Build process updates, mostly for Mac

.classpath

@@ -9,6 +9,7 @@
 	</classpathentry>
 	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
 		<attributes>
+			<attribute name="test" value="true"/>
 			<attribute name="optional" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
@@ -20,13 +21,15 @@
 	</classpathentry>
 	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
 		<attributes>
+			<attribute name="test" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="src" path="src/assembly"/>
 	<classpathentry kind="src" path="src/site"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
 		<attributes>
+			<attribute name="module" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
@@ -37,6 +40,7 @@
 	</classpathentry>
 	<classpathentry kind="src" output="target/test-classes" path="src/test/evosuite">
 		<attributes>
+			<attribute name="test" value="true"/>
 			<attribute name="optional" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>

.gitignore

@@ -7,3 +7,4 @@ test/coverage-report
 dependency-reduced-pom.xml
 maven.properties
 .evosuite
+maven-archiver

README.md

@@ -32,8 +32,16 @@ Artemis is a free genome browser and annotation tool that allows visualisation o
 
 ACT is a free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation.
 
+DNAPlotter generates images of circular and linear DNA maps.
+
+BamView is a standalone BAM/CRAM file viewer.
+
 For further information, please see the [Artemis GitHub page](http://sanger-pathogens.github.io/Artemis/)
 
+## Prerequisites
+
+Java 9+ must be installed. Ideally Java 11.
+
 ## Installation
 
 Please refer to the relevant documentation in the Documentation section below.
@@ -45,12 +53,103 @@ Please refer to the relevant documentation in the Documentation section below.
 ## Building
 
 If you would prefer to build the applications from scratch rather than use the pre-built releases in GitHub, then you will firstly need the source code from GitHub. This can be obtained by cloning the repository:
+```
+git clone https://github.com/sanger-pathogens/Artemis.git
+```
+or by downloading the source zip file for a particular release. The latest version of Apache Maven (Java 11 compatible, e.g. v3.6.0) will need to be installed beforehand, in order to build. The application jars can be built by issuing the following commands in the top-level folder:
+
+When building for the first time:
+```
+mvn validate
+```
+This is required to install some legacy libraries to the Maven repository and will be phased out in future releases.
+
+And then to build/rebuild the applications :
+```
+mvn clean package
+```
+Clean is only required if you wish to do a complete rebuild.
+If you do not wish to run tests then add the <i>-Dskip.tests=true</i> flag to the above command.
+
+Note that if you are running a build from behind a proxy you will need to add the proxy parameters to the mvn command line, e.g.
+```
+mvn -Dhttps.proxyHost=myproxyhost -Dhttps.proxyPort=myproxyport -DproxySet=true package
+```
+
+## Searching and Using Local Sequence Databases
+
+Artemis and ACT can optionally be used with local sequence databases on non-Windows systems.
+
+[Note: this may require a lot of disk space]
+
+If you wish to do this then carry out the following steps:
+
+1. To download and install BLAST+ locally, check here:
+
+  ```
+  ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
+  ```
+  to get the latest Mac OS X release:
+
+  ```
+  ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.7.1+-x64-macosx.tar.gz
+  ```
+  Uncompress, if you have downloaded a .tar.gz, e.g.
+
+  ```
+  tar -zxvf ncbi-blast-2.7.1+-x64-macosx.tar.gz
+  ```
+  For a Mac OS X install you can mount the resulting .dmg image by double-clicking it and then selecting the .pkg installer file to actually install the BLAST+ executables into the default location (/usr/local/ncbi/blast). Comprehensive installation instructions for all operating systems are provided  [here](https://www.ncbi.nlm.nih.gov/books/NBK279690/).
+
+2. To download and install Fasta locally, check here:
+
+  ```
+  ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/
+  ```
+
+  and download the latest release, e.g.
+
+  ```
+  ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/fasta3/fasta-36.3.8g.tar.gz
+  ```
+  Uncompress the tar:
+
+  ```
+  tar -zxvf fasta-36.3.8g.tar.gz
+  ```
+
+  Build the executables, e.g. for a Mac:
+
+  ```
+  cd fasta/src
+  make -f ../make/Makefile.os_x86_64 all
+  ```
+  Move the fasta folder to a convenient area, preferably /usr/local/ for Macs:
+
+3. Ensure that the BLAST+ and Fasta executables are available in your PATH and that local databases can be found by Artemis:
+
+  On the command line type:
+
+  ```
+  blastp -help
+  fasta36 -help
+  ```
+  If the executables are not found then their respective installation bin folders will need to be added to your .profile PATH variable. This can be achieved by uncommenting and setting the relevant environment variables in the **Variables for locally installed Blast databases** section of the Artemis **setenv** script. The location of the databases is assumed by default to be &lt;home directory&gt;/blast-data but this can be overridden by setting the BLASTDB and FASTLIBS variables. The setenv script should then be called from your login **.profile** file. Alternatively copy the relevant variables into your profile.
+
+  Note that database locations can also be specified directly within the Artemis/ACT applications.
+
+4. Download and format the uniprot database(s):
 
-git clone http://github.com/sanger-pathogens/Artemis.git
+  You can do this by using the Artemis etc/setup_uniprot_dbs.sh script. This script can be changed as desired, to for instance, include additional databases or create a FASTLIBS file.
 
-or by downloading the source zip file for a particular release. Apache Maven and Java 8 will need to be installed beforehand, in order to build. The applications can be built by issuing the following command in the top-level folder:
+  ```
+  mkdir $HOME/blast-data
+  cd blast-data
+  cp <Artemis folder>/etc/setup_blast_dbs.sh .
+  ./setup_blast_dbs.sh
+  ```
 
-mvn validate clean test package
+  (Note: the environment variable http_proxy may need to be set for the ftp downloads to work).
 
 ## License
 Artemis is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/artemis/blob/master/LICENSE).

act

@@ -97,8 +97,8 @@ done
 
 APPLICATION_HOME=`dirname "$PRG"`
 JAR_NAME=act.jar
-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/unix-jars/$JAR_NAME
-JAR_FILE_INSTALLED=$APPLICATION_HOME/$JAR_NAME
+JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
+JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
 
 #
 # Use a custom Java version if necessary
@@ -117,7 +117,7 @@ fi
 add_proxy_properties
 
 #
-# "-mx1g" sets the maximum amount of memory to use. 
+# "-mx2g" sets the maximum amount of memory to use. 
 # This may need to be increased when dealing with large files
 #
 if [[ "$ARTEMIS_JVM_FLAGS" = "" ]]
@@ -127,6 +127,12 @@ else
     FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
 fi
 
+#
+# Temporary flags to avoid Java 9+ reflection warnings being written to the terminal.
+# Should not be necessary when Ibatis is replaced.
+#
+FLAGS="$FLAGS --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED"
+
 PLATTMP=`uname`
 if [[ "$PLATTMP" = "Darwin" ]]
 then

art

@@ -103,8 +103,8 @@ done
 
 APPLICATION_HOME=`dirname "$PRG"`
 JAR_NAME=artemis.jar
-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/unix-jars/$JAR_NAME
-JAR_FILE_INSTALLED=$APPLICATION_HOME/$JAR_NAME
+JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
+JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
 
 #
 # Use a custom Java version if necessary
@@ -123,7 +123,7 @@ fi
 add_proxy_properties
 
 #
-# "-mx1g" sets the maximum amount of memory to use. 
+# "-mx2g" sets the maximum amount of memory to use. 
 # This may need to be increased when dealing with large files
 #
 if [[ "$ARTEMIS_JVM_FLAGS" = "" ]]
@@ -133,6 +133,13 @@ else
     FLAGS="$ARTEMIS_JVM_FLAGS -noverify"
 fi
 
+
+#
+# Temporary flags to avoid Java 9+ reflection warnings being written to the terminal.
+# Should not be necessary when Ibatis is replaced.
+#
+FLAGS="$FLAGS --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED"
+
 PLATTMP=`uname`
 if [[ "$PLATTMP" = "Darwin" ]]
 then

bamview

@@ -41,8 +41,8 @@ done
 APPLICATION_PROPERTIES="-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX $SANGER_ARTEMIS_OPTIONS"
 APPLICATION_HOME=`dirname "$PRG"`
 JAR_NAME=bamview.jar
-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/unix-jars/$JAR_NAME
-JAR_FILE_INSTALLED=$APPLICATION_HOME/$JAR_NAME
+JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
+JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
 
 #
 # Use a custom Java version if necessary
@@ -61,7 +61,7 @@ fi
 add_proxy_properties
 
 #
-# "-mx1g" sets the maximum amount of memory to use. 
+# "-mx2g" sets the maximum amount of memory to use. 
 # This may need to be increased when dealing with large files
 #
 if [[ "$ARTEMIS_JVM_FLAGS" = "" ]]
@@ -74,7 +74,7 @@ fi
 PLATTMP=`uname`
 if [[ "$PLATTMP" = "Darwin" ]]
 then
-  	APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Xdock:name=BamView"
+  	APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dapple.laf.useScreenMenuBar=true -Xdock:name=BamView"
 fi
 
 if [[ "$QUIET" = "no" ]]

dnaplotter

@@ -78,8 +78,8 @@ done
 
 APPLICATION_HOME=`dirname "$PRG"`
 JAR_NAME=dnaplotter.jar
-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/unix-jars/$JAR_NAME
-JAR_FILE_INSTALLED=$APPLICATION_HOME/$JAR_NAME
+JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
+JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
 
 #
 # Use a custom Java version if necessary
@@ -98,7 +98,7 @@ fi
 add_proxy_properties
 
 #
-# "-mx1g" sets the maximum amount of memory to use. 
+# "-mx2g" sets the maximum amount of memory to use. 
 # This may need to be increased when dealing with large files
 #
 if [[ "$ARTEMIS_JVM_FLAGS" = "" ]]

etc/writedb_entry

@@ -54,8 +54,8 @@ FLAGS="-mx2048m -ms20m -Djdbc.drivers=org.postgresql.Driver -Dibatis"
 DEFAULT_CONNECTION="-Dchado=db.genedb.org:5432/snapshot?genedb_ro -Dread_only"
 APPLICATION_HOME=`dirname "$PRG"`/..
 JAR_NAME=artemis.jar
-JAR_FILE_DEFAULT=$APPLICATION_HOME/target/unix-jars/$JAR_NAME
-JAR_FILE_INSTALLED=$APPLICATION_HOME/$JAR_NAME
+JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
+JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
 
 #
 # Use a custom Java version if necessary

lib/README

@@ -1,3 +1,5 @@
+These are old libraries and the intention is to remove or upgrade them.
+
 Lib versions:
 =============