Hi there! I have a small problem, or a suggestion for improvement, related to the use of (Mini)conda and GATK4. I'm not entirely sure if this forum is a right place to ask this because I don't really know how GATK4's Conda package is maintained, but let's give it a try!
So I'm using a wide variety of bioinformatic tools in my work which is why I prefer Conda in package management - just to make it little bit easier to handle package dependencies and package updates. I am now planning to try the new GATK4 as the version 4.0.1.1 seems to be available in Bioconda. With GATK3 I was able to launch GATK simply with command 'gatk' so I naturally tried the very same command for GATK4. However;
gatk -h
bash: gatk: command not found
gatk4 -h
bash: gatk4: command not found
I located the GATK4 .jar file and succesfully tried the command;
java -jar /home/user/miniconda3/pkgs/gatk4-4.0.1.1-py36/share/gatk4-4.0.0.1-0/gatk-package-4-0.0.1-local.jar -h
This prints all available tools as excepted. So the main problem seems to be that shortcut to this .jar file is not included in the Conda distribution. Is there any particular reason for this behaviour or is this just a bug in the package? It is, of course, possible to use GATK4 with 'java -jar' command but the use of simple 'gatk' or 'gatk4' would be easier for Conda users. For example, if I update my GATK4 in the future I must also update my pipelines so that my paths are leading to the right .jar file. If I use direct 'gatk4' command, in turn, I can simply update GATK4 with Conda and launch it with 'gatk4' command in my pipeline - without manual path updating.
Thank you!