Hi Adam Brenner,
This is my running steps.
@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
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
 
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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>>
>>
>> ___________________________________________________________
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