[galaxy-dev] error reading tool from path (epigraph.xml, epigraph_test.xml, access_libraries.xml)

2011-07-22 Thread Leon Mei
= command.get(interpreter, None) AttributeError: 'NoneType' object has no attribute 'get' ... -- Hailiang (Leon) Mei Netherlands Bioinformatics Center (http://www.nbic.nl/) Skype: leon_meiMobile: +31 6 41709231 ___ Please keep all replies

Re: [galaxy-dev] DB schema upgrade problem (79 - 85)

2011-12-05 Thread Leon Mei
... Migration script to add 'info' column to the task table. done == Thanks, Leon On Mon, Dec 5, 2011 at 9:11 PM, Nate Coraor n...@bx.psu.edu wrote: On Dec 5, 2011, at 3:02 PM, Leon Mei wrote: Dear all, Today I upgraded our NBIC server from an older release (fetched on July 5th, 2011) to the latest

[galaxy-dev] error on viewing workflow details via API

2012-01-06 Thread Leon Mei
is unsubscriptable my_IP - - [06/Jan/2012:17:46:53 +0200] GET /galaxy/api/workflows/e037fdb493429c2a?key=my_key HTTP/1.1 500 - - Python-urllib/2.6 */ Any suggestion on how to solve this problem? Thanks, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - https://wiki.nbic.nl

Re: [galaxy-dev] error on viewing workflow details via API

2012-01-09 Thread Leon Mei
? Is there perhaps a tool with no inputs in use? Thanks! -Dannon On Jan 6, 2012, at 11:59 AM, Leon Mei wrote: Hi, I received an error when I was trying to view the details of existing workflows through API. I can see 4 workflows owned by myself successfully. But viewing the details of any

[galaxy-dev] how to set FTP quota?

2012-01-16 Thread Leon Mei
, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - https://wiki.nbic.nl/index.php/Next_Generation_Sequencing Skype: leon_meiMobile: +31 6 41709231 ___ Please keep all replies on the list by using

[galaxy-dev] delete data library via API

2012-04-12 Thread Leon Mei
Hi guys, Is that possible to delete datasets in a shared data library via API? Of course when the modify permission is granted. We see delete.py in the API script folder but can't figure out how to get it work. Thanks! Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist

Re: [galaxy-dev] delete data library via API

2012-04-19 Thread Leon Mei
Dear all, Haven't heard anything back yet. So give it another try. Anyone knows if deleting dataset is supported by API? Or it will be a to-be-added feature? Thanks for any hint! Cheers, Leon On Thu, Apr 12, 2012 at 10:32 PM, Leon Mei hailiang@nbic.nl wrote: Hi guys, Is that possible

[galaxy-dev] Migrate Galaxy database from MySQL to Postgres

2012-09-04 Thread Leon Mei
experience on this. Thanks a lot, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nl Skype: leon_meiMobile: +31 6 41709231 ___ Please keep all replies on the list by using reply all

Re: [galaxy-dev] Migrate Galaxy database from MySQL to Postgres

2012-09-11 Thread Leon Mei
. Cheers, Leon On Tue, Sep 4, 2012 at 10:54 PM, Leon Mei hailiang@nbic.nl wrote: Dear list members, Did anyone migrate the Galaxy database from MySQL to Postgres lately? Any verified script available? Simple solution by adding a postgres flag in mysqldump (http://dev.list.galaxyproject.org

[galaxy-dev] missing new job lock function

2013-05-21 Thread Leon Mei
a Galaxy update, is there any other way to lock the job queue in Galaxy? Thanks, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nlhttps://wiki.nbic.nl/index.php/Next_Generation_Sequencing Skype: leon_meiMobile: +31 6 41709231

[galaxy-dev] Startup error, Galaxy DB got corrupted?

2013-06-17 Thread Leon Mei
) is not present in table workflow_step. == It seems our postgres DB got corrupted? Any suggestion on a fix? Thanks a lot! Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nlhttps://wiki.nbic.nl/index.php/Next_Generation_Sequencing Skype: leon_mei

Re: [galaxy-dev] Startup error, Galaxy DB got corrupted?

2013-06-19 Thread Leon Mei
explanations? How exactly did you perform your database backup and attempted recreation? -Dannon On Mon, Jun 17, 2013 at 5:12 PM, Leon Mei hailiang@nbic.nl wrote: Dear list, Yesterday, I noticed that the user quota setting on our Galaxy had a problem - the list of user email address

[galaxy-dev] support pbkdf2 in proftpd 1.3.5rc3

2013-07-26 Thread Leon Mei
]: checking password using SQLAuthType 'pbkdf2' 2013-07-26 13:15:06,993 mod_sql/4.3[31761]: 'pbkdf2' SQLAuthType handler reports failure What are we missing? Thanks! Rob and Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nlhttps://wiki.nbic.nl

Re: [galaxy-dev] support pbkdf2 in proftpd 1.3.5rc3

2013-08-09 Thread Leon Mei
mod_sql/4.3[32384]: cmd_auth The old user account generated before our code update still works. I wonder how it is configured at the Galaxy main server? Thanks, Leon On Thu, Aug 8, 2013 at 8:45 PM, Nate Coraor n...@bx.psu.edu wrote: On Jul 26, 2013, at 3:51 PM, Leon Mei wrote: Dear galaxy

Re: [galaxy-dev] support pbkdf2 in proftpd 1.3.5rc3

2013-08-09 Thread Leon Mei
is currently configured. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Aug 9, 2013 at 10:01 AM, Nate Coraor n...@bx.psu.edu wrote: On Aug 9, 2013, at 2:38 AM, Leon Mei wrote: Hi Nate, Thanks for the suggestion! Unfortunately, it still failed :( I got

Re: [galaxy-dev] Galaxy Release Cycle Length

2013-08-22 Thread Leon Mei
are interested in a discussion. Thanks, Dave C -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nlhttps://wiki.nbic.nl/index.php/Next_Generation_Sequencing Skype: leon_meiMobile: +31 6 41709231

[galaxy-dev] Problem with installing MAF cached dataset

2013-09-11 Thread Leon Mei
== Any hint on which step is wrong or missing is highly appreciate! Thanks, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nl Skype: leon_meiMobile: +31 6 41709231 ___ Please

Re: [galaxy-dev] Problem with installing MAF cached dataset

2013-09-11 Thread Leon Mei
that although you are only indexing (for extraction) for the specified listed species, the alignments will contain all of the species present in the original file (you list 46way multiZ as the source). Thanks for using Galaxy, Dan On Sep 10, 2013, at 6:44 PM, Leon Mei wrote: Dear

Re: [galaxy-dev] Problem with installing MAF cached dataset

2013-09-12 Thread Leon Mei
the tools included with Galaxy, or alternatively the maf_thread_for_species.py script in bx-python. Thanks for using Galaxy, Dan -- Hailiang (Leon) Mei Netherlands Bioinformatics Center BioAssist NGS Taskforce - http://ngs.nbic.nl Skype: leon_meiMobile: +31 6 41709231