I'm trying to run a basic workflow consisting of just Map with Bowtie for Illumina, Filter SAM, and SAM-to-BAM. Right now I get an error at the SAM-to-BAM step that says:
Exception: Error Setting BAM Metadata: Samtools-htslib-API: bam_index_build2() not yet implemented. I'm feeding the workflow some fastq data.
I currently have both devteam and iuc's package_samtools_0_1_19 installed on my local Galaxy instance, as well as version 1.1.4 of SAM-to-BAM owned by devteam.
I have tried uninstalling and reinstalling these tools more than once only to get the same error. I believe I have all dependencies installed as well, when I check my 'manage tools' page under Admin. Could this just the wrong mix of tools? Since there's devteam and iuc versions available, which is the right one to use, and what's the difference between them? Do I have to manually install something?