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.
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.
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
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
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