Hello,
I am designing some test and I have a problem, it works under the Galaxy
web environment, but it doesn't work when I try to use it as a test case.
Indeed I am trying other tests and they fail as well.
My test *./run_tests.sh -framework -id parallelism_bam_filter_reads* says
the next:
Hello,
I have been working in the Galaxy parallelization module and I would like
to ask you some questions that I have about how to face one problem.
I have done one pull request about splitting bams:
https://github.com/galaxyproject/galaxy/pull/184
Regarding this, I think it is useful but it
Alonso CIPF ralo...@cipf.es
wrote:
Hello,
I have been working in the Galaxy parallelization module and I would
like to
ask you some questions that I have about how to face one problem.
I have done one pull request about splitting bams:
https://github.com/galaxyproject/galaxy/pull/184
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
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
Hello,
I created a PR https://github.com/galaxyproject/galaxy/pull/149 dome days
ago, but I don't have any feedback yet, is there any problem with it? Is it
not interesting for the current Galaxy? didn't the authors realized about
it? It would be nice to have some feedback, even if it is not a
Hello,
I am writing some code in Galaxy for splitting bams. Up to know, I am
following the ideas that Marco Albuquerque proposed in this thread
http://dev.list.galaxyproject.org/Parallelism-using-metadata-td4666763.html
.
He proposed three ways of splitting:
1) by_rname - splits the bam into
://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
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 a bam in
some parts, for this I create this simple tool
parallelism method=multi split_size=3 split_mode=number_of_parts
merge_outputs=output
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 a bam in
some parts, for this I create this simple tool
parallelism method=multi split_size=3 split_mode=number_of_parts
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
Hello,
I am playing with Galaxy splitters capabilities. After some cases that
you help me out to solve I am facing a new issue, this is maybe due to my
tool configuration file, but in any case I tell you what I've done.
What I would like to do exactly, is to split paired fastq, map them and
then
,
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
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
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
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 Sequence
def get_split_commands_sequential(is_compressed, input_name, output_name,
start_sequence, sequence_count):
Does a brain-dead
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