There are two versions numbers associated with galaxy tools . There is the wrapper version and then the actual tool/binary version that is underlying. Those two numbers are wildly different and rightfully confusing (one of the unfortunate things about galaxy). I wish there was a way they would show the actual tool/binary version in the configuration GUI.
If you have only one version of bowtie installed then that would be the one used (check the PATH variable for galaxy user to see what is being sourced).
If you have only one version of bowtie installed then that would be the one used (check the PATH variable for galaxy user to see what is being sourced).
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