The bam support is regrettably different to most of Galaxy. For some reason it can not make use of Wheels installed by Galaxy but has to use native samtools. Giving very confusing error messages such as file not found if samtools is not there.
Also your bam files MUST be sorted by coordinates as BAM sorted by name is not a format supported by Galaxy. For those few tools that expect Bam sorted by name you have to sort inside that tool. Which breaks: https://toolshed.g2.bx.psu.edu/view/iuc/samtools_sort/38ea74bd4054 As it returns a bam file no longer(or never) supported by Galaxy I have wasted a number of days on these confusing behaviours. Christian University of Manchester ________________________________________ From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, March 23, 2016 8:00 AM To: Amelia Ireland; galaxy-dev@u coordinateslists.galaxyproject.org Subject: Re: [galaxy-dev] Troubleshooting BAM file upload issues Hi Amelia, can you pleae check if you have samtools installed in your PATH? Ciao, Bjoern Am 22.03.2016 um 19:28 schrieb Amelia Ireland: > I'm setting up a Galaxy instance on a new server and am having some > issues with BAM file uploads. I'm using the BAM files supplied with > JBrowse for testing purposes. I have Galaxy installed on my laptop and > file uploads are working fine, so it's evidently an issue with the > server and/or OS configuration. > > Attempting to upload a BAM file returns the message > > "The uploaded binary file contains inappropriate content" > > and the upload is empty. > > The server is running Scientific Linux and uses the Environment Modules > system for dependency management. I can successfully upload bed and > bigwig files, which suggests that samtools is being loaded and > functioning correctly. > > If someone can suggest some troubleshooting steps, I would be most grateful. > > Thanks! > Amelia > > Integrated Microbial Genomics (IMG) > JGI / LBL > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
