You might try running the python command directly, outside of galaxy, to try to track down the source of the error.  I also can't repro your issue, though out datasets differ.

Look in the log file at galaxy_dist/paster.log for something along the lines of:

galaxy.jobs.runners.local DEBUG 2010-08-05 11:24:04,018 executing: python /home/wbiesing/galaxy_dist/tools/filters/sorter.py        --input=/home/wbiesing/galaxy_dist/database/files/000/dataset_25.dat        --out_file1=/home/wbiesing/galaxy_dist/database/files/000/dataset_46.dat        --column=1       --style=alpha       --order=ASC          2         num         ASC  

Which is the output for my sort command.  Does sorting work on smaller datasets for you?
--
Jake Biesinger
Graduate Student
Xie Lab, UC Irvine
(949) 231-7587


On Thu, Aug 5, 2010 at 10:32 AM, Minh Bui <buiduyminh@gmail.com> wrote:
Hi Jacob, Guru

I tried both of your methods and Galaxy didn't give me error $'\t anymore but somehow it didn't sort (or filter) the data. 
When I sort the table (c2) , it returns a table without sorting it. 
When I filter the table (c2=='Unmapped'), it returns an empty table. 
Screenshot: http://img514.imageshack.us/img514/6047/screenshotks.png

My data after convertion looks like this: 

GIQPZ7U01A1A82-W3_11_11	Partial	99	95	chr3	17443613	17443685	-
GIQPZ7U01BM124-W3_11_11	Partial	99	89	chr3	17443521	17443685	-
GIQPZ7U01CG1P0-S3_11_11	Partial	98	65	chr2	162180459	162180499	-
GIQPZ7U01B6DQ9-S3_11_11	Chimeric
GIQPZ7U01ASQA4-NL3_10_21	Partial	99	67	chr3	17443511	17443685	-
GIQPZ7U01CB92X-W3_10_21	Partial	99	88	chr3	17443608	17443685	-
GIQPZ7U01AW16P-S3_10_23	Unmapped
GIQPZ7U01B1FV1-S3_10_21	Partial	98	75	chr16	367117	367155	-
GIQPZ7U01B2PUV-S3_11_11	Chimeric
GIQPZ7U01CC7BN-S3_10_23	Partial	97	84	chr19	18614552	18614649	-
GIQPZ7U01BOQUL-NL3_10_21	Partial	96	95	chr3	17443615	17443685	-
GIQPZ7U01CHEFR-W3_11_11	Partial	99	95	chr3	17443611	17443685	-
GIQPZ7U01B2QVH-NL3_10_21	Partial	100	67	chr16	367117	367155	-
GIQPZ7U01BH73U-S3_11_11	Unmapped
GIQPZ7U01A2OJ8-NL3_10_23	Partial	99	64	chr3	17443511	17443685	-
GIQPZ7U01B96JR-S3_10_21	Unmapped
GIQPZ7U01BSF3A-W3_10_21	Partial	99	87	chr3	17443523	17443685	-
GIQPZ7U01AY7DH-S3_10_21	Partial	99	90	chr4	38640070	38640237	+
GIQPZ7U01B3I06-S3_10_23	Full	98	100	chr19	18614567	18614647	-
GIQPZ7U01AMR6X-S3_10_23	Partial	99	85	chr19	18614551	18614649	-
GIQPZ7U01ALYU8-W3_10_21	Partial	99	78	chr3	17443625	17443685	-
GIQPZ7U01BXRZ1-W3_10_21	Partial	95	91	chr3	17443509	17443685	-
GIQPZ7U01CGAG5-W3_10_21	Partial	99	88	chr3	17443521	17443685	-
GIQPZ7U01CBIX7-S3_10_23	Partial	96	85	chr19	18614551	18614649	-
GIQPZ7U01A1RCP-S3_10_23	Partial	99	85	chr19	18614551	18614649	-
GIQPZ7U01BYXFR-W3_10_21	Partial	98	79	chr3	17443608	17443685	-
GIQPZ7U01B275Q-S3_10_21	Partial	97	67	chr16	367117	367155	-
GIQPZ7U01AXBIJ-S3_11_11	Chimeric
GIQPZ7U01BXW15-S3_10_23	Full	95	100	chr19	18614579	18614649	-
GIQPZ7U01BV1GN-W3_10_21	Partial	98	78	chr3	17443608	17443685	-
GIQPZ7U01BIYVC-S3_10_23	Partial	98	88	chr19	18614551	18614649	-
GIQPZ7U01BS3VK-S3_10_23	Unmapped
GIQPZ7U01BOGIN-NL3_10_21	Partial	99	61	chr3	17443519	17443685
.....

P.S: I am using Ubuntu. 


On Wed, Aug 4, 2010 at 12:50 PM, Jacob Biesinger <jake.biesinger@uci.edu> wrote:
I just had this exact issue.  For me, the problem was caused by my
default shell (different than login shell) being set to dash instead
of bash.  Dash doesn't respect the $'\t' trick, and so fails.  The
sorter.py script performs a system call (os.system(...)) which uses
/bin/sh.  On Ubuntu (me) and perhaps other distro's, /bin/sh is a
symbolic link to dash.

To see if this is your issue, do:
$ ls -l /bin/sh

If it points to dash, then either do:
$ sudo dpkg-reconfigure dash      # for debian-based systems like ubuntu
then choose "No-- Don't install dash"
OR
$ sudo ln -s /bin/sh bash

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



On Wed, Aug 4, 2010 at 8:58 AM, Guruprasad Ananda <gua110@bx.psu.edu> wrote:
> Hi Minh,
> Sorry for not getting back to you sooner. It looks like the sort command on
> your machine works differently from that on Galaxy, in that it doesn't
> recognize -t $'\t'as a valid option. Can you please make the following
> change and let me know if the tool ends in error state or not.
> galaxy_home_folder/tools/filters/sorter.py:
> line 42: replace
> cmd = "sort -f -t $'\t' %s %s %s" % (' '.join(cols), outputfile, inputfile)
> with
> cmd = 'TAB="\t"; sort -f -t "${TAB}" %s %s %s' % (' '.join(cols),
> outputfile, inputfile)
> Thanks,
> Guru.
> On Jul 29, 2010, at 4:22 PM, Minh Bui wrote:
>
> Hi Hans,
> This is interesting. I copied that table from Galaxy (I couldnt sort this
> table). If the big file have errors, it should give me some kind of errors
> when I Convert it.
>
> I don't know why but I still get the error. I'll run  more tests to see what
> happen.
> I also realize that when I filter C2=='Full' or 'Partial', Galaxy works fine
> and I don't get any error. But when I try to filter C2=='Chimeric' or
> 'Unmapped' ('Chimeric' and 'Unmapped' are incomplete data, they dont have
> chromosome, start-end position...), Galaxy can't filter them.
>
>
> On Thu, Jul 29, 2010 at 4:09 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
>>
>> Hi
>>
>> Does your small example really not work for you? It works fine for me
>> (after copy paste and sort on C2), see attachment.
>>
>> I suspect, there is an error in your big file?
>>
>> Hans
>>
>>
>>
>> On 07/28/2010 08:43 PM, Minh Bui wrote:
>>>
>>> And the table after I converted it to tabular format looks like this:
>>>
>>> GIQPZ7U01A1A82-W3_11_11 Full    90      100     chr3    17443613
>>>  17443686        -
>>> GIQPZ7U01BM124-W3_11_11 Partial 98      90      chr3    17443521
>>>  17443687        -
>>> GIQPZ7U01CG1P0-S3_11_11 Partial 98      65      chr2    162180459
>>> 162180499       -
>>> GIQPZ7U01B6DQ9-S3_11_11 Chimeric
>>> GIQPZ7U01ASQA4-NL3_10_21        Partial 98      67      chr3    17443511
>>>        17443686        -
>>> GIQPZ7U01CB92X-W3_10_21 Partial 98      89      chr3    17443608
>>>  17443686        -
>>> GIQPZ7U01AW16P-S3_10_23 Unmapped
>>> GIQPZ7U01B1FV1-S3_10_21 Partial 98      75      chr16   367117  367155  -
>>> GIQPZ7U01B2PUV-S3_11_11 Chimeric
>>> GIQPZ7U01CC7BN-S3_10_23 Partial 97      84      chr19   18614552
>>>  18614649        -
>>> GIQPZ7U01BOQUL-NL3_10_21        Full    86      100     chr3    17443615
>>>        17443686        -
>>> GIQPZ7U01CHEFR-W3_11_11 Full    90      100     chr3    17443611
>>>  17443686        -
>>> GIQPZ7U01B2QVH-NL3_10_21        Partial 100     67      chr16   367117
>>>  367155  -
>>> GIQPZ7U01BH73U-S3_11_11 Unmapped
>>> GIQPZ7U01A2OJ8-NL3_10_23        Partial 98      65      chr3    17443511
>>>        17443686        -
>>> GIQPZ7U01B96JR-S3_10_21 Unmapped
>>> GIQPZ7U01BSF3A-W3_10_21 Partial 99      88      chr3    17443523
>>>  17443687        -
>>> GIQPZ7U01AY7DH-S3_10_21 Partial 99      90      chr4    38640070
>>>  38640237        +
>>> GIQPZ7U01B3I06-S3_10_23 Full    98      100     chr19   18614567
>>>  18614647        -
>>> GIQPZ7U01AMR6X-S3_10_23 Partial 99      85      chr19   18614551
>>>  18614649        -
>>> GIQPZ7U01ALYU8-W3_10_21 Partial 98      80      chr3    17443625
>>>  17443687        -
>>> GIQPZ7U01BXRZ1-W3_10_21 Partial 95      92      chr3    17443509
>>>  17443686        -
>>> GIQPZ7U01CGAG5-W3_10_21 Partial 98      89      chr3    17443521
>>>  17443687        -
>>> GIQPZ7U01CBIX7-S3_10_23 Partial 96      85      chr19   18614551
>>>  18614649        -
>>> GIQPZ7U01A1RCP-S3_10_23 Partial 99      85      chr19   18614551
>>>  18614649        -
>>> GIQPZ7U01BYXFR-W3_10_21 Partial 97      80      chr3    17443608
>>>  17443686        -
>>> GIQPZ7U01B275Q-S3_10_21 Partial 97      67      chr16   367117  367155  -
>>> GIQPZ7U01AXBIJ-S3_11_11 Chimeric
>>> GIQPZ7U01BXW15-S3_10_23 Full    95      100     chr19   18614579
>>>  18614649        -
>>> GIQPZ7U01BV1GN-W3_10_21 Partial 97      80      chr3    17443608
>>>  17443687        -
>>> GIQPZ7U01BIYVC-S3_10_23 Partial 98      88      chr19   18614551
>>>  18614649        -
>>> GIQPZ7U01BS3VK-S3_10_23 Unmapped
>>> GIQPZ7U01BOGIN-NL3_10_21        Partial 99      61      chr3    17443519
>>>        17443686        -
>>> GIQPZ7U01B313G-S3_11_11 Partial 98      68      chr2    162180459
>>> 162180501       -
>>> GIQPZ7U01BCMVY-W3_10_23 Partial 99      57      chr16   367117  367155  -
>>> GIQPZ7U01BL41A-W3_10_23 Partial 95      49      chr15   50814744
>>>  50814785        +
>>> GIQPZ7U01B8EWK-NL3_10_21        Partial 98      64      chr3    17443511
>>>        17443686        -
>>> GIQPZ7U01BY5AD-NL3_10_21        Partial 97      64      chr3    17443511
>>>        17443686        -
>>> GIQPZ7U01CA6RX-S3_10_21 Unmapped
>>> GIQPZ7U01BQOHG-W3_10_21 Partial 98      89      chr3    17443521
>>>  17443686        -
>>>
>>>
>>> On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui<buiduyminh@gmail.com>  wrote:
>>>
>>>> And the table after I converted it to tabular format looks like this:
>>>>
>>>>
>>>>
>>>> On Wed, Jul 28, 2010 at 2:35 PM, Minh Bui<buiduyminh@gmail.com>  wrote:
>>>>
>>>>> Hi,
>>>>> I always get this error when I use Sort feature
>>>>> *"An error occurred running this job: sort: multi-character tab `$\t'"*
>>>>> Even I already use Text Manipulation->Convert to convert my table to
>>>>> Tabs
>>>>> format.
>>>>>
>>>>> Here is the screenshot of what happen (I want to sort C2 on job #12) :
>>>>> http://img408.imageshack.us/img408/7906/screenshotbu.png
>>>>>
>>>>>
>>>>> Could someone please show me how to fix this?
>>>>> Thank you.
>>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> _______________________________________________
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>>> galaxy-dev@lists.bx.psu.edu
>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
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