I'm not the right person to respond to this but since no one else has
I will explain my limited (probably incorrect) understanding of the
problem and what needs to be done. I believe Galaxy assumes all bam
files are coordinated sorted by default - so Galaxy's bam datatype
would be better thought of as a coordinate-sorted bam. Certain people
do not want to allow non-coordinate sorted bam files because these
would be allowed by Galaxy as valid as inputs to tools that expect
sorted bams - and things would break. For the same reason I imagine
these people would argue the bai file needs to be generated because
certain tools will depend on its existence.

I believe the proposed solution is to add an unsorted bam datatype to
Galaxy. I don't know if there is any work in progress on this but it
seems to be needed by many researchers.

Hope this clarifies things somewhat,
-John


On Mon, Jun 29, 2015 at 11:06 AM, julie dubois <dubju...@gmail.com> wrote:
> Hi all,
>
> My galaxy is the last update and I work with samtools 1.2.
> I have a bug with the sorting and the upload of bam file.
> This bug appears only when I try to upload bam sorted by name or when
> I try to sort by name.
> When I work with bam sorted by coordinate, there is no problem.
>
> So, when I try to sort a bam file by name, this error appears under
> the "bug icon" :
>
> Tool execution generated the following error message:
> [bam_sort_core] merging from 20 files...
> *** Error in `python': double free or corruption (!prev): 0x0000000002897990 
> ***
> Aborted (core dumped)
>
> The tool produced the following additional output:
>
> [E::hts_idx_push] chromosome blocks not continuous
> Galaxy attempted to build the BAM index with samtools 1.0+ but failed:
> [Errno 2] No such file or directory:
> '/data/galaxy-dist/database/job_working_directory/024/24109/__dataset_48619_metadata_temp_file_MqhjBN.bai'
>
> And the same type of error appears when I try to upload bam sorted by name.
>
>
> What I understand is that the bam can be sorted properly (The command
> line to sort is ok in a terminal with no bug and I can follow this
> step in the job_working_directory during the run) but Galaxy seems to
> fail to create a bai.
>
> For our analysis pipeline, I think the bai is not crucial, is it
> possible to avoid this creation of bai during uploading and sorting of
> bam file by name ?
>
> Is there another problem than this creation of bai ?
>
> Thanks.
>
> Julie
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