# Version June 11, 2026 # ---------------------------------------------------------------------- # 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. The following line that sets the BIRCH ## environment variable is generated during installation and ## updating. This file should never be edited manually. ## All local changes should be made in $BIRCH/local/admin ##******************************************************* BIRCH=/home/birch/BIRCH 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=$BIRCH/GenBank genbank=$GENBANK GB=$GENBANK gb=$GENBANK PIR=$BIRCH/PIR pir=$PIR RE=$BIRCH/REBASE BLASTDB=$GENBANK #databases used by standalone blast # BIRCHLIBS - libraries for Python scripts BIRCHPYLIB=$BIRCH/script/birchpylib export birch dat DOC doc TUTORIALS tutorials GENBANK \ genbank GB gb PIR pir RE BLASTDB BIRCHPYLIB #------------------------------------------------ # Use this for a more diverse server cluster # Platform-specific setup commands # BIRCH_BIN - location of BIRCH binaries # RM_CMD - file to use for 'rm' command BIRCHLIBS="" # Apple is transitioning from the Intel architecture to ARM64. # We want to put bin-macos-arm64 (BIRCH_BIN) first in the PATH, so that # native arm64 binaries are found first. If a program is not # available for arm64, the shell will search for it in # bin-osx-x86_64 (BIRCH_BIN_ALT). The Intel binaries in that directory # will be run in emulated mode by Rosetta2. BIRCH_BIN_ALT="" case "$BIRCH_PLATFORM" in solaris-sparc) BIRCH_BIN=bin-solaris-sparc RM_CMD=/usr/bin/rm ;; solaris-amd64) BIRCH_BIN=bin-solaris-amd64 RM_CMD=/usr/bin/rm ;; linux-intel) BIRCH_BIN=bin-linux-intel RM_CMD=/bin/rm ;; linux-x86_64) BIRCH_BIN=bin-linux-x86_64 RM_CMD=/bin/rm ;; linux-arm64) BIRCH_BIN=bin-linux-arm64 BIRCH_BIN_ALT=bin-linux-x86_64 RM_CMD=/bin/rm ;; osx-x86_64) BIRCH_BIN=bin-osx-x86_64 RM_CMD=/bin/rm ;; macos-arm64) BIRCH_BIN=bin-macos-arm64 BIRCH_BIN_ALT=bin-osx-x86_64 RM_CMD=/bin/rm ;; win7-64) BIRCH_BIN=bin-win7-64 RM_CMD=/bin/rm ;; *) BIRCH_BIN=bin-linux-x86_64 RM_CMD=/usr/bin/rm ;; esac export BIRCH_BIN RM_CMD # $BIRCH/script is for scripts that work on all platforms # $BIRCH_BIN is a bin directory, chosen in profile.source, # with platform-specific binaries # Check the current path for $BIRCH_BIN. Since one shell can # launch another shell, we don't want to keep adding $BIRCH_BIN each # time a new shell is spawned. COUNT=`echo $PATH | grep -c $BIRCH/$BIRCH_BIN` if [ "$COUNT" -eq "0" ] then case "$BIRCH_PLATFORM" in macos-arm64 | linux-arm64 ) PATH=$BIRCH/local/script\:$BIRCH/local/$BIRCH_BIN\:$BIRCH/local/$BIRCH_BIN_ALT\:$PATH\:$BIRCH/script\:$BIRCH/$BIRCH_BIN:$BIRCH/$BIRCH_BIN_ALT ;; * ) PATH=$BIRCH/local/script\:$BIRCH/local/$BIRCH_BIN\:$PATH\:$BIRCH/script\:$BIRCH/$BIRCH_BIN esac 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 #------------------------ BIRCH SETTINGS -------------- # Get values of environment variables if [ -f $BIRCH/admin/birch_settings_Bourne.source ] then . $BIRCH/admin/birch_settings_Bourne.source fi BIRCH_PROMPT="Y" # Personal setting for prompt overrides all other settings. if [ -f $HOME/.config/BIRCH/BIRCHsettings.source ] then result=`grep 'BIRCH_PROMPT=N' $HOME/.config/BIRCH/BIRCHsettings.source` if [ "$result" != "" ] then BIRCH_PROMPT="N" fi fi export BIRCH_PROMPT if [ "$BIRCH_PROMPT" = "Y" ] then if [ -f $BIRCH/local/admin/set_birch_prompt_Bourne.source ] then # Local settings override default settings . $BIRCH/local/admin/set_birch_prompt_Bourne.source else # default . $BIRCH/admin/set_birch_prompt_Bourne.source fi fi #------------------------ 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. # It looks like BIRCH_TMP isn't currently used in BIRCH, but # we'll keep it for now until we can be absolutely sure. # It will probably reappear as a setting that can be changed # in birchadmin. 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 #-------------------------- 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=$BL_Document export ACE_EDIT_COMMAND ACE_PDF_COMMAND ACE_PS_COMMAND ACE_BITMAP_VIEWER ACE_SPREADSHEET ACE_DOCUMENT #--------------------------- ABYSS #alias zsh=$BIRCH/bin-$BIRCH_PLATFORM/zsh #--------------------------- ARTEMIS ARTEMIS_HOME=$BIRCH/java/artemis #-------------------------- CBB HISAT2_HOME=$BIRCH/lib-$BIRCH_PLATFORM/hisat2 #-------------------------- FASTA FASTLIBS=$DAT/fasta/fastgbs export FASTLIBS #-------------------------- FSAP #-------------------------- MAPMAKER, GENEHUNTER MAPM_LIB=$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 #--------------------------- 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 is not currently used in BIRCH, but is # retained for now until we can check carefully that removing # it won't break anything. BIRCH_LOGGING=0 export BIRCH_LOGGING ################################################################ # LOCAL EXTENSIONS TO BIRCH # ################################################################ if [ -f $BIRCH/local/admin/local.profile.source ] then . $BIRCH/local/admin/local.profile.source fi ################################################################ # User Preferences that override defaults # ################################################################ BIRCHSettingsFile=$HOME/.config/BIRCH/BIRCHsettings.source if [ -f $BIRCHSettingsFile ] then . $BIRCHSettingsFile fi BLHelperFile=$HOME/.config/BIRCH/BLHelper.source if [ -f $BLHelperFile ] then . $BLHelperFile 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