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

.travis.yml

@@ -4,18 +4,18 @@ os:
   - linux
 
 jdk:
-  - oraclejdk8
+  - oraclejdk9
 
 # BeeDeeM uses graphical layers from Java/Swing. So, to enable
 # GUI app to run on Travis CI, we have to add these lines:
 # (according to https://docs.travis-ci.com/user/gui-and-headless-browsers/#Using-xvfb-to-Run-Tests-That-Require-a-GUI)
-before_script:
-  - "export DISPLAY=:99.0"
-  - "sh -e /etc/init.d/xvfb start"
-  - sleep 3 # give xvfb some time to start
+#before_script:
+#  - "export DISPLAY=:99.0"
+#  - "sh -e /etc/init.d/xvfb start"
+#  - sleep 3 # give xvfb some time to start
 
 script:
-  ant ut
+  ant makejar 
 
 after_script:
   if [ -f /home/travis/build/pgdurand/BeeDeeM/distrib/tests-result/TEST-test.unit.AllTests.txt ]; then cat /home/travis/build/pgdurand/BeeDeeM/distrib/tests-result/TEST-test.unit.AllTests.txt; fi

README.md

@@ -1,6 +1,6 @@
 # *BeeDeeM*: the Bioinformatics Databank Manager System 
 
-[![License AGPL](https://img.shields.io/badge/license-Affero%20GPL%203.0-blue.svg)](https://www.gnu.org/licenses/agpl-3.0.txt)  [![Build Status](https://travis-ci.org/pgdurand/BeeDeeM.svg?branch=master)](https://travis-ci.org/pgdurand/BeeDeeM)  [![](https://tokei.rs/b1/github/pgdurand/BeeDeeM?category=code)](https://github.com/pgdurand/BeeDeeM) [![](https://img.shields.io/badge/platform-Java--1.7+-yellow.svg)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) [![](https://img.shields.io/badge/run_on-Linux--Mac_OSX--Windows-yellowgreen.svg)]()
+[![License AGPL](https://img.shields.io/badge/license-Affero%20GPL%203.0-blue.svg)](https://www.gnu.org/licenses/agpl-3.0.txt)  [![Build Status](https://travis-ci.org/pgdurand/BeeDeeM.svg?branch=master)](https://travis-ci.org/pgdurand/BeeDeeM)  [![](https://tokei.rs/b1/github/pgdurand/BeeDeeM?category=code)](https://github.com/pgdurand/BeeDeeM) [![](https://img.shields.io/badge/platform-Java--1.8+-yellow.svg)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) [![](https://img.shields.io/badge/run_on-Linux--macOS--Windows-yellowgreen.svg)]()
 
 *BeeDeeM* is a general purpose **B**ioinformatics **D**atabank **M**anager. 
 
@@ -33,6 +33,44 @@ It provides a suite of command-line and UI softwares to install and use major se
 
 [More](https://pgdurand.gitbooks.io/beedeem/).
 
+### Use BeeDeeM from the command line
+
+Here is an example of a script to start Genbank_CoreNucleotide installation on Ifremer's [DATARMOR supercomputer](https://www.top500.org/system/178981):
+
+```
+#!/usr/bin/env bash
+#PBS -q web
+#PBS -l mem=64gb
+#PBS -l ncpus=8
+#PBS -l walltime=72:00:00
+
+# Release of BeeDeeM to use
+BDM_HOME=$SOFT/bioinfo/beedeem
+BDM_VER=latest
+
+# Load BeeDeeM environment
+module load java/1.8.0_121
+
+# Configure BeeDeeM install tool
+TASK_ARGS="-task download"
+GLOBAL_ARGS="--ftp-delay 5000 --ftp-retry 3 --task-delay 1000"
+MAILING_ARGS="--mail-smtp-host xxx --sender-mail yyy --recipient-mail zzz"
+
+# prefix of '.dsc' file that must exist in $BDM_HOME/conf/descriptor
+DESCRIPTOR="Genbank_CoreNucleotide"
+export KL_LOG_FILE=${DESCRIPTOR}.log
+$BDM_HOME/$BDM_VER/install.sh \
+   ${TASK_ARGS} ${GLOBAL_ARGS} ${MAILING_ARGS} \
+   -desc ${DESCRIPTOR} \
+   >& "$HOME/beedeem/logs/${DESCRIPTOR}-pbs.out"
+```
+
+You can easily automate bank installation using such BeeDeeM based scripts with Unix cron scheduler.
+
+### Use BeeDeeM UI
+
+Here is a screenshot of BeeDeeM user friendly interface:
+
 ![UiManager](doc/dbms_ui.png)
 
 ## Practical use cases
@@ -57,7 +95,7 @@ Among others, these databanks can be used to:
 
 ## Requirements
 
-Use a [Java Virtual Machine](http://www.oracle.com/technetwork/java/javase/downloads/index.html) 1.7 (or above) from Oracle. 
+Use a [Java Virtual Machine](http://www.oracle.com/technetwork/java/javase/downloads/index.html) 1.8 (or above) from Oracle. 
 
 *Not tested with any other JVM providers but Oracle... so there is no guarantee that the software will work as expected if not using Oracle's JVM.* [More](https://pgdurand.gitbooks.io/beedeem/) about *BeeDeeM* requirements.
 
@@ -73,4 +111,4 @@ Use a [Java Virtual Machine](http://www.oracle.com/technetwork/java/javase/downl
 It depends on several thrid-party libraries as stated in the NOTICE.txt file provided with this project.
 
 --
-(c) 2007-2019 - Patrick G. Durand and Ludovic Antin
+(c) 2007-2020 - Patrick G. Durand and Ludovic Antin

build.xml

@@ -60,6 +60,15 @@
 		<pathelement location="${distrib}/lib" />
 	</path>
 
+	<path id="class.path.test">
+	    <fileset dir="${jar}" includes="junit*.jar" />
+	</path>
+
+	<taskdef name="junit"
+	  classname="org.apache.tools.ant.taskdefs.optional.junit.JUnitTask">
+	  <classpath refid="class.path.test"/>
+	</taskdef>
+
 	<!-- ============================================================= -->
 	<target name="help">
 		<echo>This is the Ant's project file to manage BeeDeeM.</echo>
@@ -68,6 +77,9 @@
 		<echo>        makejar: only compile and package beedem jar</echo>
 		<echo>    makedistrib: prepare the full release file</echo>
 		<echo>             ut: compile beedeem and run unit tests</echo>
+	  <echo/>
+	  <echo>  Ant version: ${ant.version}</echo>
+	  <echo>  Java version: ${ant.java.version}</echo>
 		<echo />
 	</target>
 
@@ -101,6 +113,10 @@
 	<!-- ============================================================= -->
 	<!-- Prepare directory structure used to compile and package sof   -->
 	<target name="prepare" depends="checkversion">
+	  <echo/>
+	  <echo>  Ant version: ${ant.version}</echo>
+	  <echo>  Java version: ${ant.java.version}</echo>
+    <echo/>
 		<!-- Prepare the distrib directory tree -->
 		<delete dir="${distrib}" />
 		<mkdir dir="${Dsrc}" />
@@ -112,6 +128,37 @@
 		<mkdir dir="${Dexternal}" />
 	</target>
 
+	<!-- ============================================================= -->
+	<target name="is-java-eight">
+	  <condition property="java.eight">
+	      <equals arg1="${ant.java.version}" arg2="1.8"/>
+	  </condition>
+	</target>
+
+	<target name="javac8" depends="is-java-eight" if="java.eight">
+	  <javac srcdir="${Dsrc}"
+	         destdir="${Dlib}"
+	         classpathref="class.path"
+	         debug="${distribClass.path}"
+	         optimize="${compile.optimize}"
+	  	     deprecation="${compile.deprecation}"
+	         >
+	  </javac>
+	</target>
+
+	<!-- added for TravisCI -->
+	<target name="javac9" depends="is-java-eight" unless="java.eight">
+	  <javac srcdir="${Dsrc}"
+	         destdir="${Dlib}"
+	         classpathref="distribClass.path"
+	         debug="${compile.debug}"
+	         optimize="${compile.optimize}"
+	  	     deprecation="${compile.deprecation}"
+	         >
+	    <compilerarg line="--add-modules java.se.ee"/>
+	  </javac>
+	</target>
+
   <!-- ============================================================= -->
   <!-- Compile code and make software Jar                            -->
 	<target name="makejar" depends="prepare">
@@ -146,13 +193,8 @@
 			</fileset>
 		</copy>
 		<!-- Compile source code ready for distribution-->
-		<javac srcdir="${Dsrc}" 
-	           destdir="${Dlib}" 
-	           classpathref="distribClass.path" 
-	           debug="${compile.debug}" 
-	           optimize="${compile.optimize}" 
-	           deprecation="${compile.deprecation}">
-		</javac>
+	  <antcall target="javac8"/>
+	  <antcall target="javac9"/>
 		<copy todir="${Dlib}">
 			<fileset dir="${src}">
 				<include name="**/*.png" />
@@ -308,13 +350,8 @@
 			<fileset dir="${src}" />
 		</copy>
 		<!-- Compile source code ready for distribution-->
-		<javac srcdir="${Dsrc}" 
-             destdir="${Dlib}" 
-             classpathref="distribClass.path" 
-             debug="on" 
-             optimize="off" 
-             deprecation="off">
-		</javac>
+	  <antcall target="javac8"/>
+	  <antcall target="javac9"/>
 		<!-- Copy resource files -->
 		<copy todir="${Dlib}">
 			<fileset dir="${src}">

conf/dbms.config

@@ -1,11 +1,11 @@
 # KDMS main configuration file
 
 # Path where to install/manage local copies of databanks
-mirror.path = /biobanks
+mirror.path = /tmp/biobanks
 
 # Path where to prepare local installation of databanks
 # before copying them in mirror.path during install in production task
-#mirrorprepa.path = /biobanks/tmp
+#mirrorprepa.path = /tmp/biobanks/tmp
 
 # File storing the list of available databanks
 mirror.file = dbmirror.config

conf/descriptors/NCBI_nr-tax_v4.dsc

@@ -0,0 +1,25 @@
+db.name=NCBI_nr
+db.desc=NCBI nr protein databank with taxonomy. Protein sequences from GenBank CDS translations, PDB, Swiss-Prot, PIR, and PRF.
+db.type=p
+db.ldir=${mirrordir}|p|NCBI_nr
+
+db.files.include=^nr_v4.*\\d+\\.tar.gz$
+db.files.exclude=
+
+tasks.unit.post=gunzip,untar
+tasks.global.post=delgz,deltar,makealias
+
+ftp.server=ftp.ncbi.nih.gov
+ftp.port=21
+ftp.uname=anonymous
+[email protected]
+ftp.rdir=/blast/db/v4
+ftp.rdir.exclude=
+
+history=0
+
+aspera.use=true
+[email protected]
+aspera.args=-k 1 -T -l 640M
+
+

conf/descriptors/NCBI_nt-tax.dsc

@@ -1,14 +1,13 @@
 db.name=NCBI_nt-tax
-db.desc=NCBI nt databank. Nucleotide sequences from several sources, including GenBank, RefSeq, TPA and PDB. Not non-redundant.
+db.desc=NCBI nt databank with taxonomy. Blast v4 bank format. Nucleotide sequences from several sources, including GenBank, RefSeq, TPA and PDB. Not non-redundant.
 db.type=n
 db.ldir=${mirrordir}|n|NCBI_nt-tax
 
-#db.files.include=^nt.*\\d+\\.tar.gz$
-db.files.include=nt.00.tar.gz,nt.01.tar.gz
+db.files.include=^nt_v4.*\\d+\\.tar.gz$
 db.files.exclude=
 
 tasks.unit.post=gunzip,untar
-tasks.global.post=makealias
+tasks.global.post=delgz,deltar,makealias
 
 ftp.server=ftp.ncbi.nih.gov
 ftp.port=21

conf/descriptors/PDB_proteins.dsc

@@ -13,6 +13,6 @@ db.ldir=${mirrordir}|p|PDB_proteins
 ftp.rdir.exclude=
 ftp.rdir=/blast/db/FASTA/
 history=0
-db.desc=PDB Protein databank\: sequences from 3D protein structures (no annotations).
+db.desc=PDB Protein databank (no taxonomy).
 db.files.exclude=
 db.type=p

conf/descriptors/PDB_proteins_task.dsc

@@ -0,0 +1,29 @@
+#PDB_proteins
+#Fri Sep 15 13:47:28 CEST 2017
+
+db.name=PDB_proteins
+db.desc=PDB Protein databank; illustrate use of external script call
+db.type=p
+db.ldir=${mirrordir}|p|PDB_proteins
+
+db.files.include=pdbaa_v4.tar.gz
+db.files.exclude=
+
+tasks.global.post=makealias,delgz,deltar,script(name=HelloWorld;path=hello_world.sh)
+tasks.unit.post=gunzip,untar,script(name=HelloWorld;path=hello_world.sh)
+
+ftp.uname=anonymous
+[email protected]
+ftp.server=ftp.ncbi.nih.gov
+ftp.port=21
+ftp.rdir=/blast/db/v4
+ftp.rdir.exclude=
+
+depends=
+
+history=0
+
+aspera.use=true
+[email protected]
+aspera.args=-k 1 -T -l 640M
+

conf/descriptors/PDB_proteins_v4.dsc

@@ -0,0 +1,29 @@
+#PDB_proteins
+#Fri Sep 15 13:47:28 CEST 2017
+
+db.name=PDB_proteins
+db.desc=PDB Protein databank (Blast v4 db format)
+db.type=p
+db.ldir=${mirrordir}|p|PDB_proteins
+
+db.files.include=pdbaa_v4.tar.gz
+db.files.exclude=
+
+tasks.global.post=makealias,delgz,deltar
+tasks.unit.post=gunzip,untar
+
+ftp.uname=anonymous
+[email protected]
+ftp.server=ftp.ncbi.nih.gov
+ftp.port=21
+ftp.rdir=/blast/db/v4
+ftp.rdir.exclude=
+
+depends=
+
+history=0
+
+aspera.use=true
+[email protected]
+aspera.args=-k 1 -T -l 640M
+

conf/descriptors/Pfam-hmm.dsc

@@ -0,0 +1,20 @@
+db.name=Pfam-hmm
+db.desc=Large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)
+db.type=d
+db.ldir=${mirrordir}|d|Pfam-hmm
+
+db.files.include=Pfam-A.hmm.gz
+db.files.exclude=
+
+tasks.unit.post=gunzip
+# by default, post-process script is located in ../scripts path
+tasks.global.post=delgz,script(name=hmmpress;path=pfam-hmm.sh)
+
+ftp.server=ftp.ebi.ac.uk
+ftp.port=21
+ftp.uname=anonymous
+[email protected]
+ftp.rdir=/pub/databases/Pfam/current_release
+ftp.rdir.exclude=
+
+history=0

conf/scripts/hello_world.sh

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+
+# This is a BeeDeeM external task script template.
+#
+# This script illustrates the use of external tasks.
+# Such a task is called from a bank descriptor; e.g. see
+# for instance ../descriptors/PDB_proteins_task.dsc
+#
+# Such a BeeDeeM script is called by the task engine and
+# with up to two arguments: -d <path> -f <path>
+#
+#  -d <path>: <path> is the bank installation path.
+#             provided for both unit and global tasks.
+#  -f <path>: <path> is the path to file under unit task processing
+#             only provided with unit task.
+
+echo "Executing an external script"
+echo "Arguments coming from BeeDeeM are:"
+echo $@
+