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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