Dear all, Are we the only ones that are missing bam index files (the .bai) when exporting a history that contains for instance bowtie mapped reads. In the original history we can save the bam and bai files but after export to a file (tgz) and later import into another (or the same) galaxy instance, the bai files cannot be accessed/saved anymore.... Alex
Are we the only ones that are missing bam index files (the .bai) when exporting a history that contains for instance bowtie mapped reads.
Bam indices are deliberately left out because they can be regenerated. However, it's reasonable that there should be an option to download BAIs; I've added it to the card for improving history import/export.
In the original history we can save the bam and bai files but after export to a file (tgz) and later import into another (or the same) galaxy instance, the bai files cannot be accessed/saved anymore....
This is a bug and has been fixed in -central changeset 3a71d40d7b99 J.
Thanks. We'll test it shortly. These are usually small files (not the actual index). Alex -----Oorspronkelijk bericht----- Van: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Verzonden: vrijdag 14 december 2012 17:59 Aan: Bossers, Alex CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] bai file missing in history export?!
Are we the only ones that are missing bam index files (the .bai) when exporting a history that contains for instance bowtie mapped reads.
Bam indices are deliberately left out because they can be regenerated. However, it's reasonable that there should be an option to download BAIs; I've added it to the card for improving history import/export.
In the original history we can save the bam and bai files but after export to a file (tgz) and later import into another (or the same) galaxy instance, the bai files cannot be accessed/saved anymore....
This is a bug and has been fixed in -central changeset 3a71d40d7b99 J.
participants (2)
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Bossers, Alex -
Jeremy Goecks