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/ |
|---|
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