Merge branch 'docker-bash' into development

Author: julesjacobsen

exomiser-cli/README.md

@@ -235,6 +235,24 @@ ${docker.repository}/exomiser-cli           latest           f39698e3f36b  53 ye
 ${docker.repository}/exomiser-cli           ${project.version} f39698e3f36b  53 years ago   274 MB
 ```
 
+### <a id="docker-environment-variables"></a>Docker environment variables
+
+Exomiser will require at least two environment variables to be set. These can be provided using `-e` or `--env`
+or by creating a `.env` file.
+
+```shell
+ # -e EXOMISER_DATA_DIRECTORY=/exomiser-data # This variable is automatically set in the docker image
+-e EXOMISER_HG19_DATA_VERSION=2512 \
+-e EXOMISER_PHENOTYPE_DATA_VERSION=2512
+```
+
+These variables can also be specified in the `application.properties` file which should be made available via a mounted
+volume. 
+
+```shell
+-e SPRING_CONFIG_LOCATION=/path/to/your/application.properties
+```
+
 ### <a id="working-with-the-distroless-image"></a>Working with the distroless image (no shell)
 
 Distroless images are the default image and come without a shell. These are can be pulled using 
@@ -246,24 +264,14 @@ If you choose to run the distroless image use the following command:
  docker run -v "/path/to/exomiser-data:/exomiser-data" \
  -v "/path/to/exomiser/exomiser-config/:/exomiser"  \
  -v "/path/to/exomiser/results:/results"  \
+ -e SPRING_CONFIG_LOCATION=/exomiser/application.properties
  ${docker.repository}/exomiser-cli:${project.version}  \
- analyse --analysis /exomiser/test-analysis-exome.yml  \
- --spring.config.location=/exomiser/application.properties
+ exomiser analyse --analysis /exomiser/examples/preset-exome-analysis-human-only.yml \
+ --vcf /exomiser/examples/Pfeiffer.vcf.gz --assembly hg19 \
+ --sample /exomiser/examples/pfeiffer-phenopacket.yml \
+ --output-directory /results --output-format=PARQUET --output-filename docker-test
 ```
 
-or using Spring configuration arguments instead of the `application.properties`:
-
-```shell
- docker run -v "/path/to/exomiser-data:/exomiser-data" \
- -v "/path/to/exomiser/exomiser-config/:/exomiser"  \
- -v "/path/to/exomiser/results:/results"  \
- ${docker.repository}/exomiser-cli:${project.version}  \
- analyse --analysis /exomiser/test-analysis-exome.yml  \
- # minimal requirements for an hg19 exome sample
- --exomiser.data-directory=/exomiser-data \
- --exomiser.hg19.data-version=${genome.data.version} \
- --exomiser.phenotype.data-version=${phenotype.data.version}
-```
 -----
 
 In both cases, to run the image you will need the standard Exomiser directory layout to mount as separate volumes as in the CLI and
@@ -281,46 +289,44 @@ exomiser.data-directory=/exomiser-data
 ### <a id="working-with-the-docker-bash-image"></a>Working with the docker bash images
 
 Running the image with the following command will open the shell and create volumes with
-links to the exomiser data and connects the results to your local machine. `/results` should be an empty directory,
-where Exomiser will write the results into.
-
+links to the exomiser data and connect the results to your local machine. `/results` should be a directory,
+where Exomiser will write the results into. The host path `/path/to/exomiser-data` should contain the unpacked data
+directories `2512_hg19` and `2512_phenotype`.
 
 ```shell
 docker run -v "/path/to/exomiser-data:/exomiser-data" \
  -v "/path/to/exomiser/exomiser-config/:/exomiser" \
  -v "/path/to/exomiser/results:/results"  \
- ${docker.repository}/exomiser-cli:${project.version}-bash  
+ -e EXOMISER_HG19_DATA_VERSION=2512 \
+ -e EXOMISER_PHENOTYPE_DATA_VERSION=2512 \
+ -it ${docker.repository}/exomiser-cli:${project.version}-bash  
 ```
 
 Here the contents of `/path/to/exomiser/exomiser-config` is simply the `application.properties` file and the example files
-to test all is working correctly.
+to test all is working correctly. The `application.properties` file can be omitted if the genomic and phenotype data
+versions have been provided as environment variables.
 
 ```shell
 $ tree /path/to/exomiser/exomiser-config/
 exomiser-config/
 ├── application.properties
 ├── Pfeiffer.vcf.gz
 ├── Pfeiffer.vcf.gz.tbi
-└── test-analysis-exome.yml
+├── pfeiffer-phenopacket.yml
+└── preset-exome-analysis-human-only.yml
 ```
 
 #### Running Exomiser from the bash shell
-After running the following commands Exomiser will be started from the containers shell.
+
+The entrypoint for the image is `/bin/bash` and the command to run Exomiser is:
 
 ```shell
- source enable_exomiser.sh
- bash enable_exomiser.sh
- exomiser analyse --analysis /exomiser/test-analysis-exome.yml \
- --spring.config.location=/exomiser/application.properties
+ exomiser analyse --analysis /exomiser/examples/preset-exome-analysis-human-only.yml \
+ --vcf /exomiser/examples/Pfeiffer.vcf.gz --assembly hg19 \
+ --sample /exomiser/examples/pfeiffer-phenopacket.yml \
+ --output-directory /results --output-format=PARQUET --output-filename docker-test
 ```
 
-or using Spring configuration arguments instead of the `application.properties`:
+If successful, the results will be written to `/results/docker-test.parquet`.
 
-```shell
- exomiser --analysis /exomiser/test-analysis-exome.yml  \
- # minimal requirements for an hg19 exome sample
- --exomiser.data-directory=/exomiser-data \
- --exomiser.hg19.data-version=${genome.data.version} \
- --exomiser.phenotype.data-version=${phenotype.data.version}
-```
 -----

exomiser-cli/pom.xml

@@ -210,7 +210,7 @@
         <profile>
             <id>docker:bash</id>
             <properties>
-                <docker.base.image>eclipse-temurin:25.0.2_10-jre</docker.base.image>
+                <docker.base.image>eclipse-temurin:25.0.2_10-jre@sha256:ff82c74a630c08b417502c4c18189e62074edbb28eb1f2d31b799ac138c01058</docker.base.image>
             </properties>
             <build>
                 <plugins>
@@ -234,11 +234,6 @@
                                                 <os>linux</os>
                                                 <architecture>arm64</architecture>
                                             </platform>
-                                            <!-- No longer provided was this for MacOS? -->
-<!--                                            <platform>-->
-<!--                                                <os>linux</os>-->
-<!--                                                <architecture>arm</architecture>-->
-<!--                                            </platform>-->
                                             <platform>
                                                 <os>linux</os>
                                                 <architecture>amd64</architecture>
@@ -258,16 +253,26 @@
                                         <entrypoint>
                                             <arg>/bin/bash</arg>
                                         </entrypoint>
+                                        <environment>
+                                            <EXOMISER_DATA_DIRECTORY>/exomiser-data</EXOMISER_DATA_DIRECTORY>
+                                        </environment>
                                         <volumes>
                                             <volume>/exomiser-data</volume>
                                             <volume>/exomiser</volume>
                                             <volume>/results</volume>
                                         </volumes>
                                     </container>
                                     <extraDirectories>
+                                        <paths>
+                                            <path>
+                                                <from>src/main/jib</from>
+                                                <into>/usr/local/bin</into>
+                                                <includes>exomiser</includes>
+                                            </path>
+                                        </paths>
                                         <permissions>
                                             <permission>
-                                                <file>/entrypoint.sh</file>
+                                                <file>/usr/local/bin/exomiser</file>
                                                 <mode>755</mode>
                                             </permission>
                                         </permissions>
@@ -320,6 +325,9 @@
                                         </tags>
                                     </to>
                                     <container>
+                                        <environment>
+                                            <EXOMISER_DATA_DIRECTORY>/exomiser-data</EXOMISER_DATA_DIRECTORY>
+                                        </environment>
                                         <volumes>
                                             <volume>/exomiser-data</volume>
                                             <volume>/exomiser</volume>

exomiser-cli/src/main/jib/enable_exomiser.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+java $JAVA_OPTS -cp @/app/jib-classpath-file @/app/jib-main-class-file "$@"

exomiser-cli/src/main/jib/exomiser

@@ -184,6 +184,9 @@
                                         </tags>
                                     </to>
                                     <container>
+                                        <environment>
+                                            <EXOMISER_DATA_DIRECTORY>/exomiser-data</EXOMISER_DATA_DIRECTORY>
+                                        </environment>
                                         <volumes>
                                             <volume>/exomiser-data</volume>
                                             <volume>/exomiser</volume>