Stable Galaxy for local install
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.
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/
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/
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.
___________________________________________________________ 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/
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.
___________________________________________________________ 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/
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.
___________________________________________________________ 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/
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.
___________________________________________________________ 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/
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, cngbgalaxy@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:aebrenne@uci.edu> *Date:* 2013-09-12 10:47 *To:* cngbgalaxy@gmail.com <mailto:cngbgalaxy@gmail.com> *CC:* joachim.jacob <mailto:joachim.jacob@vib.be>; galaxy-dev@lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu>; galaxy-dev <mailto:galaxy-dev@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/ 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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___________________________________________________________ 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/
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participants (6)
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Adam Brenner -
cngbgalaxy -
cngbgalaxy＠gmail.com
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Hans-Rudolf Hotz -
Joachim Jacob | VIB | -
test galaxy