[galaxy-dev] metadata in parallelization

Hello, I am writing some code to enable parallelization for some tool wrappers. First, I did it for simple bwa wrapper, but now I am modifying toolshed.g2.bx.psu.edu/repos/devteam/bwa/c71dd035971e/bwa/bwa-mem.xml to check if the code would work with this wrapper. So, I wrote some code that I

[galaxy-dev] join bam results in one file

hand, is this related with the last email of John Chilton and the 15.03 release? Best Regards -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain

Re: [galaxy-dev] problems splitting

justify future investment in maintaining it. Sorry about not following up on this - I think I might have assumed you would take care of it. Unfortunately I won't be able to test the obvious fix until at least a week later... Peter -- Roberto Alonso Functional Genomics Unit Bioinformatics

Re: [galaxy-dev] problems splitting

, Regards On 25 February 2015 at 11:13, Roberto Alonso CIPF ralo...@cipf.es wrote: Hello, I just changed for the CDATA format, but the problem still remains. When I split by 2, there is no problem, but when I go for 3, it happens the problem commented before. Here it is the link to the sam

Re: [galaxy-dev] problems splitting

On 24 February 2015 at 17:49, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Feb 24, 2015 at 4:43 PM, Roberto Alonso CIPF ralo...@cipf.es wrote: Hello again, first of all thanks for your help, it is being very useful. What I have done up to now is to copy this method to the class

Re: [galaxy-dev] problems splitting

everything is fine with this line. The other problem still remains Regards, sorry for the confusion On 25 February 2015 at 11:40, Roberto Alonso CIPF ralo...@cipf.es wrote: Hello again, this is something that I consider important, when I see the log I see this output: galaxy.jobs.runners.tasks DEBUG

[galaxy-dev] question about splitting bams

, but this would be inside the Bam class, under *binary.py* file. Could you please guide me before I mess things up? Thanks so much -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico

Re: [galaxy-dev] question about splitting bams

should use both files in order to create the bam sub-files, but this would be inside the Bam class, under *binary.py* file. Could you please guide me before I mess things up? Thanks so much -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe

Re: [galaxy-dev] question about splitting bams

://dev.list.galaxyproject.org/Parallelism-using-metadata-td4666763.html . -John On Thu, Apr 23, 2015 at 11:55 AM, Roberto Alonso CIPF ralo...@cipf.es wrote: Hello, I ma trying ti write some code in order to give the possibility of parallelize some tasks. Now, I was with the problem of splitting

Re: [galaxy-dev] PR 149

splitting pull request - is merging useful on its own without the other piece you are working on. -John On Wed, Apr 29, 2015 at 11:04 AM, Roberto Alonso CIPF ralo...@cipf.es wrote: Hello, I created a PR https://github.com/galaxyproject/galaxy/pull/149 dome days ago, but I don't

[galaxy-dev] splitting bams bai

, if you find that I am doing something wrong, or you have a better idea of implementing this, please don't hesitate to contact me. Best regards -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic

[galaxy-dev] PR 149

if it is not a convenient PR. Thanks so much, Best regards -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain Tel: +34 963289680 Ext. 1021 Fax: +34 963289574

[galaxy-dev] bam split and gatk calling

This solution does not convince me too much because it is a bit intrusive in the tool definition and also because you have to trust that the *region.bed* file exists. Do you have any opinion, suggestion...? Thanks a lot! Best regards -- Roberto Alonso Functional Genomics Unit Bioinformatics

Re: [galaxy-dev] bam split and gatk calling

you have any opinion, suggestion...? Thanks a lot! Best regards -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C./Eduardo Primo Yúfera (Científic), nº 3 (junto Oceanografico) 46012 Valencia, Spain Tel

Re: [galaxy-dev] bam split and gatk calling

files, the only way to parallelize their execution is through smaller bams Regards On 6 May 2015 at 15:00, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, May 6, 2015 at 11:33 AM, Roberto Alonso CIPF ralo...@cipf.es wrote: Hello, I agree, what you say fits perfectly for GATK, but as I

[galaxy-dev] error executing test

than it tries to migrate the database each time I try a test case and it takes too long. I have seen that you can use --db postgres but it doesn't work, I think this option should be user with --dockerize (that is not my case). would you have any idea of what is going on? Best regards -- Roberto

[galaxy-dev] metadata in parallelization

it doesn't execute this. I see that Galaxy have to do something with metada attributes, but what is t trying to do? is there any way to solve this? Thank you very much Regards, -- Roberto Alonso Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF) C