[mira_talk] Re: Run MIRA in Galaxy....

On Mon, Dec 19, 2011 at 10:16 AM, Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx> wrote:
>
> The segmentation fault is probably a MIRA problem.
> However, the prior "uname: write error: Broken pipe"
> might be something to do with Galaxy though.
>
> ..
>
> I did see the  "uname: write error: Broken pipe" on my
> machine, but it doesn't seem to be consistent.

I'm still not sure, but I suspect a new Galaxy feature
for capturing the version number is to blame, see:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007890.html

> I have not seen the "Missing .wig output file" issue,
> which is a message from my wrapper, which treats
> this as an error condition (so the history in Galaxy
> will go red). In this case the MIRA log should help
> explain what went wrong.

I realised the wrapper would only report the first
missing file (here the wiggle file), and not tell you
if the other files were missing (e.g. the ACE output).
I've fixed that now.

Please could you update mira.xml, mira.py, mira.txt
once more and retest? If this sees to be working I'll
publish it on the Galaxy Tool Shed this week:

https://bitbucket.org/peterjc/galaxy-central/src/e061fcaaba43/tools/sr_assembly

Thanks!

Peter

P.S. On a related issue, would you prefer FASTQ
output instead of QUAL for the contig qualities for
any downstream analysis within Galaxy?

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