hello, maybe this work: change (in HOMEGALAXY/tools/filters/sorter.py) this line cmd = "sort -f -t $'\t' %s %s %s" % (' '.join(cols), outputfile, inputfile) to cmd = "sort -f -t'\t' %s %s %s" % (' '.join(cols), outputfile, inputfile) and restart galaxy 2010/8/25 Isabelle Phan <isabelle.phan@seattlebiomed.org>:

Hello,

I installed galaxy-dev using hg clone -r 60448575467f http://bitbucket.org/galaxy/galaxy-central galaxy-dist

since http://www.bx.psu.edu/hg/galaxy seems down.

I started galaxy, uploaded a fasta file, computed sequence lengths, then sorted on c2. The sort fails with the error:

Tool execution generated the following error message:

sort: multi-character tab `$\t'

I created a tab-delimited test file with 2 column, one letter in the first, one digit in the second, then sorted on c1: got the same error.

The sorter.py is doing a system call to the unix sort function (I have sort (GNU coreutils) 7.4). I tested my shell by running this on the command line

/usr/bin/sort -f -t $'\t' test-file

and it worked. I modified sorter.py to use /usr/bin/sort, restarted galaxy... and still get the same error.

So there is something wrong in the way the shell escapes the $'\t' in the sorter.py line: os.system(cmd)

Any help greatly appreciated.

Isabelle

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