# Version June 22, 2015 # ---------------------------------------------------------------------- # This file is called by .profile to initialize environment variables # and set up the path. ################################################################ # PLATFORM-SPECIFIC SETTINGS # ################################################################ # BIRCH_DEBUG = 1 will cause each successive profile.source, platform.profile.source # etc. to each print progress messages. BIRCH_DEBUG=0 if [ $BIRCH_DEBUG -eq 1 ] then echo Running profile.source fi ##******************************************************* ## LOCATION OF BIRCH. This should be the only line you ## need to change in this file. All local changes should ## be made in $BIRCH/local/admin ##******************************************************* BIRCH=/home/psgendb/BIRCHDEV export BIRCH # Get critical platform-specific settings, which will # govern how other settings are made. If you have additional # commands that you want to override commands in this file, # put them in $BIRCH/local/admin/local.profile.source, which is called # at the end of this file. . $BIRCH/local/admin/platform.profile.source ################################################################ # GLOBAL SETTINGS # ################################################################ #----------------- BIRCH ENVIRONMENT VARIABLES --------------------- #useful environment variables for sequence work # both upper and lowercase equivalents are permitted birch=$BIRCH LOCAL=$BIRCH/local local=$LOCAL # Documentation and data directories DOC=$BIRCH/doc doc=$DOC DAT=$BIRCH/dat dat=$DAT TUTORIALS=$BIRCH/tutorials tutorials=$TUTORIALS # Databases GENBANK=$BIRCH/GenBank GENPEPT=$BIRCH/GenPept genbank=$GENBANK GB=$GENBANK gb=$GENBANK GP=$GENPEPT gp=$GENPEPT PIR=$BIRCH/PIR pir=$PIR RE=$BIRCH/REBASE # BIRCHLIBS - libraries for Python scripts BIRCHPYLIB=$BIRCH/script/birchpylib # Default appplications # # Older versions of netscape/mozilla need to be called using the # openURL() argument, if you try to launch a new page while # a copy of the browser is already running. The variable BROWSER_OPENURL # is set to 0 by default. If you are using an older browser # such as Netscape 7.1 and earlier, BROWSER_OPENURL should be set # to 1. # This variable is only used by browser.sh, which is a BOURNE shell # script. It is not needed for csh, tcsh etc. #BL_Browser=firefox #BROWSER_OPENURL=0 export birch dat DOC doc TUTORIALS tutorials GENBANK GENPEPT \ genbank GB gb GP gp PIR pir RE #------------------------------------------------ # Use this for a more diverse server cluster # Platform-specific setup commands # RM_CMD - file to use for 'rm' command BIRCHLIBS="" case "$BIRCH_PLATFORM" in solaris-sparc) BIRCH_BIN=bin-solaris-sparc BIRCHLIBS="/usr/dt/lib\:/usr/openwin/lib\:/usr/local/qt/lib\:$BIRCH/lib-solaris-sparc\:$BIRCH/local/lib-solaris-sparc" RM_CMD=/usr/bin/rm ;; solaris-amd64) BIRCH_BIN=bin-solaris-amd64 BIRCHLIBS="/usr/dt/lib\:/usr/openwin/lib\:/usr/local/qt/lib\:$BIRCH/lib-solaris-amd64\:$BIRCH/local/lib-solaris-amd64" RM_CMD=/usr/bin/rm ;; linux-intel) BIRCH_BIN=bin-linux-intel BIRCHLIBS=$BIRCH/lib-linux-intel\:$BIRCH/lib-linux-intel/openwin/lib\:$BIRCH/local/lib-linux-intel RM_CMD=/bin/rm ;; linux-x86_64) BIRCH_BIN=bin-linux-x86_64 BIRCHLIBS=$BIRCH/lib-linux-x86_64\:$BIRCH/lib-linux-x86_64/openwin/lib\:$BIRCH/local/lib-linux-x86_64 RM_CMD=/bin/rm ;; osx-x86_64) BIRCH_BIN=bin-osx-x86_64 BIRCHLIBS=$BIRCH/lib-osx-x86_64\:$BIRCH/lib-osx-x86_64/openwin/lib\:$BIRCH/local/lib-osx-x86_64 RM_CMD=/bin/rm ;; winxp-32) BIRCH_BIN=bin-winxp-32 BIRCHLIBS=$BIRCH/lib-winxp-32\:$BIRCH/local/lib-winxp-32 RM_CMD=/bin/rm ;; win7-64) BIRCH_BIN=bin-win7-64 BIRCHLIBS=$BIRCH/lib-win7-64\:$BIRCH/local/lib-win7-64 RM_CMD=/bin/rm ;; AIX) BIRCH_BIN=bin-AIX ;; HP) BIRCH_BIN=bin-HP ;; *) BIRCH_BIN=bin-linux-x86_64 RM_CMD=/usr/bin/rm ;; esac export BIRCH_BIN RM_CMD # Set path and MANPATH # $BIRCH/script is for scripts that work on all platforms # $BIRCH_BIN is a bin directory, chosen in profile.source, # with platform-specific binaries COUNT=`echo $PATH | grep -c $BIRCH/$BIRCH_BIN` if [ "$COUNT" -eq "0" ] then # PATH=$PATH\:$BIRCH/script\:$BIRCH/$BIRCH_BIN:$BIRCH/local/script\:$BIRCH/local/$BIRCHBIN PATH=$BIRCH/local/script\:$BIRCH/local/$BIRCH_BIN\:$PATH\:$BIRCH/script\:$BIRCH/$BIRCH_BIN fi export PATH # Set Manual path case "$BIRCH_PLATFORM" in solaris-*) if [ -z "$MANPATH" ] then MANPATH=$BIRCH\:$BIRCH/local else COUNT=`echo "$MANPATH" | grep -c $BIRCH` if [ "$COUNT" -eq "0" ] then MANPATH=$MANPATH\:$BIRCH\:$BIRCH/local fi fi export MANPATH ;; # On Debian Linux, man -w doesn't work, and there is no alternative # switch that works for linux distributions. For now the workaround # is just to check the $MANPATH variable. # linux-*) # MANPATH=`man -w`\:$BIRCH\:$BIRCH/local # export MANPATH # ;; *) # This is probably safest when we don't know how # man works on a system.If you try setting MANPATH # on a system that uses /etc/man.config, you clobber # all manual pages other than the BIRCH pages. if [ ! -z "$MANPATH" ] then COUNT=`echo "$MANPATH" | grep -c $BIRCH` if [ "$COUNT" -eq "0" ] then MANPATH=$MANPATH\:$BIRCH\:$BIRCH/local fi fi export MANPATH ;; esac #------------------------ TEMPORARY DIRECTORIES -------------- # This variable may be changed in local.profile.source, # telling where temporary files may be written for some # scripts which run programs that generate very large # temporary files. BIRCH_TMP="" export BIRCH_TMP #---------------------------- OTHER SETTINGS ----------------- # noclobber must be off so that files can be overwritten # unset noclobber # unset noclobber appeears not to work on some linux systems, # so we do it this way. set +o noclobber # Limit core files to 0 bytes ulimit -c 0 # Printer variables PSPRINT=ccp export PSPRINT ################################################################ # APPLICATION-SPECIFIC SETTINGS # ################################################################ #-------------------------- BioLegato programs: eg. birch, bldna, blprotein, blmarker, bltree... if [ -f $BIRCH/admin/setblenv.profile.$BIRCH_PLATFORM.source ] then . $BIRCH/admin/setblenv.profile.$BIRCH_PLATFORM.source fi case $BIRCH_PLATFORM in "solaris-sparc") BLBIRCH_HELP_DIR=$dat/blbirch BLDNA_HELP_DIR=$dat/bldna BLPROTEIN_HELP_DIR=$dat/blprotein BLDATA_HELP_DIR=$dat/bldata BLTREE_HELP_DIR=$dat/bltree BLMARKER_HELP_DIR=$dat/blmarker ;; "solaris-amd64") BLBIRCH_HELP_DIR=$dat/blbirch BLDNA_HELP_DIR=$dat/bldna BLPROTEIN_HELP_DIR=$dat/blprotein BLDATA_HELP_DIR=$dat/bldata BLTREE_HELP_DIR=$birch/dat/bltree BLMARKER_HELP_DIR=$birch/dat/blmarker ;; "linux-intel") BLBIRCH_HELP_DIR=$dat/blbirch BLDNA_HELP_DIR=$dat/bldna BLPROTEIN_HELP_DIR=$dat/blprotein BLDATA_HELP_DIR=$dat/bldata BLTREE_HELP_DIR=$dat/bltree BLMARKER_HELP_DIR=$dat/blmarker ;; "linux-x86_64") BLBIRCH_HELP_DIR=$dat/blbirch BLDNA_HELP_DIR=$dat/bldna BLPROTEIN_HELP_DIR=$dat/blprotein BLDATA_HELP_DIR=$dat/bldata BLTREE_HELP_DIR=$dat/bltree BLMARKER_HELP_DIR=$dat/blmarker ;; "osx-x86_64") BLBIRCH_HELP_DIR=$dat/blbirch BLDNA_HELP_DIR=$dat/bldna BLPROTEIN_HELP_DIR=$dat/blprotein BLDATA_HELP_DIR=$dat/bldata BLTREE_HELP_DIR=$dat/bltree BLMARKER_HELP_DIR=$dat/blmarker ;; "winxp-32") BLBIRCH_HELP_DIR=$dat/blbirch BLDNA_HELP_DIR=$dat/bldna BLPROTEIN_HELP_DIR=$dat/blprotein BLDATA_HELP_DIR=$dat/bldata BLTREE_HELP_DIR=$dat/bltree BLMARKER_HELP_DIR=$dat/blmarker ;; "win7-64") BLBIRCH_HELP_DIR=$dat/blbirch BLDNA_HELP_DIR=$dat/bldna BLPROTEIN_HELP_DIR=$dat/blprotein BLDATA_HELP_DIR=$dat/bldata BLTREE_HELP_DIR=$dat/bltree BLMARKER_HELP_DIR=$dat/blmarker ;; *) # These are lowest commen denominator choices, most likely to # be on all Unix systems, but generally pretty poor choices. # Choose better ones by commenting out lines in # $BIRCH/local/admin/local.cshrc.source BLBIRCH_HELP_DIR=$dat/blbirch BLDNA_HELP_DIR=$dat/bldna BLPROTEIN_HELP_DIR=$dat/blprotein BLDATA_HELP_DIR=$dat/bldata BLTREE_HELP_DIR=$dat/bltree BLMARKER_HELP_DIR=$dat/blmarker ;; esac export BLBIRCH_HELP_DIR BLDNA_HELP_DIR BLPROTEIN_HELP_DIR BLDATA_HELP_DIR BLTREE_HELP_DIR BLMARKER_HELP_DIR #-------------------------- ACEDB ACEDB=$BIRCH/acedb ACE_EDIT_COMMAND=$BL_TextEditor ACE_PDF_COMMAND=$BL_PDFViewer ACE_PS_COMMAND=$BL_PSViewer ACE_BITMAP_VIEWER=$BL_ImageViewer ACE_SPREADSHEET=$BL_Spreadsheet ACE_DOCUMENT=$BL_Document export ACE_EDIT_COMMAND ACE_PDF_COMMAND ACE_PS_COMMAND ACE_BITMAP_VIEWER ACE_SPREADSHEET ACE_DOCUMENT #--------------------------- ARTEMIS ARTEMIS_HOME=$BIRCH/java/artemis #-------------------------- BOXSHADE BOXDIR=$dat/boxshade export BOXDIR #-------------------------- FASTA # ...also, see THREADING above FASTLIBS=$DAT/fasta/fastgbs export FASTLIBS #-------------------------- FSAP #-------------------------- GeneParser GP_HOME=$dat/geneparser export GP_HOME #-------------------------- MAPMAKER, GENEHUNTER MAPM_LIB=$DAT/mapmaker GH_DIR=$DAT/genehunter #GS_LIB=$MAPM_LIB/ghostscript export MAPM_LIB GH_DIR #-------------------------- NCBI NCBI=$BIRCH/pkg/NCBI CN3D_HOME=$NCBI export NCBI CN3D_HOME #--------------------------- PRIMER3 PRIMER_BIN=$BIRCH/$BIRCH_BIN export PRIMER_BIN #-------------------------- TACG TACGLIB=$dat/tacg export TACGLIB #--------------------------- TIGR TM4 # If your system has enough memory, set this to at least 512 or 1024 TMEV_JAVA_MEMORY=256 export TMEV_JAVA_MEMORY #--------------------------- XYLEM XYLEM_PLATFORM=$BIRCH_PLATFORM export XYLEM_PLATFORM ################################################################ # SYSTEM STATISTICS # # # # Put code here for recording user traffic etc. # ################################################################ BIRCH_LOGGING=0 export BIRCH_LOGGING ################################################################ # LOCAL EXTENSIONS TO BIRCH # ################################################################ if [ -f $BIRCH/local/admin/local.profile.source ] then . $BIRCH/local/admin/local.profile.source fi ################################################################ # FIRST TIME LOGIN PROCEDURES # # This simulates a .login file for sh and similar shells # ################################################################ # Only run the login script once. # This one didn't seem to work. # We can test this by seeing if BIRCH has been added to the PATH. #COUNT=`echo $PATH | grep -c $BIRCH` #if [ "$COUNT" -eq "0" ] # then # . $BIRCH/admin/profile.login.source #fi # Another approach: # We can test this by seeing if BIRCH_LOGGEDIN has been set. if [ -z "$BIRCH_LOGGEDIN" ] then BIRCH_LOGGEDIN=1 export BIRCH_LOGGEDIN . $BIRCH/admin/profile.login.source fi