One thing to try: see if your shell is 'dash' (which is the default is recent Ubuntus) and switch it to 'bash' . Make sure to change not only your currently running shell, but also the "/bin/sh" link . "dash" does not respect the $'\t' trick . -gordon Jacob Biesinger wrote, On 08/03/2010 06:01 PM:
Hi! On my local galaxy_dist, doing a simple sort on a bed file is failing. I think the culprit is a tab expansion of the system call on line 42 of tools/filters/sorter.py.
The Galaxy command that is being run is: python /home/wbiesing/galaxy_dist/tools/filters/sorter.py --input=/home/wbiesing/galaxy_dist/database/files/000/dataset_171.dat --out_file1=/home/wbiesing/galaxy_dist/database/files/000/dataset_190.dat --column=1 --style=alpha --order=DESC 2 num DESC
and the stderr output from galaxy is: sort: multi-character tab `$\t'
I can repro the system call within python: In [1]: import os In [3]: cmd = "sort -f -t $'\t' -k1,1 -k2,2n -o /home/wbiesing/galaxy_dist/database/files/000/dataset_190.dat /home/wbiesing/galaxy_dist/database/files/000/dataset_171.dat" In [5]: os.system(cmd) sort: multi-character tab `$\t' Out[5]: 512
Running python2.6.5 with recent co of galaxy_dist. Ubuntu 10.04 x86_64.
-- Jake Biesinger Graduate Student Xie Lab, UC Irvine (949) 231-7587
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