Question: bam_index_build2() not yet implemented exception on local Galaxy instance - sam-to-bam
gravatar for nhung
7 months ago by
University of Maryland, College Park
nhung10 wrote:


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?

ADD COMMENTlink modified 7 months ago by Jennifer Hillman Jackson25k • written 7 months ago by nhung10
gravatar for Jennifer Hillman Jackson
7 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Which Galaxy version are you running? If not at the most current, try upgrading:

Bowtie for Illumina has been deprecated. Use Bowtie2 instead.

For devteam and iuc tools, pick the one that is the most current (by tool revision or date). There is some overlap between the groups and the ownership/development repositories.

If upgrading Galaxy doesn't work, let us know and we can troubleshoot more here or you can ask the developers directly at Gitter (often faster): or

Thanks! Jen, Galaxy team

ADD COMMENTlink written 7 months ago by Jennifer Hillman Jackson25k
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