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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