Hi Ryan (and list membres),

In first place, thank you very much for answering my question, and, moreover, in a detailed way.

I've checked user`s shell and it's bash (the Ubuntu default), and tried sort command directly on a terminal:

sort -k 4 -t $'\t' -o item3sorted.interval item3.interval

In fact, I've saved Galaxy's history datasets to a folder, sorted them by using the above command and uploaded again just to follow the screencast... Thus, I guess there is some other reason for the error.

This week, I've been requested to switch Ubuntu for Fedora, because this will be the actual compilation we will be using. If I run over that problem again I'll let the mailing list know... except if you think this issue deserves more investigation/tests.

Best regards,

Jordi Rambla Universitat de Barcelona

-----Mensaje original----- De: Ry4an Brase [mailto:ry4an-galaxy@msi.umn.edu] Enviado el: lunes, 26 de abril de 2010 7:38 Para: Jordi Rambla CC: galaxy-dev@bx.psu.edu Asunto: Re: [galaxy-dev] grouping and sorting error at a bare local installation

That error message is coming out of the sort(1) unix command, not from galaxy/python. In filters/sorter.py the command line being invoked looks like:

cmd = "sort -f -t $'\t' %s %s %s" % (' '.join(cols), outputfile, inputfile)

ignoring the python stuff that $'\t' is supposed to be interpreted as a TAB character by your shell:

Words of the form $'string' are treated specially. The word expands to string, with backslash-escaped characters replaced as specified by the ANSI C standard. Backslash escape sequences, if present, are decoded as follows: \a alert (bell) \b backspace \e an escape character \f form feed \n new line \r carriage return \t horizontal tab

(from the bash(1) manpage)

Is it possible the user under which you're running galaxy doesn't have sh or bash as it's shell?

I've never seen that listed as a requirement, but failure to interpret $'\t' seems to be what's happening so nearly as I can tell.

On Sat, Apr 24, 2010 at 10:51:19AM +0200, Jordi Rambla wrote:

Hi,

I'm quite new to Galaxy and Python, but I have near 25 years of experience at computing (development, databases, web development, systems.)

I've performed a local installation in order to learn Galaxy and it's "internals".

In order to test the installation, I'm reproducing the Galaxy screencast tutorials locally.

When reproducing the screencast named : "Finding Exons with the highest number of nucleotide polymorphisms", at step 4 (grouping and

counting).

I'm receiving the following error: "An error occurred running this job: Sorting input dataset resulted in error: 512: sort: multi-character tab `$\t'".

Just to doublecheck, I've tried to just sort the dataset on column 4 (Name), and I'm receiving a quite similar error ("An error occurred running this job: sort: multi-character tab `$\t'").

I've tried to locate the error source at the configuration/ source code files. but found nothing promising on filters/sorter.py nor stats/grouping.py.

Thus, I'm asking for a tip on where to look at.

Thanks in advance.

Jordi Rambla

Universitat de Barcelona

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