-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy path.bash_profile
More file actions
66 lines (46 loc) · 3.39 KB
/
.bash_profile
File metadata and controls
66 lines (46 loc) · 3.39 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
# .bash_profile
# Get the aliases and functions
if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi
# User specific environment and startup programs
alias l="ll -hrt"
alias les="less -S"
alias qsub='/opt/gridengine/bin/lx26-amd64/qsub -q rna.q -q all.q'
alias qsub1='/opt/gridengine/bin/lx26-amd64/qsub'
SOFT=/PUBLIC/software/public
MY=/PROJ/RNA/lilin
RNASOFT=/PUBLIC/software/RNA
WORK=/WORK/RNA/lilin
BJ=/BJPROJ/RNA/lilin
LNC=/PUBLIC/source/RNA/lncRNA/lncRNA_v1
MAF=/PUBLIC/database/RNA/maf/genome
# PATH EV
PATH=$RNASOFT/msort/bin:$SOFT/Alignment/bowtie2-2.0.6:$SOFT/Alignment/bowtie2-2.2.2:$SOFT/Alignment/bowtie-1.0.1:$RNASOFT/tophat-2.0.9/:$SOFT/Alignment/blast-2.2.26:$RNASOFT/cufflinks-2.1.1:$SOFT/Alignment/ncbi-blast-2.2.28+/bin:$SOFT/Alignment/blat:$RNASOFT/ruby/bin:$SOFT/VarCall/samtools/samtools-0.1.18:$SOFT/System/sqlite3/bin:$RNASOFT/ViennaRNA-1.8.5/bin:$RNASOFT/mfold-3.5/bin:$RNASOFT/mirdeep2:$RNASOFT/ImageMagick-6.8.9-0/bin:$RNASOFT/psRobot_v1.2/bin:$RNASOFT/tRNAscan-SE/bin:$RNASOFT/randfold-2.0:$RNASOFT/srna-tools-cli:$RNASOFT/tRNA-scan-SE/bin:$SOFT/System/Perl-5.18.2/bin/:$SOFT/System/Python-2.7.6/bin/:$SOFT/System/R-2.15.3/bin/:$RNASOFT/circos-0.62-1/bin:$SOFT/System/mysql-5.1.62/bin:/PUBLIC/software/public/Annotation/hmmer-3.1b1/bin:$PATH:$HOME/bin
export PATH
# Python path EV
export PYTHONPATH=$SOFT/System/Python-2.7.6/lib/python2.7/site-packages/:/PUBLIC/software/public/Annotation/kobas2.0-20120208/src:/PUBLIC/software/RNA/galaxy/galaxy-dist2/galaxy-dist/lib:$PYTHONPATH
# Link dynamic lib path EV
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$SOFT/System/R-2.15.3/lib64/R/lib:$SOFT/System/Python-2.7.6/lib/:$SOFT/System/atlas:$SOFT/System/blas:$SOFT/System/pcre/lib
# Perl lib EV
export PERL5LIB=$SOFT/System/Perl-5.18.2/lib/perl5/5.18.2/:$RNASOFT/psRobot_v1.2/lib/:$RNASOFT/mirdeep2/lib/:$RNASOFT/srna-tools-cli/lib/:$RNASOFT/tRNAscan-SE/bin:$SOFT/System/Perl-5.18.2/lib/perl5/site_perl/5.18.2/x86_64-linux/:/PUBLIC/software/RNA/PfamScan:$PERL5LIB
#export
export MIREVO=/PUBLIC/software/RNA/miREvo
export MANPATH=/PUBLIC/software/RNA/tRNAscan-SE/man
#for c c++
export CPLUS_INCLUDE_PATH=$SOFT/System/boost_1_49_0
export C_INCLUDE_PATH=$SOFT/System/boost_1_49_0
export ATLAS=$SOFT/System/atlas
#Language
export LANG=en_US.UTF-8
PS1="\[\033[0;32m\]\A \[\033[0;31m\]\u\[\033[0;34m\]@\[\033[0;35m\]\h\[\033[0;34m\]:\[\033[00;36m\]\w\[\033[0;33m\] \n$\[\033[0m\]"
### old EV ##############################################################
#export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$SOFT/pcre/lib:$SOFT/R/lib64/R/lib:$SOFT/libgtextutils/lib:$SOFT/tre/lib:$SOFT/blas:$SOFT/pcre-8.32:$SOFT/atlas:$SOFT/python/lib:/usr/local/lib:/PROJ/RNA/share/software/MCR_R2012b/v80/runtime/glnxa64:/PROJ/RNA/share/software/MCR_R2012b/v80/bin/glnxa64:/PROJ/RNA/share/software/MCR_R2012b/v80/sys/os/glnxa64:/PROJ/RNA/share/software/MCR_R2012b/v80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/PROJ/RNA/share/software/MCR_R2012b/v80/sys/java/jre/glnxa64/jre/lib/amd64/server:/PROJ/RNA/share/software/MCR_R2012b/v80/sys/java/jre/glnxa64/jre/lib/amd64
#export PKG_CONFIG_PATH=$SOFT/libgtextutils/lib/pkgconfig:$SOFT/tre/lib/pkgconfig:$PKG_CONFIG_PATH
#export
#export MIREVO=/PROJ/RNA/share/software/miREvo
#export C_INCLUDE_PATH=$SOFT/boost_1_49_0
## perl library
#export PERL5LIB=$SOFT/TGICL-2.1/lib:$SOFT/mirdeep2/lib:$PERL5LIB #$SOFT/perl/lib/5.18.0
#for MATLAB MCR
#export XAPPLRESDIR=/PROJ/RNA/share/software/MCR_R2012b/v80/X11/app-defaults