diff --git a/.classpath b/.classpath index cb5e8f166..b940f9666 100644 --- a/.classpath +++ b/.classpath @@ -9,6 +9,7 @@ + @@ -20,13 +21,15 @@ + - + + @@ -37,6 +40,7 @@ + diff --git a/.gitignore b/.gitignore index 33df0f4a3..af1c7913d 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,4 @@ test/coverage-report dependency-reduced-pom.xml maven.properties .evosuite +maven-archiver diff --git a/README.md b/README.md index 4c02249ba..0139ddf7b 100644 --- a/README.md +++ b/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 -Dskip.tests=true 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 <home directory>/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 $HOME/blast-data + cd blast-data + cp /etc/setup_blast_dbs.sh . + ./setup_blast_dbs.sh + ``` -mvn validate clean test package + (Note: the environment variable http_proxy may need to be set for the ftp downloads to work). ## License Artemis is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/artemis/blob/master/LICENSE). diff --git a/act b/act index 882862501..b46b8edf0 100755 --- a/act +++ b/act @@ -97,8 +97,8 @@ done APPLICATION_HOME=`dirname "$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 diff --git a/art b/art index 85930e5a1..1bdb3b262 100755 --- a/art +++ b/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 diff --git a/bamview b/bamview index cf64667a0..4299619a3 100755 --- a/bamview +++ b/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 [[ "$QUIET" = "no" ]] diff --git a/dnaplotter b/dnaplotter index fe9e835fa..6c9cb5292 100755 --- a/dnaplotter +++ b/dnaplotter @@ -78,8 +78,8 @@ done APPLICATION_HOME=`dirname "$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 [[ "$ARTEMIS_JVM_FLAGS" = "" ]] diff --git a/etc/writedb_entry b/etc/writedb_entry index 60c9e46cc..299381581 100755 --- a/etc/writedb_entry +++ b/etc/writedb_entry @@ -54,8 +54,8 @@ FLAGS="-mx2048m -ms20m -Djdbc.drivers=org.postgresql.Driver -Dibatis" DEFAULT_CONNECTION="-Dchado=db.genedb.org:5432/snapshot?genedb_ro -Dread_only" APPLICATION_HOME=`dirname "$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 diff --git a/icons/Readme.txt b/icons/Readme.txt deleted file mode 100644 index de05238ce..000000000 --- a/icons/Readme.txt +++ /dev/null @@ -1,83 +0,0 @@ - -Artemis, ACT & DNAPlotter -========================= - -Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. - -ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based on Artemis. - -DNAPlotter generates images of circular and linear DNA maps. - -BamView is a standalone BAM/CRAM file viewer. - -Installation on MacOSX -====================== - -1. Drag and drop the Artemis, ACT, DNAPlotter and BamView icons to an Applications directory, for example an 'Applications' directory in your home directory. - -2. Then eject the disk image (right click and select 'Eject'). - -3. Drag the icons from where you have installed them, into your dock. - -4. To run 'art' and 'act' from the command line add the following to your UNIX PATH: - -$ARTEMIS/Artemis.app/Contents - -where $ARTEMIS is the directory you have installed to. This can be done by adding a line to ~/.bashrc (if you are using bash shell) for example: - -PATH=~/Applications/Artemis.app/Contents; export PATH - -Searching and Using Local Sequence Databases (Optional) -======================================================= - -1. Download and install BLAST: - -ftp://ftp.ncbi.nih.gov/blast/executables/release/ - -get the latest release, e.g.: - -ftp://ftp.ncbi.nih.gov/blast/executables/release/2.2.18/blast-2.2.18-universal-macosx.tar.gz - -Untar and add the contents of the bin directory into Artemis.app/Contents/blast. - -2. Download and install Fasta -ftp://ftp.ebi.ac.uk/pub/software/unix/fasta - -Get the latest, e.g.: - -ftp://ftp.ebi.ac.uk/pub/software/unix/fasta/fasta3/fasta-34.26.5.shar.Z - -Put this in Artemis.app/Contents/fasta and unwrap and compile: -uncompress fasta-34.26.5.shar.Z -cat fasta-34.26.5.shar | sh -make -f Makefile.os_x all - -3. Download and format uniprot database - -You can do this by using the setup_dbs.sh script in Artemis.app/Contents/blast-data - -cd Artemis.app/Contents/blast-data -./setup_dbs.sh - -(Note the environment variable http_proxy may need to be set for the download to work). - -Additional databases can be added here. -To select to run searches locally ensure that under the 'Options' menu 'Send Searches via SSH' is not toggled. - -BamView CRAM reference lookup -============================= - -BamView now has the ability to download CRAM reference sequences if none is specified on startup. -This behaviour can be further governed using two environment variables REF_PATH and REF_CACHE. -The usage of these variables is the same as for samtools. Please refer to this article for details: - -http://www.htslib.org/workflow/ - - -References: -=========== - -"K. Rutherford, J. Parkhill, J. Crook, T. Horsnell, P. Rice, M-A. Rajandream and B. Barrell (2000) Artemis: sequence visualisation and annotation." Bioinformatics 16 (10) 944-945. - -T.J. Carver, K.M. Rutherford, M. Berriman, M-A. Rajandream, B.G. Barrell and J. Parkhill, "ACT: the Artemis Comparison Tool", Bioinformatics, 2005. - diff --git a/lib/README b/lib/README index 459ee8055..a8ca756ae 100644 --- a/lib/README +++ b/lib/README @@ -1,3 +1,5 @@ +These are old libraries and the intention is to remove or upgrade them. + Lib versions: ============= diff --git a/pom.xml b/pom.xml index d793f89dd..5fec389ee 100644 --- a/pom.xml +++ b/pom.xml @@ -67,12 +67,16 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys ${project.basedir}/etc/versions + 2018 Wellcome Trust Sanger Institute + ${env.EMBOSS_ROOT} Artemis + ${artemis.application.name} (CHADO) ACT + ${act.application.name} (CHADO) Circular-Plot BamView @@ -89,10 +93,12 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys uk.ac.sanger.artemis.circular.DNADraw - 1.8 - 1.8 - https://docs.oracle.com/javase/8/docs/api/ - ${env.JAVA_HOME}/../.. + 9 + + /Library/Java/JavaVirtualMachines/jdk-10.0.2.jdk + ${project.basedir}/maven-lib/appbundler-1.0ea.jar + Artemis_Tools + Artemis_Tools_Chado src/test/evosuite @@ -125,23 +131,35 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys -Dartemis.environment=UNIX -Dcom.apple.mrj.application.apple.menu.about.name -Xdock:name + -Dapple.laf.useScreenMenuBar=true -Dchado="localhost:5432/databasename?username" -Dibatis -Dsanger_options=yes - -Dj2ssh + -Dblack_belt_mode=false 8000 - 2 - -Xmx4g ${noverify.command.line.arg} ${postgres.command.line.arg} -Dtimeout=${unit.test.timeout.ms} -Duse_separate_classloader=false -DEMBOSS_ROOT=${emboss.installation.root} - + 1 + -Xmx4g ${noverify.command.line.arg} ${postgres.command.line.arg} -DEMBOSS_ROOT=${emboss.installation.root} --illegal-access=warn + ${default.tests.surefireArgLine} -Dtimeout=${unit.test.timeout.ms} -Duse_separate_classloader=false + **/log4j*.xml META-INF/* **/.DS_Store **/._* *.seq *.fasta *.embl *.tab *.crunch *.genbank + ${project.basedir}/icons + ${project.basedir}/images + + + false + **/*_ESTest* + true + true + true + true @@ -435,7 +453,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys j2ssh-core 0.2.9 jar - ${project.basedir}/lib/j2ssh/j2ssh-core.jar + ${project.basedir}/lib/j2ssh-core.jar true @@ -477,36 +495,6 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys - - - - - maven-compiler-plugin - 3.7.0 - - ${java.source.version} - ${java.target.version} - - - - - - - org.apache.maven.plugins - maven-jar-plugin - 3.1.0 - - - - false - - - all-permissions - * - - - - @@ -515,26 +503,10 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys maven-resources-plugin 3.0.2 - - - copy-test-data - process-test-resources - - copy-resources - - - ${project.build.testOutputDirectory}/data - - - ${project.basedir}/test/data - - - - copy-property-files - process-test-resources + process-resources copy-resources @@ -547,46 +519,13 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys - - copy-image-folder - process-test-resources - - copy-resources - - - ${project.build.outputDirectory}/images - - - ${project.basedir}/images - - - - - - - - copy-icons-to-target-folder - package - - copy-resources - - - ${jarsigner.skip} ${project.build.directory}/icons @@ -598,43 +537,38 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys - - + + + + + maven-compiler-plugin + 3.8.0 + + false + true + + ${java.compatibility.major.version} + + + + - org.apache.maven.plugins - maven-surefire-plugin - 2.20.1 - - ${skip.tests} - false - ${surefire.num.forks} - false - ${ignore.test.failures} - @{surefireArgLine} - - - - - ${evosuite.exclude.filter} - - org/gmod/** - **/RunBlastAtNCBITest.* - **/j2ssh/** - - - - - - - - - listener - org.evosuite.runtime.InitializingListener - - - - + org.apache.maven.plugins + maven-jar-plugin + 3.1.0 + + + + false + + + all-permissions + * + + + + @@ -657,13 +591,39 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys + + + + + + org.apache.maven.plugins + maven-surefire-plugin + 2.22.1 + + ${skip.tests} + true + ${surefire.num.forks} + false + ${ignore.test.failures} + @{default.tests.surefireArgLine} + + + **/*ESTest* + + + **/RunBlastAtNCBITest.* + **/TestIbatisDAO.* + **/TestJdbcDAO.* + + + org.jacoco jacoco-maven-plugin - 0.8.0 + 0.8.1 ${skip.coverage.reporting} @@ -709,13 +669,13 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys 3.1.0 - package-nonunix-artemis-jar + package-win-artemis-jar package shade - target/jars/${artemis.jar.name} + target/win-jars/${artemis.jar.name} false false @@ -750,13 +710,13 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys - package-unix-artemis-jar + package-default-artemis-jar package shade - target/unix-jars/${artemis.jar.name} + target/jars/${artemis.jar.name} false false @@ -791,13 +751,13 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys - package-nonunix-act-jar + package-win-act-jar package shade - target/jars/${act.jar.name} + target/win-jars/${act.jar.name} false false @@ -832,13 +792,13 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys - package-unix-act-jar + package-default-act-jar package shade - target/unix-jars/${act.jar.name} + target/jars/${act.jar.name} false false @@ -873,13 +833,13 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys - package-nonunix-dnaplotter-jar + package-win-dnaplotter-jar package shade - target/jars/${dnaplotter.jar.name} + target/win-jars/${dnaplotter.jar.name} false false @@ -915,13 +875,13 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys - package-unix-dnaplotter-jar + package-default-dnaplotter-jar package shade - target/unix-jars/${dnaplotter.jar.name} + target/jars/${dnaplotter.jar.name} false false @@ -957,13 +917,13 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys - package-nonunix-bamview-jar + package-win-bamview-jar package shade - target/jars/${bamview.jar.name} + target/win-jars/${bamview.jar.name} false false @@ -999,13 +959,13 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys - package-unix-bamview-jar + package-default-bamview-jar package shade - target/unix-jars/${bamview.jar.name} + target/jars/${bamview.jar.name} false false @@ -1055,7 +1015,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys 1.4 - sign-non-unix-jars + sign-win-jars package sign @@ -1065,7 +1025,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys false false false - target/jars + target/win-jars ${signer-keystore-path} ${signer-keystore-type} ${signer-keystore-alias} @@ -1076,7 +1036,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys - sign-unix-jars + sign-default-jars package sign @@ -1086,7 +1046,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys false false false - target/unix-jars + target/jars ${signer-keystore-path} ${signer-keystore-type} ${signer-keystore-alias} @@ -1195,6 +1155,17 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys + + + + org.codehaus.mojo + versions-maven-plugin + 2.7 + + false + + + - + - dev - + old-java8-profile-deprecated + + - true - + 1.8 + - false - **/*_ESTest* - true - true - true - true - - dev + java8-profile + + + + + + maven-compiler-plugin + 3.8.0 + + false + 1.8 + 1.8 + + + + + org.apache.maven.plugins + maven-surefire-plugin + 2.22.1 + + ${skip.tests} + true + ${surefire.num.forks} + false + ${ignore.test.failures} + @{surefireArgLine} + + + + ${evosuite.exclude.filter} + org/gmod/** + **/j2ssh/** + + + + **/RunBlastAtNCBITest.* + **/TestIbatisDAO.* + **/TestJdbcDAO.* + + + + + + + listener + org.evosuite.runtime.InitializingListener + + + + + + + + + mac-osx-dmg-packaging + + + + mac + + + + mac-osx-dmg-packaging + + + + + + org.apache.maven.plugins + maven-antrun-plugin + 1.8 + + + build-macosx + verify + + ${skip.artifact.creation} + + + + + + + + + run + + + + + + + + + release @@ -1287,335 +1351,16 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys false - **/*_ESTest* + false false false false release - - - - - - - - sh.tak.appbundler - appbundle-maven-plugin - 1.1.0 - - - create-artemis-osx-app - package - - bundle - - - ${skip.artifact.creation} - ${project.version} - ${osx.app.folder} - false - ${artemis.application.name} - ${osx.jdk.path} - ${artemis.main.class} - ${project.build.directory}/icons/artemis.icns - ${java.target.version} - - ${maxheap.command.line.arg} - ${initialheap.command.line.arg} - ${noverify.command.line.arg} - ${unixenv.command.line.arg} - ${macosx.menuname.command.line.arg}=${artemis.application.name} - ${macosx.dock.command.line.arg}=${artemis.application.name} - ${sangeroptions.command.line.arg} - ${j2ssh.command.line.arg} - - - - ${project.build.directory}/icons - - Readme.txt - - - - - - - create-act-osx-app - package - - bundle - - - false - ${project.version} - ${osx.app.folder} - false - ${act.application.name} - ${osx.jdk.path} - ${act.main.class} - ${project.build.directory}/icons/act.icns - ${java.target.version} - - ${maxheap.command.line.arg} - ${initialheap.command.line.arg} - ${noverify.command.line.arg} - ${unixenv.command.line.arg} - ${macosx.menuname.command.line.arg}=${act.application.name} - ${macosx.dock.command.line.arg}=${act.application.name} - ${sangeroptions.command.line.arg} - ${j2ssh.command.line.arg} - - - - ${project.build.directory}/icons - - Readme.txt - - - - - - - create-dnaplotter-osx-app - package - - bundle - - - false - ${project.version} - ${osx.app.folder} - false - ${dnaplotter.application.name} - ${osx.jdk.path} - ${dnaplotter.main.class} - ${project.build.directory}/icons/dnaplotter.icns - ${java.target.version} - - ${maxheap.command.line.arg} - ${initialheap.command.line.arg} - ${noverify.command.line.arg} - ${unixenv.command.line.arg} - ${macosx.menuname.command.line.arg}=${dnaplotter.application.name} - ${macosx.dock.command.line.arg}=${dnaplotter.application.name} - ${sangeroptions.command.line.arg} - ${j2ssh.command.line.arg} - - - - ${project.build.directory}/icons - - Readme.txt - - - - - - - - create-bamview-osx-app - package - - bundle - - - false - ${project.version} - ${osx.app.folder} - true - ${osx.app.folder}/${osx.release.filename}.dmg - ${bamview.application.name} - ${osx.jdk.path} - ${bamview.main.class} - ${project.build.directory}/icons/bamview.icns - ${java.target.version} - - ${maxheap.command.line.arg} - ${initialheap.command.line.arg} - ${noverify.command.line.arg} - ${unixenv.command.line.arg} - ${macosx.menuname.command.line.arg}=${bamview.application.name} - ${macosx.dock.command.line.arg}=${bamview.application.name} - ${sangeroptions.command.line.arg} - ${j2ssh.command.line.arg} - - - - ${project.build.directory}/icons - - Readme.txt - - - - - - - - - - create-artemis-osx-app-CHADO - package - - bundle - - - ${skip.artifact.creation} - ${project.version} - ${osx.app.chado.folder} - false - ${artemis.application.name} (CHADO) - ${osx.jdk.path} - ${artemis.main.class} - ${project.build.directory}/icons/artemis.icns - ${java.target.version} - - ${postgres.command.line.arg} - ${chado.command.line.arg} - ${ibatis.command.line.arg} - ${maxheap.command.line.arg} - ${initialheap.command.line.arg} - ${noverify.command.line.arg} - ${unixenv.command.line.arg} - ${macosx.menuname.command.line.arg}=${artemis.application.name} - ${macosx.dock.command.line.arg}=${artemis.application.name} - ${sangeroptions.command.line.arg} - ${j2ssh.command.line.arg} - - - - ${project.build.directory}/icons - - Readme.txt - - - - - - - create-act-osx-app-CHADO - package - - bundle - - - false - ${project.version} - ${osx.app.chado.folder} - false - ${act.application.name} (CHADO) - ${osx.jdk.path} - ${act.main.class} - ${project.build.directory}/icons/act.icns - ${java.target.version} - - ${postgres.command.line.arg} - ${chado.command.line.arg} - ${ibatis.command.line.arg} - ${maxheap.command.line.arg} - ${initialheap.command.line.arg} - ${noverify.command.line.arg} - ${unixenv.command.line.arg} - ${macosx.menuname.command.line.arg}=${act.application.name} - ${macosx.dock.command.line.arg}=${act.application.name} - ${sangeroptions.command.line.arg} - ${j2ssh.command.line.arg} - - - - ${project.build.directory}/icons - - Readme.txt - - - - - - - create-dnaplotter-osx-app-CHADO - package - - bundle - - - false - ${project.version} - ${osx.app.chado.folder} - false - ${dnaplotter.application.name} - ${osx.jdk.path} - ${dnaplotter.main.class} - ${project.build.directory}/icons/dnaplotter.icns - ${java.target.version} - - ${maxheap.command.line.arg} - ${initialheap.command.line.arg} - ${noverify.command.line.arg} - ${unixenv.command.line.arg} - ${macosx.menuname.command.line.arg}=${dnaplotter.application.name} - ${macosx.dock.command.line.arg}=${dnaplotter.application.name} - ${sangeroptions.command.line.arg} - ${j2ssh.command.line.arg} - - - - ${project.build.directory}/icons - - Readme.txt - - - - - - - - create-bamview-osx-app-CHADO - package - - bundle - - - false - ${project.version} - ${osx.app.chado.folder} - true - ${osx.app.chado.folder}/${osx.chado.release.filename}.dmg - ${bamview.application.name} - ${osx.jdk.path} - ${bamview.main.class} - ${project.build.directory}/icons/bamview.icns - ${java.target.version} - - ${maxheap.command.line.arg} - ${initialheap.command.line.arg} - ${noverify.command.line.arg} - ${unixenv.command.line.arg} - ${macosx.menuname.command.line.arg}=${bamview.application.name} - ${macosx.dock.command.line.arg}=${bamview.application.name} - ${sangeroptions.command.line.arg} - ${j2ssh.command.line.arg} - - - - ${project.build.directory}/icons - - Readme.txt - - - - - - - - - + - + diff --git a/src/assembly/macosx-release-assembly.xml b/src/assembly/macosx-release-assembly.xml new file mode 100644 index 000000000..8268c61aa --- /dev/null +++ b/src/assembly/macosx-release-assembly.xml @@ -0,0 +1,326 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + NOTE: hdiutil must be installed to create a Mac .dmg image file... + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + NOTE: hdiutil must be installed to create a Mac .dmg image file... + + + + + + + + + + + + + + + + diff --git a/src/assembly/unix-release-assembly.xml b/src/assembly/unix-release-assembly.xml index e2a3d2b10..b35ed9c91 100644 --- a/src/assembly/unix-release-assembly.xml +++ b/src/assembly/unix-release-assembly.xml @@ -15,8 +15,8 @@ - target/unix-jars - ${unix.assembly.folder} + target/jars + ${unix.assembly.folder}/dist *.jar @@ -27,7 +27,6 @@ etc/** 0755 - 0755 unix @@ -37,6 +36,7 @@ LICENSE README* + unix ${unix.assembly.folder} diff --git a/src/assembly/windows-release-assembly.xml b/src/assembly/windows-release-assembly.xml index 3b992a81c..afe74552c 100644 --- a/src/assembly/windows-release-assembly.xml +++ b/src/assembly/windows-release-assembly.xml @@ -14,7 +14,7 @@ - target/jars + target/win-jars ${windows.assembly.folder} *.jar