Galaxy stores a BAI for each BAM internally; you can access it in a tool
wrapper like this (assuming the name of your input dataset is 'input_bam':
${input_bam.metadata.bam_index}
Once you have the file path, you can set up a symbolic link to it and the tool
should work fine.
Good luck,
J.
On May 22, 2013, at 4:05 AM, Michiel Van Bel wrote:
> Hi,
>
> I would like to inquire whether anyone has attempted to implement the
> idxstats tool from samtools into Galaxy?
> The xml-file for idxstats is not present in the Galaxy source code, which led
> me to try and implement it myself.
> However, the main problem I face is that the idxstats tool silently relies on
> having an index file available (within the same directory) for the bam file
> you which to print the stats for.
> E.g. samtools idxstats PATH/test.bam
> searches for PATH/test.bam.bai and gives an error when this file is not
> present. And somehow I cannot model this behavior in Galaxy.
>
> A different solution would of course be to ask the author(s) of samtools to
> have an option available where the user can directly indicate the path to the
> index file.
>
> regards,
> Michiel
>
> PS: I've searched the mailing list archives for this problem but did not find
> any matches. Apologies if I somehow missed the answer.
>
> --
> ==================================================================
> Michiel Van Bel, PhD
> Expert Bioinformatician
> Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809
> VIB Department of Plant Systems Biology, Ghent University
> Technologiepark 927, 9052 Gent, BELGIUM
> mi...@psb.vib-ugent.be http://www.psb.vib-ugent.be
> http://bioinformatics.psb.ugent.be
> ==================================================================
>
>
>
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