Well would you look a that. $ ls -l /bin/sh lrwxrwxrwx 1 root root 4 2010-05-28 12:07 /bin/sh -> dash

I assumed having bash set in /etc/passwd was enough-- I guess that's only for login shells? This also explains why I've always had trouble starting galaxy --> `sh run.sh` would not have environment variables, etc so I always did `bash run.sh` After: $ sudo rm /bin/sh $ sudo ln -s /bin/bash /bin/sh

Things work wonderfully. Thanks for that. Perhaps there should be a disclaimer on the wiki somewhere? I imagine Ubuntu is fairly large portion of galaxy's target audience, and it sure can cause funny errors... -- Jake Biesinger Graduate Student Xie Lab, UC Irvine (949) 231-7587

On Tue, Aug 3, 2010 at 3:30 PM, Assaf Gordon gordon@cshl.edu wrote:

I don't think so. It actually shows that your "sh" is not "bash".

run:  $ ls -l /bin/sh

and see if you get:  /bin/sh -> bash or  /bin/sh -> dash

Jacob Biesinger wrote, On 08/03/2010 06:27 PM:

...

No, my default shell (listed in /etc/passwd) is definitely /bin/bash and I can run the sort command just fine from the command line: $ 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

Though running just sh, the command fails: $ sh $ sort -f -t $'\t' -k1,1 -k2,2n -o /home/wbiesing/galaxy_dist/database/files/000/dataset_190.dat /home/wbiesing/galaxy_dist/database/files/000/dataset_171.dat sort: multi-character tab `$\t'

Seems like python's os.system(...) is the weak link.

Jake Biesinger Graduate Student Xie Lab, UC Irvine (949) 231-7587

On Tue, Aug 3, 2010 at 3:16 PM, Assaf Gordon gordon@cshl.edu wrote:

...

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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