Merge pull request #11 from pgdurand/prepV5

Prep v5

conda/build.sh

@@ -11,16 +11,16 @@ cp -R ${SRC_DIR}/external $PREFIX
 cp -R ${SRC_DIR}/license $PREFIX
 
 # Copy BeeDeeM scripts and update them with default config
-cp ${SRC_DIR}/scripts/*.sh $PREFIX/bin
-sed -i 's/@KL_WORKING_DIR@/\/beedeem-wk/g' $PREFIX/bin/*.sh
-sed -i 's/@JAVA_ARGS@/-Xms128M -Xmx2048M -Djava.io.tmpdir=\$KL_WORKING_DIR -DKL_LOG_TYPE=console/g' $PREFIX/bin/*.sh
+cp ${SRC_DIR}/scripts/bdm.sh $PREFIX/bin/bdm
+sed -i 's/@KL_WORKING_DIR@/\/beedeem-wk/g' $PREFIX/bin/bdm
+sed -i 's/@JAVA_ARGS@/-Xms128M -Xmx4G -Djava.io.tmpdir=\$KL_WORKING_DIR -DKL_LOG_TYPE=console/g' $PREFIX/bin/bdm
 
 # Copy the BeeDeeM master configuration file and update it
 cp ${SRC_DIR}/scripts/dbms.config $PREFIX/conf
 sed -i 's/@BIOBASE_ROOTDIR@/\/beedeem-db/g' $PREFIX/conf/dbms.config
 
 # Ensure executables have valid exec permission
-chmod +x $PREFIX/bin/*.sh
+chmod +x $PREFIX/bin/bdm
 chmod +x $PREFIX/external/bin/linux/*
 chmod +x $PREFIX/external/bin/macos/*
 chmod +x $PREFIX/conf/scripts/*.sh

conda/run_test.sh

@@ -17,7 +17,7 @@ mkdir -p $KL_WORKING_DIR
 # path
 DESC_LIST="PDB_proteins,SwissProt_human"
 # Start installation
-install.sh -desc $DESC_LIST
+bdm install -desc $DESC_LIST
 
 # Note: by design of this script, we DO NOT delete
 # $KL_WORKING_DIR... please, do it yourself.

docker/Dockerfile

@@ -47,10 +47,10 @@ RUN \
 
 RUN \
   cd /opt/beedeem && \
-  cp scripts/*.sh . && \
+  cp scripts/bdm.sh ./bdm && \
   cp scripts/dbms.config conf && \
   sed -i 's/@BIOBASE_ROOTDIR@/\/beedeem-db/g' conf/dbms.config && \
-  chmod +x *.sh && \
+  chmod +x bdm && \
   chmod +x /opt/beedeem/external/bin/linux/* && \
   chmod +x /opt/beedeem/conf/scripts/*.sh && \
   cd /opt/beedeem/external/bin && rm -rf macos windows

scripts/install.bat → scripts/bdm.bat

@@ -1,12 +1,16 @@
 @echo off
 
 rem
-rem DBMS program to install databanks ; for Mac/Linux
-rem Copyright (c) - Patrick G. Durand, 2007-2017
+rem BeeDeeM starter command for Windows
+rem Copyright (c) - Patrick G. Durand, 2007-2022
 rem -------------------------------------------------------------------
 rem User manual:
 rem   https://pgdurand.gitbooks.io/beedeem/
 rem -------------------------------------------------------------------
+rem Command use: 
+rem  bdm.bat -h: to get help
+rem  bdm.bat <command> [options]: to start a command
+rem
 rem In addition, some parameters can be passed to the JVM for special 
 rem configuration purposes:<br>
 rem -DKL_DEBUG=true ; if true, if set, log will be in debug mode<br>
@@ -18,7 +22,8 @@ rem -DKL_CONF_DIR=an_absolute_path ; the absolute path to a home-made
 rem  conf directory. If not set, use ${user.dir}/conf.
 rem -DKL_LOG_TYPE=none|console|file(default)
 rem
-rem Proxy configuration: update configuration file: ${beedeemHome}/conf/system/network.config.
+rem Proxy configuration: update configuration file: 
+rem      ${beedeemHome}/conf/system/network.config.
 
 rem *** Application home
 set KL_APP_HOME=@KL_INSTALL_DIR@
@@ -35,4 +40,4 @@ set FILES=
 for /F %%f in ('dir /b %KL_APP_HOME%\bin\*.jar') do set FILES=!FILES!;%KL_APP_HOME%\bin\%%f
 
 rem *** Start application
-java.exe %KL_JAVA_ARGS% -classpath "%FILES%" bzh.plealog.dbmirror.main.CmdLineInstaller %*
+java.exe %KL_JAVA_ARGS% -classpath "%FILES%" bzh.plealog.dbmirror.main.BeeDeeMain %*

scripts/install.sh → scripts/bdm.sh

@@ -1,12 +1,16 @@
 #!/usr/bin/env bash
 #
 # -------------------------------------------------------------------
-# DBMS program to install databanks ; for Mac/Linux
+# BeeDeeM starter command for macOS/Linux
 # Copyright (c) - Patrick G. Durand, 2007-2022
 # -------------------------------------------------------------------
 # User manual:
 #   https://pgdurand.gitbooks.io/beedeem/
 # -------------------------------------------------------------------
+# Command use: 
+#    bdm -h: to get help
+#    bdm <command> [options]: to start a command
+#
 # In addition, some parameters can be passed to the JVM for special 
 # configuration purposes:<br>
 # -DKL_DEBUG=true ; if true, if set, log will be in debug mode<br>
@@ -22,7 +26,8 @@
 #  env variables before calling this script. Additional JRE arguments
 #  can also be passed in to this script using env variable KL_JRE_ARGS.
 #
-# Proxy configuration: update configuration file: ${beedeemHome}/conf/system/network.config.
+# Proxy configuration: update configuration file: 
+#      ${beedeemHome}/conf/system/network.config.
 
 # *** Application home
 KL_APP_HOME=$( cd -P -- "$(dirname -- "$(command -v -- "$0")")" && pwd -P )
@@ -57,6 +62,6 @@ KL_JAR_LIST_TMP=`\ls $KL_APP_HOME/bin/*.jar`
 KL_JAR_LIST=`echo $KL_JAR_LIST_TMP | sed 's/ /:/g'`
 
 # *** start application
-KL_APP_MAIN_CLASS=bzh.plealog.dbmirror.main.CmdLineInstaller
+KL_APP_MAIN_CLASS=bzh.plealog.dbmirror.main.BeeDeeMain
 java $KL_JAVA_ARGS -classpath $KL_JAR_LIST $KL_APP_MAIN_CLASS $@
 

scripts/beedeem_info.xml

@@ -8,8 +8,8 @@
         <requirement type="package" version="@PRG_VERSION@">beedeem</requirement>
     </requirements>
     <command><![CDATA[ 
-	info.sh -f galaxy -d n >& $my_blastn_db;
-        info.sh -f galaxy -d p >& $my_blastp_db
+	bdm info -f galaxy -d n >& $my_blastn_db;
+        bdm info -f galaxy -d p >& $my_blastp_db
     ]]></command>
     <outputs>
         <data format="beedeemn" name="my_blastn_db" label="My nucleotide BLAST databases" />