Hi cngbgalaxy

May be there is an issue with the version of grep you are using on the server Galaxy is running on? I vaguely remember discussions on the mailing list related to grep/sort/etc


what happens when do it on the command line, ie:

[hrh@foo]$ grep "^@" foo.sam
@HD VN:1.0 SO:coordinate
@SQ SN:chr1 LN:10001
@SQ SN:chr2 LN:100001
@SQ SN:chr3 LN:10001
@SQ SN:chr4 LN:1001
@RG ID:rg1 SM:s1
@RG ID:rg2 SM:s3
[hrh@foo]$ grep -v "^@" foo.sam
bar:record:4    77      chr1    1       0       *       *       0       0       
AAAAAAAAAAAAA   1111111111111   RG:Z:rg1
bar:record:6    77      chr1    1       0       *       *       0       0       
AAAAAAAAAAAAA   1111111111111   RG:Z:rg2
[haruhotz@xenon1 20130912]$



Alternatively, if everything fails, and all you wanna do is just removing the seven lines at the top of the sam file, you can also use the tool: "Text Manipulation" -> "Remove beginning of a file"



Regards, Hans-Rudolf


On 09/12/2013 06:07 AM, cngbgal...@gmail.com wrote:
Hi Adam Brenner,
This is my running steps.

  * I got my sam file (as follow) upload:

        @HD VN:1.0 SO:coordinate

        @SQ SN:chr1 LN:10001

        @SQ SN:chr2 LN:100001

        @SQ SN:chr3 LN:10001

        @SQ SN:chr4 LN:1001

        @RG ID:rg1 SM:s1

        @RG ID:rg2 SM:s3

        bar:record:4

        

        77

        

        chr1

        

        1

        

        0

        

        *

        

        *

        

        0

        

        0

        

        AAAAAAAAAAAAA

        

        1111111111111

        

        RG:Z:rg1

        bar:record:6

        

        77

        

        chr1

        

        1

        

        0

        

        *

        

        *

        

        0

        

        0

        

        AAAAAAAAAAAAA

        

        1111111111111

        

        RG:Z:rg2

        bar:record:1

        

        77

        

        chr1

        

        10

        

        0

        

        *

        

        *

        

        0

        

        0

        

        AAAAAAAAAAAAA

        

        1111111111111

        

        RG:Z:rg1

        bar:record:3

        

        77

        

        chr1

        

        10

        

        0

        

        *

        

        *

        

        0

        

        0

        

        AAAAAAAAAAAAA

        

        1111111111111

        

        RG:Z:rg2

        bar:record:5

        

        141

        

        chr3

        

        40

        

        0

        

        *

        

        *

        

        0

        

        0

        

        CCCCCCCCCCCCC

        

        2222222222222

        

        RG:Z:rg1

        bar:record:9

        

        77

        

        chr4

        

        10

        

        0

        

        *

        

        *

        

        0

        

        0

        

        AAAAAAAAAAAAA

        

        1111111111111

        

        RG:Z:rg1

        bar:record:7

        

        141

        

        chr4

        

        20

        

        0

        

        *

        

        *

        

        0

        

        0

        

        CCCCCCCCCCCCC

        

        2222222222222

        

        RG:Z:rg1

        bar:record:5

        

        77

        

        chr1

        

        40

        

        0

        

        *

        

        *

        

        0

        

        0

        

        AAAAAAAAAAAAA

        

        1111111111111

        

        RG:Z:rg2

        bar:record:6

        

        141

        

        chr1

        

        50

        

        0

        

        *

        

        *

        

        0

        

        0

        

        CCCCCCCCCCCCC

        

        2222222222222

        

        RG:Z:rg2

        bar:record:2

        

        77

        

        chr2

        

        10

        

        0

        

        *

        

        *

        

        0

        

        0

        

        AAAAAAAAAAAAA

        

        1111111111111

        

        RG:Z:rg1

        bar:record:2

        

        141

        

        chr2

        

        30

        

        0

        

        *

        

        *

        

        0

        

        0

        

        CCCCCCCCCCCCC

        

        2222222222222

        

        RG:Z:rg2

        bar:record:3

        

        141

        

        chr3

        

        20

        

        0

        

        *

        

        *

        

        0

        

        0

        

        CCCCCCCCCCCCC

        

        2222222222222

        

        RG:Z:rg1

        bar:record:9

        

        141

        

        chr4

        

        60

        

        0

        

        *

        

        *

        

        0

        

        0

        

        CCCCCCCCCCCCC

        

        2222222222222

        

        RG:Z:rg1

        bar:record:1

        

        141

        

        chr1

        

        20

        

        0

        

        *

        

        *

        

        0

        

        0

        

        CCCCCCCCCCCCC

        

        2222222222222

        

        RG:Z:rg1

        bar:record:7

        

        77

        

        chr1

        

        20

        

        0

        

        *

        

        *

        

        0

        

        0

        

        AAAAAAAAAAAAA

        

        1111111111111

        

        RG:Z:rg2

        bar:record:8

        

        77

        

        chr1

        

        30

        

        0

        

        *

        

        *

        

        0

        

        0

        

        AAAAAAAAAAAAA

        

        1111111111111

        

        RG:Z:rg2

        bar:record:4

        

        141

        

        chr1

        

        40

        

        0

        

        *

        

        *

        

        0

        

        0

        

        CCCCCCCCCCCCC

        

        2222222222222

        

        RG:Z:rg1

        bar:record:8

        

        141

        

        chr3

        

        20

        

        0

        

        *

        

        *

        

        0

        

        0

        

        CCCCCCCCCCCCC

        

        2222222222222

        

        RG:Z:rg1

  *   I use "Select" in "Filter and Sort"  to sort my sam file.But I got
    "no peek" under "Matching pattern: ^@" ,while I got the same sam
    file under "NOT Matching pattern: ^@" .No other error message
    produce.I useps aux|grep weiyan to see the commands run in background :

        root      4021  0.0  0.0 88092  3348 ?        Ss 11:07   0:00
        sshd: weiyan [priv]
        weiyan    4023  0.0  0.0  88092 1756 ?        S 11:07   0:00
        sshd: weiyan@pts/0
        weiyan    4024  0.0  0.0  11052 1688 pts/0    Ss+  11:07   0:00
        -bash
        root      5248  0.0  0.0 88092  3340 ?        Ss 11:14   0:00
        sshd: weiyan [priv]
        weiyan    5250  0.0  0.0  88232 1768 ?        S 11:14   0:00
        sshd: weiyan@pts/1
        weiyan    5251  0.0  0.0  11052 1688 pts/1    Ss+  11:14   0:00
        -bash
        root      5282  0.0  0.0 88092  3348 ?        Ss 11:14   0:00
        sshd: weiyan [priv]
        weiyan    5284  0.0  0.0  88092 1756 ?        S 11:14   0:00
        sshd: weiyan@pts/2
        weiyan    5285  0.0  0.0  11052 1692 pts/2    Ss   11:14   0:00
        -bash
        root      5357  0.0  0.0 43892  1256 pts/2    S 11:17   0:00 su
        weiyan
        weiyan    5358  0.0  0.0  11048 1692 pts/2    S    11:17   0:00 bash
        weiyan    5559  6.9  0.8 650404 152076 ?       Sl   11:18   1:19
        python ./scripts/paster.py serve universe_wsgi.ini --daemon
        root      5683  0.0  0.0 88984  3348 ?        Ss 11:30   0:00
        sshd: weiyan [priv]
        weiyan    5685  0.0  0.0  88984 1760 ?        S 11:30   0:00
        sshd: weiyan@pts/3
        weiyan    5686  0.0  0.0  11052 1692 pts/3    Ss+  11:30   0:00
        -bash
        weiyan    5819  0.3  0.0 8688  1120 ? S    11:36   0:00 /bin/sh
        /software/009088d5e76f/galaxy-dist/set_metadata.sh
        ./database/files
        
/software/009088d5e76f/galaxy-dist/database/job_working_directory/000/280
        . /software/009088d5e76f/galaxy-dist/universe_wsgi.ini
        /software/009088d5e76f/galaxy-dist/database/tmp/tmpX6UZ_g
        
/software/009088d5e76f/galaxy-dist/database/job_working_directory/000/280/galaxy.json
        
/software/009088d5e76f/galaxy-dist/database/job_working_directory/000/280/metadata_in_HistoryDatasetAssociation_740_BwkeHD,/software/009088d5e76f/galaxy-dist/database/job_working_directory/000/280/metadata_kwds_HistoryDatasetAssociation_740_I_2FUY,/software/009088d5e76f/galaxy-dist/database/job_working_directory/000/280/metadata_out_HistoryDatasetAssociation_740_kJiXq5,/software/009088d5e76f/galaxy-dist/database/job_working_directory/000/280/metadata_results_HistoryDatasetAssociation_740_M58ii4,,/software/009088d5e76f/galaxy-dist/database/job_working_directory/000/280/metadata_override_HistoryDatasetAssociation_740_p2WIO0
        weiyan    5821 79.3  0.3 177984 55452 ?        R 11:36   0:02
        python ./scripts/set_metadata.py ./database/files
        
/software/009088d5e76f/galaxy-dist/database/job_working_directory/000/280
        . /software/009088d5e76f/galaxy-dist/universe_wsgi.ini
        /software/009088d5e76f/galaxy-dist/database/tmp/tmpX6UZ_g
        
/software/009088d5e76f/galaxy-dist/database/job_working_directory/000/280/galaxy.json
        
/software/009088d5e76f/galaxy-dist/database/job_working_directory/000/280/metadata_in_HistoryDatasetAssociation_740_BwkeHD,/software/009088d5e76f/galaxy-dist/database/job_working_directory/000/280/metadata_kwds_HistoryDatasetAssociation_740_I_2FUY,/software/009088d5e76f/galaxy-dist/database/job_working_directory/000/280/metadata_out_HistoryDatasetAssociation_740_kJiXq5,/software/009088d5e76f/galaxy-dist/database/job_working_directory/000/280/metadata_results_HistoryDatasetAssociation_740_M58ii4,,/software/009088d5e76f/galaxy-dist/database/job_working_directory/000/280/metadata_override_HistoryDatasetAssociation_740_p2WIO0
        weiyan    5828  0.0  0.0 10480   924 pts/2    R+ 11:36   0:00 ps aux
        weiyan    5829  0.0  0.0 6056   756 pts/2    S+ 11:36   0:00
        grep --color weiyan

      I see nothing in
    /software/009088d5e76f/galaxy-dist/database/job_working_directory/000/:

        $ ll
        /software/009088d5e76f/galaxy-dist/database/job_working_directory/000/
            total 0

  *
    Actually,I can got the correct results in Galaxy main by running the
    above steps.

I don't know what is wrong with my local Gaalxy.Thank you.
------------------------------------------------------------------------
cngbgalaxy
*From:* Adam Brenner <mailto:aebre...@uci.edu>
*Date:* 2013-09-12 10:47
*To:* cngbgal...@gmail.com <mailto:cngbgal...@gmail.com>
*CC:* joachim.jacob <mailto:joachim.ja...@vib.be>;
galaxy-dev@lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu>;
galaxy-dev <mailto:galaxy-...@bx.psu.edu>
*Subject:* Re: [galaxy-dev] Stable Galaxy for local install
 > What I want to do in a hurry is to fix the problem of "Select" in "Filter
 > and Sort" .It is a step very important for me to Sort SAM file for
 > Cufflinks.Thank you very much for all of your help.
Per my last email:.....
$ hg clone https://bitbucket.org/galaxy/galaxy-dist/
$ cd galaxy-dist
$ hg update stable
If you are running into issues, can you be more specific...provide
error message? Steps on how to reproduce your issue?
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu
On Wed, Sep 11, 2013 at 6:58 PM, cngbgal...@gmail.com
<cngbgal...@gmail.com> wrote:
 > Hi all,
 > What I want to do in a hurry is to fix the problem of "Select" in "Filter
 > and Sort" .It is a step very important for me to Sort SAM file for
 > Cufflinks.Thank you very much for all of your help.
 >
 > ________________________________
 > cngbgalaxy
 >
 > From: Adam Brenner
 > Date: 2013-09-12 00:41
 > To: cngbgalaxy
 > CC: joachim.jacob; galaxy-dev@lists.bx.psu.edu; galaxy-...@bx.psu.edu
 > Subject: Re: [galaxy-dev] Stable Galaxy for local install
 > Galaxy development occurs in two repositories, galaxy-central and
 > galaxy-dist. Changes are stabilized in galaxy-central and then pushed
 > to galaxy-dist roughly once a month.[1]
 >
 > So....
 >
 > $ hg clone https://bitbucket.org/galaxy/galaxy-dist/
 > $ cd galaxy-dist
 > $ hg update stable
 >
 > [1]: http://wiki.galaxyproject.org/Admin/Get%20Galaxy
 >
 > --
 > Adam Brenner
 > Computer Science, Undergraduate Student
 > Donald Bren School of Information and Computer Sciences
 >
 > Research Computing Support
 > Office of Information Technology
 > http://www.oit.uci.edu/rcs/
 >
 > University of California, Irvine
 > www.ics.uci.edu/~aebrenne/
 > aebre...@uci.edu
 >
 >
 > On Wed, Sep 11, 2013 at 8:42 AM, cngbgalaxy <cngbgal...@gmail.com> wrote:
 >> Hi Joachim,
 >> Thank you very much for your help.
 >> Actually I find some problems about such versions of Galaxy in
 >> https://bitbucket.org/galaxy/galaxy-dist/downloads .
 >> We can not view the data in history by clicking the eyes icon on the
 >> c42567f43aa7 version.The "Select" in "Filter and Sort" fail to work
on the
 >> 1ae95b3aa98d (release_2013.08.12 ) version and the 524f246ca853
 >> (release_2013.06.03 ),though I don't know whether it is a bug or not.
 >> As a result,I feel confused about which version of Galaxy to install and
 >> avoid the above problems.
 >>
 >> ________________________________
 >> cngbgalaxy
 >>
 >> From: Joachim Jacob | VIB |
 >> Date: 2013-09-11 22:38
 >> To: test galaxy
 >> CC: galaxy-dev; galaxy-dev
 >> Subject: Re: [galaxy-dev] Stable Galaxy for local install
 >> The latest code from the 'stable' branch of Galaxy is preferred. See the
 >> news brief accompanying the update (release_2013.08.12) on
 >> http://wiki.galaxyproject.org/DevNewsBriefs/2013_08_12
 >>
 >> You need mercurial (http://mercurial.selenic.com/) for installing
 >> Galaxy. Report bugs at https://trello.com/b/75c1kASa/galaxy-development
 >>
 >> Cheers
 >> Joachim
 >>
 >> Joachim Jacob
 >> Contact details: http://www.bits.vib.be/index.php/about/80-team
 >>
 >>
 >> On 09/11/2013 03:55 AM, test galaxy wrote:
 >>> Hi everyone,
 >>> I want to install my local Galaxy with less bugs,and I don't know
 >>> which version is more stable and work well.Could anyone give same
 >>> advise?Thank you very much.
 >>>
 >>>
 >>> ___________________________________________________________
 >>> Please keep all replies on the list by using "reply all"
 >>> in your mail client.  To manage your subscriptions to this
 >>> and other Galaxy lists, please use the interface at:
 >>>    http://lists.bx.psu.edu/
 >>>
 >>> To search Galaxy mailing lists use the unified search at:
 >>> http://galaxyproject.org/search/mailinglists/
 >>
 >>
 >> ___________________________________________________________
 >> Please keep all replies on the list by using "reply all"
 >> in your mail client.  To manage your subscriptions to this
 >> and other Galaxy lists, please use the interface at:
 >>   http://lists.bx.psu.edu/
 >>
 >> To search Galaxy mailing lists use the unified search at:
 >> http://galaxyproject.org/search/mailinglists/


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