Re: [galaxy-dev] Fwd: How to Clean up Old Data
Hello, Regards your comment about keeping history but deleting data, I suggest you convert your history into a Workflow. You could then delete the history and therefore all files attached to it but keep a copy of the protocol for future use. Hope it helps Best Jean-François Also is there a way a user can keep her history around as a record of what was done and be able to rerun it later, but still delete the actual data? I don't think that is possible at the moment. Cheers, Bjoern -- # Jean-François Taly Bioinformatician Bioinformatics Core Facility http://biocore.crg.cat CRG - Centre de Regulació Genòmica (Room 439) Parc de Recerca Biomèdica de Barcelona (PRBB) Doctor Aiguader, 88 08003 Barcelona Spain email: jean-francois.t...@crg.eu phone: +34 93 316 0202 fax: +34 93 316 0099 # ___ 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/
Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails
Dear all, I am having the same problem as Linda with a fresh installation of version 20130603. In the thread of her mail Dannon Baker said : That said, this doesn't resolve the mysql index issues, which I'm currently working on. I hope to have a fix for them available soon, though. I would like to know if what is the status of this thread. Should I use the solution provided in Linda's mail (CREATE INDEX ix_history_slug ON history (slug(1000));) Thx a lot for your help Best Jean-François On 06/05/2013 05:12 PM, Linda Cham wrote: Hi. I am new to the Galaxy forum and I am trying to setup a new local Galaxy instance with MySQL on RH6.2 x86_64. On a newly installed OS node, using the hg clone command (hg clone _https://bitbucket.org/galaxy/galaxy-dist#stable_ https://bitbucket.org/galaxy/galaxy-dist) which gets the current Galaxy 20130603 image, I am getting the following errors when running run.sh: File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173, in execute self.errorhandler(self, exc, value) File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line 36, in defaulterrorhandler raise errorclass, errorvalue OperationalError: (OperationalError) (1170, BLOB/TEXT column 'slug' used in key specification without a key length) 'CREATE INDEX ix_history_slug ON history (slug)' () Reading the forum, someone stated it can be bypass by running the CREATE INDEX. mysql CREATE INDEX ix_history_slug ON history (slug(1000)); Query OK, 0 rows affected (0.09 sec) Records: 0 Duplicates: 0 Warnings: 0 -- # Jean-François Taly Bioinformatician Bioinformatics Core Facility http://biocore.crg.cat CRG - Centre de Regulació Genòmica (Room 439) Parc de Recerca Biomèdica de Barcelona (PRBB) Doctor Aiguader, 88 08003 Barcelona Spain email: jean-francois.t...@crg.eu phone: +34 93 316 0202 fax: +34 93 316 0099 # ___ 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/
Re: [galaxy-dev] Installation of 20130603 Galaxy image with MySQL fails
Thanks Dannon, I indeed managed to have the galaxy-central version installed. I already see some problems but I will open another thread if necessary. Regards the DB engine, this new Galaxy I am deploying now is only a toy server I want to use in the Galaxy meeting in Oslo. I would like to have the same configuration as the other server we already have which using MySQL. Thx a lot for your help JF On 06/21/2013 11:26 AM, Dannon Baker wrote: Hi Jean-François, The index issues preventing a new instance from starting are resolved in the stable branch of galaxy-central; if you pull updates from that branch you should be able to start a new instance. While the instance will start and run, there are other peculiarities I still need to resolve and I'd really recommend using postgres for a new instance at this time if you're at all able to do so. -Dannon On Fri, Jun 21, 2013 at 5:07 AM, jean-François Taly jean-francois.t...@crg.eu mailto:jean-francois.t...@crg.eu wrote: Dear all, I am having the same problem as Linda with a fresh installation of version 20130603. In the thread of her mail Dannon Baker said : That said, this doesn't resolve the mysql index issues, which I'm currently working on. I hope to have a fix for them available soon, though. I would like to know if what is the status of this thread. Should I use the solution provided in Linda's mail (CREATE INDEX ix_history_slug ON history (slug(1000));) Thx a lot for your help Best Jean-François On 06/05/2013 05:12 PM, Linda Cham wrote: Hi. I am new to the Galaxy forum and I am trying to setup a new local Galaxy instance with MySQL on RH6.2 x86_64. On a newly installed OS node, using the hg clone command (hg clone _https://bitbucket.org/galaxy/galaxy-dist#stable_ https://bitbucket.org/galaxy/galaxy-dist) which gets the current Galaxy 20130603 image, I am getting the following errors when running run.sh: File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py, line 173, in execute self.errorhandler(self, exc, value) File build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py, line 36, in defaulterrorhandler raise errorclass, errorvalue OperationalError: (OperationalError) (1170, BLOB/TEXT column 'slug' used in key specification without a key length) 'CREATE INDEX ix_history_slug ON history (slug)' () Reading the forum, someone stated it can be bypass by running the CREATE INDEX. mysql CREATE INDEX ix_history_slug ON history (slug(1000)); Query OK, 0 rows affected (0.09 sec) Records: 0 Duplicates: 0 Warnings: 0 -- # Jean-François Taly Bioinformatician Bioinformatics Core Facility http://biocore.crg.cat CRG - Centre de Regulació Genòmica (Room 439) Parc de Recerca Biomèdica de Barcelona (PRBB) Doctor Aiguader, 88 08003 Barcelona Spain email:jean-francois.t...@crg.eu mailto:jean-francois.t...@crg.eu phone:+34 93 316 0202 tel:%2B34%2093%20316%200202 fax:+34 93 316 0099 tel:%2B34%2093%20316%200099 # ___ 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/ -- # Jean-François Taly Bioinformatician Bioinformatics Core Facility http://biocore.crg.cat CRG - Centre de Regulació Genòmica (Room 439) Parc de Recerca Biomèdica de Barcelona (PRBB) Doctor Aiguader, 88 08003 Barcelona Spain email:jean-francois.t...@crg.eu phone: +34 93 316 0202 fax: +34 93 316 0099 # ___ 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-dev] drmaa and JSV
',
'h_rt' = '6:00:00'
},
'shell' = 'n',
'pe_min' = '2',
'USER' = 'www-bi',
'binding_socket' = '0',
'e' = {
'/scratch/nfs/galaxy.crg.es/job_working_directory/000/195/195.drmerr' =
undef
},
'GROUP' = 'www-bi',
'binding_core' = '0',
'pe_max' = '2',
'CMDARGS' = '0',
'q_hard' = {
'www-el6' = undef
},
'pe_name' = 'smp',
'CLIENT' = 'drmaa',
'b' = 'y',
'R' = 'y',
'VERSION' = '1.0',
'CONTEXT' = 'client',
'o' = {
'/scratch/nfs/galaxy.crg.es/job_working_directory/000/195/195.drmout' =
undef
}
};
There's a core binding strategy.
The problem is that second job submission is inheriting submission
parameters from the first job, and, as the JSV script does not allow to
specify
core binding strategy by the user, the job is rejected.
If you wait some time (600 seconds), the new submit works again...
We are wondering if anyone can help us to understand why the submission
parameters been inherit by each job?
Maybe the DRMAA session is not properly closed? or the environment not
cleaned?
Thank you for your help
Best
Jean-François
$hg summary
parent: 8795:9fd7fe0c5712
merge from stable
branch: default
commit: 1 modified, 59 unknown
update: (current)
--
#
Jean-François Taly
Bioinformatician
Bioinformatics Core Facility
http://biocore.crg.cat
CRG - Centre de Regulació Genòmica (Room 439)
Parc de Recerca Biomèdica de Barcelona (PRBB)
Doctor Aiguader, 88
08003 Barcelona
Spain
email: jean-francois.t...@crg.eu
phone: +34 93 316 0202
fax: +34 93 316 0099
#
___
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:
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To search Galaxy mailing lists use the unified search at:
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[galaxy-dev] list of multithreaded tools
Dear All, Could you please tell where or how I could get the list of multi-threaded tools and the amount of threads they open by default? Thanks a lot Jean-François PS: I have collected the following list by hands: #Tool_idNum_thread gatk_count_covariates4 gatk_realigner_target_creator4 gatk_unified_genotyper4 gatk_variant_eval4 gatk_variant_recalibrator4 gatk_variant_select4 bfast_wrapper4 bowtie24 bowtie_color_wrapper4 bowtie_wrapper4 bwa_color_wrapper4 bwa_wrapper4 cuffdiff4 cufflinks4 cuffmerge4 tophat24 tophat_color4 tophat4 -- # Dr Jean-François Taly Bioinformatician Bioinformatics Core Facility http://biocore.crg.cat CRG - Centre de Regulació Genòmica (Room 439) Parc de Recerca Biomèdica de Barcelona (PRBB) Doctor Aiguader, 88 08003 Barcelona Spain email: jean-francois.t...@crg.eu phone: +34 93 316 0202 fax: +34 93 316 0099 # ___ 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/
