adding skesa version 2.5.1

[erinyoung]

Skesa has actually had a new version for awhile, I just didn't notice because of their tag. It looks like I wasn't the only one confused (ncbi/SKESA#39).

Closes #748

To add to the confusion or reduce the confusion, I vote we tag this image as skesa.2.4.0_saute.1.3.0_2, which is the same tag as their github repo. It's actually for skesa version 2.5.1 - which I guess we could use as well. (Does that mean we would tag this as skesa.2.4.0_saute.1.3.0_2, 2.5.1, and latest?)

I completely changed things from the prior Dockerfile. I added a builder, app, and test stage, CMD line, and some tests. I also added a tool-specific readme where it lists the versions of all the tools installed.

I opted to not use the pre-compiled executables because their url changes too much (i.e. https://github.com/ncbi/SKESA/releases/download/skesa.2.4.0_saute.1.3.0_2/gfa_connector.centos.7.9.2009 and https://github.com/ncbi/SKESA/releases/download/2.4.0/gfa_connector.centos7.7), which is why I put together the builder stage.

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
  • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[Kincekara]

I saw a few missing libraries in the build log. Certain things may not work.
Could you add flex bison doxygen libxml2 default-jdk (or any Java you want) to the builder?

#8 24.69 -- Could NOT find FLEX (missing: FLEX_EXECUTABLE) (Required is at least version "2.6")
#8 24.69 -- Could NOT find BISON (missing: BISON_EXECUTABLE) (Required is at least version "3")
#8 24.79 -- Found Python3: /usr/bin/python3 (found version "3.10.12") found components: Interpreter 
#8 24.79 -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) 

#8 192.6 -- Could NOT find FLEX (missing: FLEX_EXECUTABLE) (Required is at least version "2.6")
#8 192.6 -- Could NOT find BISON (missing: BISON_EXECUTABLE) (Required is at least version "3")
#8 192.6 -- Could NOT find LibXml2 (missing: LIBXML2_LIBRARY LIBXML2_INCLUDE_DIR) 
#8 192.6 -- Could NOT find Java (missing: Java_JAVA_EXECUTABLE Java_JAVAC_EXECUTABLE Java_JAR_EXECUTABLE Java_JAVADOC_EXECUTABLE Java_JAVAH_EXECUTABLE Development) 

[erinyoung]

I added those dependencies!

[Kincekara]

Thank you for putting all this together!
You can check the image deployment from here: https://github.com/StaPH-B/docker-builds/actions/runs/8331979883.