Merge branch 'master' of https://github.com/pgdurand/BeeDeeM

NOTICE.txt

@@ -1,4 +1,4 @@
-This product includes software developed by:
+This software includes software developed by:
 
   The Plealog Team (http://www.plealog.com)
     Plealog license 1 is here: http://www.apache.org/licenses/LICENSE-2.0
@@ -34,3 +34,6 @@ This product includes software developed by:
     Biojava license is here: http://www.gnu.org/copyleft/lesser.html
     It targets: biojava, bytecode
 
+  The Informas Annotation framework 
+    License is here: https://github.com/rmuller/infomas-asl
+    It targets: eu.informas.annotation package

TODOs.txt

@@ -1,6 +1,3 @@
-- MaJ descripteurs avec dépendances ; temporairement virer pfam (marche plus ?)
-- MaJ doc: formatdb->makeblastdb 
-
 remote: warning: GH001: Large files detected. You may want to try Git Large File Storage - https://git-lfs.github.com.
 remote: warning: See http://git.io/iEPt8g for more information.
 remote: warning: File tests/junit/databank/fasta_multi2/fasta4.faa is 64.63 MB; this is larger than GitHub's recommended maximum file size of 50.00 MB

build.xml

@@ -38,13 +38,8 @@
 
 	<property name="rootpkg" value="bzh.plealog.dbmirror.main" />
 	<property name="KLMirrorClass" value="${rootpkg}.CmdLineInstaller" />
-	<property name="KLUIMirrorClass" value="${rootpkg}.UiInstaller" />
-	<property name="KLQueryMirrorClass" value="${rootpkg}.CmdLineQuery" />
-	<property name="KLMirrorAnnot" value="${rootpkg}.Annotate" />
-  <property name="KLMirrorInfo" value="${rootpkg}.DumpBankList" />
-  <property name="KLMirrorDelete" value="${rootpkg}.DeleteBank" />
-  <property name="KLMirrorCheck" value="${rootpkg}.AutoCheckDescriptors" />
-
+	<property name="KANT_ZIP" value="ant-1.9.4.zip" />
+
 	<path id="class.path">
 		<pathelement path="${classpath}" />
 		<fileset dir="${jar}">
@@ -216,77 +211,9 @@
 	<!-- ============================================================= -->
   <!-- Compile code and make software dustribution package           -->
 	<target name="makedistrib" depends="makejar">
-		<!-- Copy the DBMS scripts for Mac, Linux and Windows -->
-		<copy file="${scripts}/install.sh" todir="${Dscripts}">
-			<filterset>
-				<filter token="APP_MAIN_CLASS" value="${KLMirrorClass}" />
-			</filterset>
-		</copy>
-		<copy file="${scripts}/UiInstall.sh" todir="${Dscripts}">
-			<filterset>
-				<filter token="APP_MAIN_CLASS" value="${KLUIMirrorClass}" />
-			</filterset>
-		</copy>
-		<copy file="${scripts}/query.sh" todir="${Dscripts}">
-			<filterset>
-				<filter token="APP_MAIN_CLASS" value="${KLQueryMirrorClass}" />
-			</filterset>
-		</copy>
-		<copy file="${scripts}/annotate.sh" todir="${Dscripts}">
-			<filterset>
-				<filter token="APP_MAIN_CLASS" value="${KLMirrorAnnot}" />
-			</filterset>
-		</copy>
-		<copy file="${scripts}/info.sh" todir="${Dscripts}">
-			<filterset>
-				<filter token="APP_MAIN_CLASS" value="${KLMirrorInfo}" />
-			</filterset>
-		</copy>
-    <copy file="${scripts}/delete.sh" todir="${Dscripts}">
-      <filterset>
-        <filter token="APP_MAIN_CLASS" value="${KLMirrorDelete}" />
-      </filterset>
-    </copy>
-    <copy file="${scripts}/check.sh" todir="${Dscripts}">
-      <filterset>
-        <filter token="APP_MAIN_CLASS" value="${KLMirrorCheck}" />
-      </filterset>
-    </copy>
-		<copy file="${scripts}/install.bat" todir="${Dscripts}">
-			<filterset>
-				<filter token="APP_MAIN_CLASS" value="${KLMirrorClass}" />
-			</filterset>
-		</copy>
-		<copy file="${scripts}/UiInstall.bat" todir="${Dscripts}">
-			<filterset>
-				<filter token="APP_MAIN_CLASS" value="${KLUIMirrorClass}" />
-			</filterset>
-		</copy>
-		<copy file="${scripts}/query.bat" todir="${Dscripts}">
-			<filterset>
-				<filter token="APP_MAIN_CLASS" value="${KLQueryMirrorClass}" />
-			</filterset>
-		</copy>
-		<copy file="${scripts}/annotate.bat" todir="${Dscripts}">
-			<filterset>
-				<filter token="APP_MAIN_CLASS" value="${KLMirrorAnnot}" />
-			</filterset>
-		</copy>
-		<copy file="${scripts}/info.bat" todir="${Dscripts}">
-			<filterset>
-				<filter token="APP_MAIN_CLASS" value="${KLMirrorInfo}" />
-			</filterset>
-		</copy>
-    <copy file="${scripts}/delete.bat" todir="${Dscripts}">
-      <filterset>
-        <filter token="APP_MAIN_CLASS" value="${KLMirrorDelete}" />
-      </filterset>
-    </copy>
-    <copy file="${scripts}/check.bat" todir="${Dscripts}">
-      <filterset>
-        <filter token="APP_MAIN_CLASS" value="${KLMirrorCheck}" />
-      </filterset>
-    </copy>
+		<!-- Copy the DBMS scripts for Mac, Linux -->
+		<copy file="${scripts}/bdm.sh" todir="${Dscripts}" />
+    <copy file="${scripts}/test_bdm.sh" todir="${Dscripts}" />
 		<!-- Galaxy wrapper to list available DBs -->
     <copy file="${scripts}/beedeem_info.xml" todir="${Dconf}/system">
       <filterset>
@@ -316,7 +243,6 @@
 		<!-- Copy the DBMS Ant installer files -->
 		<copy file="${scripts}/config-std.properties" tofile="${distrib}/config.properties" />
 		<copy file="${scripts}/envDBMS" todir="${distrib}" />
-		<copy file="${scripts}/install-std.txt" tofile="${distrib}/INSTALL.txt" />
 		<copy file="${scripts}/deploy-std.xml" tofile="${distrib}/deploy.xml">
 			<filterset>
 				<filter token="KDBMS_TBALL" value="${apptar}.gz" />
@@ -326,7 +252,7 @@
 		<!-- in case Ant will not be available on the target system,
          we provide it. -->
 		<mkdir dir="${distrib}/ant" />
-		<copy file="${scripts}/ant-1.9.4.zip" todir="${distrib}/ant" />
+		<copy file="${scripts}/${KANT_ZIP}" todir="${distrib}/ant" />
 		<!-- Package the whole stuff in a zip (natively readable on 
 		     all OS, including Windows)
 		 -->

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