I am not on my computer right now but ill give you the report as soon as I am back home. Thank you.

On Thu, Aug 5, 2010 at 2:27 PM, Jacob Biesinger <jake.biesinger@uci.edu> wrote:

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.
>>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> galaxy-dev mailing list
>>> galaxy-dev@lists.bx.psu.edu
>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
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