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:477chr110**00AAAAAAAAAAAAA1111111111111RG:Z:rg1 bar:record:677chr110**00AAAAAAAAAAAAA1111111111111RG:Z:rg2 bar:record:177chr1100**00AAAAAAAAAAAAA1111111111111RG:Z:rg1 bar:record:377chr1100**00AAAAAAAAAAAAA1111111111111RG:Z:rg2 bar:record:5141chr3400**00CCCCCCCCCCCCC2222222222222RG:Z:rg1 bar:record:977chr4100**00AAAAAAAAAAAAA1111111111111RG:Z:rg1 bar:record:7141chr4200**00CCCCCCCCCCCCC2222222222222RG:Z:rg1 bar:record:577chr1400**00AAAAAAAAAAAAA1111111111111RG:Z:rg2 bar:record:6141chr1500**00CCCCCCCCCCCCC2222222222222RG:Z:rg2 bar:record:277chr2100**00AAAAAAAAAAAAA1111111111111RG:Z:rg1 bar:record:2141chr2300**00CCCCCCCCCCCCC2222222222222RG:Z:rg2 bar:record:3141chr3200**00CCCCCCCCCCCCC2222222222222RG:Z:rg1 bar:record:9141chr4600**00CCCCCCCCCCCCC2222222222222RG:Z:rg1 bar:record:1141chr1200**00CCCCCCCCCCCCC2222222222222RG:Z:rg1 bar:record:777chr1200**00AAAAAAAAAAAAA1111111111111RG:Z:rg2 bar:record:877chr1300**00AAAAAAAAAAAAA1111111111111RG:Z:rg2 bar:record:4141chr1400**00CCCCCCCCCCCCC2222222222222RG:Z:rg1 bar:record:8141chr3200**00CCCCCCCCCCCCC2222222222222RG: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 use ps 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 Date: 2013-09-12 10:47 To: cngbgalaxy@gmail.com CC: joachim.jacob; galaxy-dev@lists.bx.psu.edu; galaxy-dev 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/ aebrenne@uci.edu On Wed, Sep 11, 2013 at 6:58 PM, cngbgalaxy@gmail.com <cngbgalaxy@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-dev@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/ aebrenne@uci.edu
On Wed, Sep 11, 2013 at 8:42 AM, cngbgalaxy <cngbgalaxy@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.
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