Samtools index for indexing .bam files.

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#1

I would like to use the Samtools index tool. Is that possible for you to install on the Galaxy platform? Thank you for your help in advance.

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#2

If you download your own Galaxy (http://getgalaxy.org) you can install any tools that are available at https://toolshed.g2.bx.psu.edu/

In case the tool you want is not there, you might need to wrap it yourself, tutorial: https://planemo.readthedocs.io/en/latest/writing_standalone.html

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#3

For this specific tool also note that there should be no need for it when using Galaxy, and that it is not offered as a separate tool on public servers on purpose.

Whenever you generate a BAM dataset in Galaxy, the server, transparently to you, uses samtools index to generate the index for that BAM already, and every tool requiring an indexed BAM as input should either use that pregenerated index or create its own on the fly. If you find a tool maintained by devteam or the iuc that does not adhere to this standard, you should report this as a bug.
If you need to download a BAM and also its index, that is possible, too. When you click on the download icon of any BAM dataset, you should see a menu pop up, which offers you the choice to download the BAM itself or its index.

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#4

Thank you very much for your help marten and wm75 !!!

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