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Annotation of /ReleaseTools/sysbiorc.csh

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Revision 1.2 - (view) (download) (as text)

1 : efrank 1.1 ###
2 :     # env setup so must be sourced, not run
3 :     #
4 :     # This is a sample of a typical system-level configuration that users
5 :     # could source and thereafter be ready to use the ReleaseTools. The
6 :     # key thing is the block of environment variables, RTROOT, etc. (see below).
7 :     #
8 :     ###
9 :    
10 :     ##
11 :     # Release tools stuff
12 :     ##
13 :    
14 :     setenv RTCURRENT rtBoot
15 : efrank 1.2 setenv RTROOT ~efrank/KahRoot
16 : efrank 1.1 setenv RTDIST ${RTROOT}/dist
17 : efrank 1.2 setenv RTARCH linux-gentoo
18 : efrank 1.1
19 :     alias rtpath 'source $RTDIST/releases/$RTCURRENT/ReleaseTools/RTPath.csh'
20 :     ##
21 :     # Stuff for external dependencies. These are software that we need, but
22 :     # do not ship.
23 :     ##
24 :    
25 :     setenv EXTERNAL_REL 0.0.2
26 : efrank 1.2 set EXTERNAL=$RTROOT/external/releases/$EXTERNAL_REL
27 : efrank 1.1
28 :     ##
29 :     # make sure they have some sort of path, but see also RTPath.csh
30 :     ##
31 :    
32 :     set path=( $EXTERNAL/bin $path $EXTERNAL/AccessGrid/bin )
33 :     rtpath
34 :    
35 :     ##
36 :     # CVS Repo. You can also do :ext:username@biocvs if you need to, but this
37 :     # should work in general:
38 :     ##
39 :    
40 :     setenv CVSROOT :ext:biocvs.mcs.anl.gov:/disks/cvs/bio
41 :     setenv CVS_RSH ssh
42 :    
43 :     setenv CYTOSCAPE_HOME /homes/SysBio/external/packages/Cytoscape1.1.1/
44 :     setenv CYTOSCAPE_COMMAND $CYTOSCAPE_HOME/cytoscape.sh
45 :     if ( $?DOTFONTPATH ) then
46 :     setenv CYTOSCAPE_DISPLAY $DISPLAY
47 :     endif
48 :    
49 :    
50 :    
51 :     ###
52 :     # What follows are set up as appends so that earlier configs can supercede.
53 :     ##
54 :    
55 :     # systems dot lacks fonts. we dumped needed fonts here:
56 :    
57 :    
58 :     if ( $?DOTFONTPATH ) then
59 :     setenv DOTFONTPATH ${DOTFONTPATH}:/homes/SysBio/external/X11R6/lib/X11/fonts/truetype
60 :     else
61 :     setenv DOTFONTPATH /homes/SysBio/external/X11R6/lib/X11/fonts/truetype
62 :     endif
63 :    
64 :    
65 :     if ( $?PYTHONPATH ) then
66 :     setenv PYTHONPATH ${PYTHONPATH}:/homes/SysBio/external/releases/${EXTERNAL_REL}/lib/python2.2/site-packages
67 :     else
68 :     setenv PYTHONPATH /homes/SysBio/external/releases/${EXTERNAL_REL}/lib/python2.2/site-packages
69 :     endif
70 :    
71 :    
72 :     if ( $?LD_LIBRARY_PATH ) then
73 :     setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${EXTERNAL}/lib/:/soft/com/packages/oracle/OraHome1/lib
74 :     else
75 :     setenv LD_LIBRARY_PATH ${EXTERNAL}/lib/:/soft/com/packages/oracle/OraHome1/lib
76 :     endif
77 :    
78 :     ##
79 :     # Configure shared AG installation
80 :     ##
81 :    
82 : efrank 1.2 # only needed for build, not for run
83 :     #source $EXTERNAL/AccessGrid/env-init.csh
84 : efrank 1.1

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