I would think the correct approach would be to allow any bam file and if a tool requires a coordinate sorted bam and one is not provided it would make sense for the tool to fail with an error.

Does galaxy itself require a coordinate sorted bam or this this so the majority of tools can function properly?

Sent from my iPhone

> On Jul 17, 2015, at 11:08 AM, John Chilton <jmchilton@gmail.com> wrote:
>
> 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 <dubjulie@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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