Unverified Commit 28b487d8 authored by kpepper's avatar kpepper Committed by GitHub
Browse files

Merge pull request #270 from sanger-pathogens/build-process-upgrade-merge

Merge build 18.0.0 changes to master
parents 3e43d27e 91a091bb
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry excluding="ant-build|cobertura-lib|coverage-report|data|docs|evosuite-dependencies|evosuite-libs|evosuite-tests|jacoco-lib|lib|evosuite-tests/" including="uk/**" kind="src" output="eclipse-classes" path="test"/>
<classpathentry including="uk/**" kind="src" output="eclipse-classes" path="test/evosuite-tests"/>
<classpathentry excluding="main/" kind="src" path="ant-build/src"/>
<classpathentry excluding="ant-build/classes/|ant-build/src/|docs|test|test/evosuite-tests/|uk/ac/sanger/artemis/ExternalProgramUtils.java" including="org/|uk/" kind="src" path=""/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="lib" path="lib/jemAlign.jar"/>
<classpathentry kind="lib" path="lib/jakarta-regexp-1.2.jar"/>
<classpathentry kind="lib" path="lib/biojava.jar"/>
<classpathentry kind="lib" path="lib/j2ssh/j2ssh-core.jar"/>
<classpathentry kind="lib" path="lib/j2ssh/j2ssh-artemis-plugin.jar"/>
<classpathentry kind="lib" path="lib/j2ssh/commons-logging.jar"/>
<classpathentry kind="lib" path="lib/ibatis/ibatis-2.3.4.726.jar"/>
<classpathentry kind="lib" path="lib/ibatis/log4j-1.2.14.jar"/>
<classpathentry kind="lib" path="lib/postgresql-8.4-701.jdbc3.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-awt-util.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-codec.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-dom.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-ext.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-svggen.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-util.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-xml.jar"/>
<classpathentry kind="lib" path="lib/commons-lang-2.6.jar"/>
<classpathentry kind="lib" path="test/lib/junit-4.11.jar"/>
<classpathentry kind="lib" path="/Users/kp11/workspace/applications/Artemis/eclipse-classes"/>
<classpathentry kind="lib" path="test/evosuite-lib/evosuite-1.0.5.jar"/>
<classpathentry kind="lib" path="lib/commons-net-3.6.jar"/>
<classpathentry kind="lib" path="lib/picard/picard.jar"/>
<classpathentry kind="output" path="eclipse-classes"/>
<classpathentry excluding="data/**" kind="src" output="eclipse-classes" path="test"/>
<classpathentry kind="src" output="target/classes" path="src/main/java">
<attributes>
<attribute name="optional" value="true"/>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</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>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</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-11">
<attributes>
<attribute name="module" value="true"/>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
<attributes>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</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>
</classpathentry>
<classpathentry kind="output" path="target/classes"/>
</classpath>
*.class
.settings
ant-build
test/ant-build
**/.DS_Store
**/*.log
test/coverage-report
jar_build
tar_build
artemis_compiled.tar
/eclipse-classes/
/test-kjp/
/target/
dependency-reduced-pom.xml
maven.properties
.evosuite
maven-archiver
......@@ -10,8 +10,14 @@
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.m2e.core.maven2Builder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
</natures>
</projectDescription>
This diff is collapsed.
language: java
jdk:
- openjdk8
- oraclejdk8
sudo: false
env:
global:
- BUILD_CMD='make'
- RUN_TESTS=false
- BUILD_CMD='mvn -Dskip.tests=true clean package'
- RUN_TESTS=true
sudo: true
matrix:
include:
- jdk: oraclejdk8
- jdk: oraclejdk9
env:
- BUILD_CMD='ant -f build.xml'
- RUN_TESTS=true
- TEST_EXCLUDES="**/*_ESTest*"
- jdk: openjdk9
env:
- TEST_EXCLUDES="**/*_ESTest*"
- jdk: openjdk11
env:
- TEST_EXCLUDES="**/*_ESTest*"
cache:
directories:
- "${HOME}/dependencies"
- "${HOME}/.m2"
before_install:
- "export CASHER_TIME_OUT=300"
- "export DISPLAY=:99.0"
- "sh -e /etc/init.d/xvfb start"
- "source install_dependencies.sh"
- mvn validate
install:
- "$BUILD_CMD"
script:
- if [ "$RUN_TESTS" == "true" ]; then
cd test;
ln -s $(pwd)/../etc/log4j.properties .;
./RunDefaultUnitTests.sh | tee test.log && [ -z "$(grep 'Failures:\s[^0]\|Errors:\s[^0]' test.log)" ];
fi
./RunTravisTests.sh -e "$TEST_EXCLUDES" | tee test.log && [ -z "$(grep 'Failures:\s[^0]\|Errors:\s[^0]' test.log)" ];
fi
\ No newline at end of file
Tim Carver (path-help@sanger.ac.uk)
Sascha Steinbiss (path-help@sanger.ac.uk)
Kim Rutherford (path-help@sanger.ac.uk)
Kevin Pepper (path-help@sanger.ac.uk)
Tim Carver
Sascha Steinbiss
Kim Rutherford
Kevin Pepper (artemis-help@sanger.ac.uk)
Version 17.0.2-test - TBD next release
1) Added bamview_use_htsjdk_file_index_caching property to allow switching off of htsjdk caching for bam files.
This gets around a bug for large bams whereby parts of the bam fail to get loaded - RT ticket #624271.
See htsjdk GitHub issue 1127 for details.
Version 17.0.1
Version 18
1) Switched build process to use Apache Maven. Changed directory structure. Removed ant and Make files. Most jar files are now pulled directly from the Maven repository.
2) Upgraded Java version as Java 8 will be going out of support. Artemis will now only build/run with Java versions 9 to 11 (RT ticket #589103).
3) Upgraded to Picard 2.18.14 jar, which has a number of important bug fixes, including:
i) RT tickets #625730 - Loading bams into Artemis
ii) RT ticket #624271 - Problems with some bams loaded into Artemis causing data not to be viewable
4) Removed broken documentation functionality.
HTML/PDF manuals are now stored in Github gh-pages branch and exported from word docs (RT ticket #618907).
5) Added run menu option to execute an InterPro sequence search for a selected feature - RT ticket #643820.
6) Updated application scripts.
7) Fixed broken Amigo, GO term, Uniprot (RT ticket #639930) and UniprotKB URLs, used in the Artemis gene builder/feature edit windows.
8) Updated README.md
9) Fix for RT ticket #400288: "GO term warnings in Artemis" - we now no longer put out a warning for ISM, as it's optional in certain cases
[http://wiki.geneontology.org/index.php/Inferred_from_Sequence_Model_(ISM)].
10) Removed the INSTALL document as the content is now covered elsewhere.
11) Changed error message displayed when multiple features are selected for pfam/rfam search.
12) Added temporary Java 9+ --add-opens flags to art/act scripts. These will be removed when Ibatis is replaced.
13) Added unit tests for Chado access to enable Postgres 10 testing (RT ticket #632896).
14) Added Mockito for unit test mocking.
15) Updated/fixed run_blast<..> scripts in the etc folder. Running blast from the run menu now uses blast+. Removed options to run Smart, Jalview, fasta & fastx.
Results are displayed using View->Search Results.
Related RT ticket #596281 also closed.
16) Removed the old icons/Readme doc for local blast setup and added an updated version to the main README.md.
17) Updated setup_blast_dbs.sh script and added to etc folder, for setup of a local blast environment (detailed in the README.md and manuals).
18) Removed ability to run remote blast, fasta34 etc using SSH. This functionality is being retired.
19) Removed old ".sanger" and ".sanger.linux" scripts from etc folder - these were very out of date, with incorrect file paths etc.
20) Fixed RT ticket #642350: "GO term evidence codes in chado Artemis" - Added HTP, HDA, HMP, HGI, HEP GO evidence codes to Artemis.
21) Added fix for Java 9 JDK-8181568 issue across all apps, related to display of application icons on Macs.
22) Fixed incorrect Pfam URL, used in Feature Edit and Evidence Viewer screens.
23) Fixed error handling on Run->Pfam/Rfam search (RT ticket #420623).
24) Enabled ability to drag and drop data files on to Artemis and BamView apps [Mac OS X] for immediate display.
25) Fixed RT ticket #642944: "ACT crunch-m8 file generation". ACT can now handle tblastx hit table files produced from comparisons
on the NCBI Blast web site. This is an alternative to Web ACT / Double ACT.
[e.g. https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastx&PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&LINK_LOC=blasttab&LAST_PAGE=tblastx&BLAST_INIT=blast2seq]
26) Removed the /lustre/scratch101/blastdb/Pathogen/Kineto_aa run->blast menu option. This database path no longer exists.
27) RT ticket #472601: Artemis RPKM and read count broken since version 16.0.6. Fixed bug related to intron region reads. New unit tests added.
Version 17.0.2-test - patch release for Sanger. Changes incorporated into GitHub master.
1) Added bamview_use_htsjdk_file_index_caching property to allow switching off of htsjdk caching for bam files.
This gets around a bug for large bams whereby parts of the bam fail to get loaded - RT ticket #624271.
See htsjdk GitHub issue 1127 for details.
Version 17
Artemis/ACT and associated applications have been upgraded to Java 8. Java 7/6/5 are now no longer supported - RT ticket #589103
......
Installation instructions for UNIX
==================================
1. change to /some/directory
2. uncompress and untar the artemis_compiled.tar.gz file
On UNIX the command is: tar xzvf artemis_compiled.tar.gz
This will create a "artemis" directory containing all the java classes. On
Unix the easiest way to run the program is to run the script called art in the
diana directory:
/some/directory/artemis/art
If all goes well you will be presented with a small window with two
menus. From the File menu you can open a flat file containing an
entry. If it reads the entry successfully a new window will open,
which shows the sequence and features for the entry.
Download and Install from GitHub
================================
Installation instructions for GitHub download
1. Download:
git clone http://github.com/sanger-pathogens/Artemis.git
2. Compile the code:
cd Artemis
make
3. Run Artemis:
./art
or ACT:
./act
Makefile targets
================
make - compile code
make jar - create Artemis (jar_build/artemis.jar) and ACT
(jar_build/act.jar) jar files.
make dist - create a tar ball of the Artemis/ACT distribution
Creating signed jar files for Artemis/ACT Java Web Start launch
===============================================================
Use 'make jar' to create jar_build/artemis.jar. See the following pages
for a description of deploying and signing jar files:
http://java.sun.com/docs/books/tutorial/deployment/webstart/deploying.html
http://java.sun.com/docs/books/tutorial/deployment/jar/signing.html
Use the Java keytool to generate a keystore (e.g. artemisstore below) file:
keytool -genkey -alias signFiles -dname "CN=$NAME, \
OU=$ORGU, O=$ORG, L=$LOC, S=$STATE, C=$CODE" \
-keypass $KEYPASS -storepass $STOREPASS -keystore artemisstore -validity $VALID
The following can be used to view the key store and list entry details:
keytool -list -v -keystore artemisstore
Then use the following to create a signed jar to use in the JNLP file:
jarsigner -keystore artemisstore -storepass $STOREPASS -keypass $KEYPASS \
-signedjar sartemis.jar artemis.jar signFiles
Running the test suite
======================
cd test
RunDefaultUnitTests.sh - this runs all hand-written unit tests.
RunEvoSuiteUnitTests.sh - this runs all EvoSuite generated unit tests. It will take well over 30 mins to run.
RunAllUnitTests.sh - this runs all hand-written and EvoSuite generated unit tests. It will take well over 30 mins to run.
This software is Copyright (c) 2018 by Wellcome Trust Sanger Institute.
This software is Copyright (c) 2019 by Wellcome Trust Sanger Institute.
This is free software, licensed under:
......
Manifest-Version: 1.0
Main-Class: uk.ac.sanger.artemis.components.ArtemisMain
# This is a GNU Makefile for Artemis
SHELL=/bin/sh
#OPT_FLAGS = -g -deprecation
JAVAC := javac -source 1.8 -target 1.8 $(OPT_FLAGS) $(EXTRA_FLAGS)
REAL_CLASSPATH := CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:.
ARTEMIS_DIRS = uk/ac/sanger/artemis \
uk/ac/sanger/artemis/chado \
uk/ac/sanger/artemis/circular \
uk/ac/sanger/artemis/circular/digest \
uk/ac/sanger/artemis/components \
uk/ac/sanger/artemis/components/alignment \
uk/ac/sanger/artemis/components/database \
uk/ac/sanger/artemis/components/filetree \
uk/ac/sanger/artemis/components/genebuilder \
uk/ac/sanger/artemis/components/genebuilder/cv \
uk/ac/sanger/artemis/components/genebuilder/gff \
uk/ac/sanger/artemis/components/genebuilder/ortholog \
uk/ac/sanger/artemis/components/variant \
uk/ac/sanger/artemis/components/ref \
uk/ac/sanger/artemis/editor \
uk/ac/sanger/artemis/io \
uk/ac/sanger/artemis/j2ssh \
uk/ac/sanger/artemis/plot \
uk/ac/sanger/artemis/sequence \
uk/ac/sanger/artemis/util
SOURCES := $(foreach DIR,$(ARTEMIS_DIRS),$(wildcard $(DIR)/*.java))
CLASSES := $(SOURCES:%.java=%.class)
all: code
# Utils needs to be built before controller
uk/ac/sanger/artemis/circular/digest/CircularGenomeController.class:uk/ac/sanger/artemis/circular/digest/Utils.class
$(REAL_CLASSPATH) $(JAVAC) $(@:%.class=%.java)
code: $(CLASSES)
topdown:
$(REAL_CLASSPATH) $(JAVAC) uk/ac/sanger/artemis/components/ArtemisMain.java
%.class : %.java
$(REAL_CLASSPATH) $(JAVAC) $<
doc :
$(REAL_CLASSPATH) javadoc -J-mx200m -version \
AppGlobal.java \
uk.ac.sanger.artemis uk.ac.sanger.artemis.components \
uk.ac.sanger.artemis.sequence uk.ac.sanger.artemis.plot \
uk.ac.sanger.artemis.util uk.ac.sanger.artemis.io
manual :
(cd docs; make)
CLASS_FILES := `find org uk -name '*.class' -print`
OTHER_FILES := `find images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md`
dist :
rm -rf artemis_compiled.tar.gz tar_build
mkdir tar_build
mkdir tar_build/artemis
tar cf - $(OTHER_FILES) act art dnaplotter bamview setenv Makefile etc | (cd tar_build/artemis; tar xf -)
tar cf - artemis_sqlmap dnaplotter uk org lib | (cd tar_build/artemis; tar xf -)
(cd tar_build; find . -name 'CVS' -print | xargs rm -rf; find . -name '.svn' -print | xargs rm -rf; tar cvf ../artemis_compiled.tar artemis)
jar : all artemis.jar
artemis.jar : $(CLASSES)
mkdir -p jar_build/build
rm -f *.jar
cd jar_build/build; \
for fileJar in ../../lib/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
for fileJar in ../../lib/j2ssh/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
for fileJar in ../../lib/ibatis/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
for fileJar in ../../lib/batik/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
for fileJar in ../../lib/picard/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
cp -R ../../lib/LICENSE.* ../../uk ../../org ../../etc ../../images ../../lib/j2ssh/j2ssh.properties \
../../images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg ../../images/icon.gif ../../README.md ../../artemis_sqlmap .
find jar_build/build -name '*.java' -print | xargs rm -f
find jar_build/build -name '.svn' -print | xargs rm -rf
find jar_build/build -name '*.DS_Store' -print | xargs rm -rf
cd jar_build/build; \
rm -rf META-INF/MANIFEST.MF; \
echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain" > manifest-art; \
echo "Permissions: all-permissions" >> manifest-art; \
jar cmf manifest-art ../artemis.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \
artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \
echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw" > manifest-circular; \
echo "Permissions: all-permissions" >> manifest-circular; \
jar cmf manifest-circular ../dnaplotter.jar images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg README.md etc \
org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \
echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView" > manifest-bamview; \
echo "Permissions: all-permissions" >> manifest-bamview; \
jar cmf manifest-bamview ../bamview.jar META-INF/services etc org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE; \
echo "Main-Class: uk.ac.sanger.artemis.components.ActMain" > manifest-act; \
echo "Permissions: all-permissions" >> manifest-act; \
jar cmf manifest-act ../act.jar META-INF/services images/Wellcome_Sanger_Institute_Logo_Landscape_Digital_RGB_Full_Colour.jpg images/icon.gif README.md etc \
artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \
rm -rf jar_build/build;
clean :
-rm -rf *.html artemis.jar resources uk/ac/sanger/jcon/ jar_build tar_build artemis_compiled.tar
-rm -rf TAGS* *.o
-find . -name '*.class' -print | xargs rm -f
......@@ -16,6 +16,7 @@ The Artemis Software is a set of software tools for genome browsing and annotati
* [Introduction](#introduction)
* [Installation](#installation)
* [Usage](#usage)
* [Building](#building)
* [License](#license)
* [Documentation](#documentation)
......@@ -31,15 +32,119 @@ 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.
For further information, please see the [Artemis GitHub page](http://sanger-pathogens.github.io/Artemis/)
DNAPlotter generates images of circular and linear DNA maps.
BamView is a standalone BAM/CRAM file viewer.
For further information and details on how to download the Artemis software, please see the [Artemis GitHub page](http://sanger-pathogens.github.io/Artemis/)
## Prerequisites
Java 9+ must be installed. Ideally Java 11.
## Installation
For instructions on how to install Artemis, please see the [Artemis manual](ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf).
Please refer to the relevant documentation in the Documentation section below.
## Usage
For instructions please see the [Artemis manual](ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf)
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, 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
```
This will build the application jars and place them in target/jars and win-jars folders. The win-jars jars have the etc folder files bundled in, for Windows.
## Building Release artifacts
To build .zip or .gz installables with unsigned jars, use the following command:
```
mvn -Djarsigner.skip=true clean package -P release
```
If building on a Mac then .app packages and a .dmg image can additionally be produced using:
```
mvn -Djarsigner.skip=true clean package verify -P release
```
The release artifacts can then be found in the target/release-artifacts directory.
Jar signing can be included in the build cycle by <b>not</b> supplying a -Djarsigner.skip flag. A <i>maven.properties</i> file needs to be placed in the top-level Artemis folder containing the following keystore properties:
```
signer-keystore-path=<The path to a .jks keystore>
signer-keystore-alias=<certificate alias name>
signer-keystore-password=<keystore password>
signer-keystore-type=JKS
```
## 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. Ensure that the BLAST+ executables are available in your PATH and that local
databases can be found by Artemis:
On the command line type:
```
blastp -help
```
If the executables are not found then their installation bin folder 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 variable (See Blast+ documentation). 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 using the run menu - set options functionality.
4. Download and format the uniprot database(s):
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.
```
mkdir $HOME/blast-data
cd blast-data
cp <Artemis folder>/etc/setup_blast_dbs.sh .
./setup_blast_dbs.sh
```
(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).
......@@ -49,15 +154,13 @@ For more information on how to download Artemis, please see the [Artemis GitHub
## Documentation
The Artemis user manual is at:
http://www.sanger.ac.uk/science/tools/artemis
http://sanger-pathogens.github.io/Artemis/Artemis/
The ACT user manual is at:
http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act
The DNA plotter user manual is at:
http://www.sanger.ac.uk/science/tools/dnaplotter
The BAM View user manual is at:
http://www.sanger.ac.uk/science/tools/bamview
http://sanger-pathogens.github.io/Artemis/ACT/
The DNA plotter documentation is at:
http://sanger-pathogens.github.io/Artemis/Artemis/DNAPlotter/
The BAM View documentation is at:
http://sanger-pathogens.github.io/Artemis/Artemis/BamView/
log4j.rootLogger=info,stdout
log4j.appender.stdout=org.apache.log4j.ConsoleAppender
log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
log4j.appender.stdout.layout.ConversionPattern=%p\t%d{ISO8601}\t%r\t%c\t[%t]\t%m%n
log4j.logger.org.evosuite=info, stdout
......@@ -5,7 +5,6 @@
#
QUIET=no
PRG=$0
usage () {
echo "SYNOPSIS"
......@@ -58,17 +57,16 @@ add_proxy_properties() {
}
#
# Resolve links - $0 may be a link
# Resolve script path (inc symlinks)
#
while [ -h "$PRG" ] ; do
ls=`ls -ld "$PRG"`
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '.*/.*' > /dev/null; then
PRG="$link"
else
PRG="`dirname $PRG`/$link"
fi
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
SOURCE="$(readlink "$SOURCE")"
[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
# Special Sanger override on chado PGUSER
if [[ "$ARTEMIS_SANGER_DBUSER" != "" ]]
......@@ -95,9 +93,10 @@ do
shift
done