[galaxy-user] Cleanup script error - guess_dialect_for_url

Hello, I'm working on a local instance of Galaxy-dist and I just updated it. Right after the update I tried to run the cleanup scripts. Unfortunately what I'm getting is the following error: # sh delete_datasets.sh -d 0 -r Traceback (most recent call last):   File

[galaxy-user] How can I sort BAM/SAM file by read names?

Hi, I need to sort a BAM file by read names, I was wondering if this is possible with a tool included in Galaxy? I know any BAM file produced inside Galaxy will be sorted by coordinates, but I couldn't find an option to change this to queryname in any tool. Picard has the tool SortSam[1],

Re: [galaxy-user] How can I sort BAM/SAM file by read names?

Hello Carlos, Start by converting your BAM file to SAM, with NGS: SAM Tools - BAM-to-SAM. It is probably best to include the header if you plan to use the SAM file in downstream tools later on. If not, you can skip the step where it is saved. Next, to save back the SAM header into a

Re: [galaxy-user] Cleanup script error - guess_dialect_for_url

Hi Rocco, To help us get oriented, which galaxy-dist pull did you start from and which did you update to? If you have the release date/hg pull numbers, that would be great. If you need to reference, these are the prior distributions: http://wiki.g2.bx.psu.edu/DevNewsBriefs Ideally, you