTML installation folder. Have to be under the web working directory /var/www/ncPROseq/
CGI_DIR CGI installation folder. Have to be under the CGI working directory /usr/lib/cgi-bin/ncPROseq/
WWW_RES Results path for local web version /home/ncPROseq/www_results
PBS_MODE 0/1. If 1, the job are send to the PBS job scheduler using the qsub command 0
PBS_OPT Options to give to qsub at job submission -m ae -M bioinfo.ncproseq@curie.fr -j oe -l nodes=1:ppn=6,mem=20gb
PBS_PATH Absolute path to PBS (qsub) command /usr/bin
R_PATH Absolute path to R binary folder /usr/local/R/R/bin/
AWK_PATH Absolute path to awk executable folder /usr/bin/
BOWTIE_PATH Absolute path to bowtie executable folder /usr/local/bowtie-0.12.7/
BOWTIE_INDEXES_PATH Installation folder of Bowtie indexes /home/Apps/Bowtie_indexes/
BEDTOOLS_PATH Installation folder of BedTools binaries /home/Apps/BEDTools-Version-2.15.0/bin/
SAMTOOLS_PATH Installation folder of samtools binary /home/nservant/Apps/samtools/
CONVERT_PATH Utilities used to create thumbnail for html report /usr/bin/
BAM_MAPCT_PATH Installation folder of the bamMapCount program. Distributed with the BEDTools-version10.0 /home/Apps/BEDTools-Version-2.10.0/bin/
PERL_PATH Perl installation folder /usr/local/bin
MAILX_PATH Optional - mailx excutable path to send email at the end of the analysis /usr/bin/
   

Once the config-system.txt is ready, go to the sources directory, and simply use the following command: 

> make CONFIG_SYS=config-system.txt install

This command will install the sources in the folder specified in the config-system.txt file. Note that if some of the paths from the config-system.txt are not correct (or unknown), the installation program will try to find them on the system.
In most of the cases, the installation of ncPRO-seq required administrator rigths, especially for the installation under the web directories.

next up previous contents
Next: How to use it Up: Requirements and Installation Previous: Required softwares   Contents
Nicolas Servant 2012-05-31