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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