Hi John,
I'm using your bitbucket fork.I still didn't finish all the needed job but
meanwhile it works great.
The two tools you add: multi-upload & split - works great too - and are all
what I needed.
(I had only one patch which I had to add somewhere - I'm still trying to
understand the galaxy code there.)

The difference between tool which accepts input file and a tool which
accepts multi-input-file is nice.
Currently, I'm gone use this. I hope the official release will have similar
feature in the future.

Thanks,
Hagai


On Wed, Feb 13, 2013 at 9:56 AM, Hagai Cohen <haga...@gmail.com> wrote:

>
> John, that's seems great.
> I will read this stuff and see if  I can use it (The bed format isn't that
> essential, bowtie can bam instead).
>
> If it wont work I will try the other solution which doesn't need to change
> the galaxy own code (Creating hundreds of workflow run, linking to their
> outputs and running last workflow with the merging tool - this solution
> also distribute in a better way).
>
> Because galaxy is used a lot on sequencers output, I think someday it
> should support this kind of jobs internally.
> When I will have a running solution, I will publish what solution I have
> used.
>
> Its really great to know I'm not the first one to attack this problem.
> Thanks for the advices.
> Hagai
>
>
>
>
>
> On Tue, Feb 12, 2013 at 5:42 PM, Joachim Jacob |VIB| <joachim.ja...@vib.be
> > wrote:
>
>> You cannot directly couple different workflows.
>>
>> But you could indeed copy all outputs of the different workflows into one
>> history, and create a separate workflow with your tool to work on all those
>> input files.
>>
>> Cheers,
>>
>> Joachim
>>
>> Joachim Jacob
>>
>> Rijvisschestraat 120, 9052 Zwijnaarde
>> Tel: +32 9 244.66.34
>> Bioinformatics Training and Services (BITS)
>> http://www.bits.vib.be
>> @bitsatvib
>>
>> On 02/12/2013 04:31 PM, Hagai Cohen wrote:
>>
>>>
>>> Thanks for your answer.
>>> I figured that there is an option to run a workflow on multiple files,
>>> but I can't merge the outputs afterwardsl. I would like the workflow to
>>> return one final output.
>>>
>>> But you gave me another idea.
>>> Can I somehow tell one workflow to run on other workflow output?
>>> If this can be done, I can run 100 different workflows with bowtie &
>>> statistics, each working on one fastq file, than run another workflow which
>>> gets 100 xls inputs and merge them to one.
>>>
>>>
>>>
>>>
>>> On Tue, Feb 12, 2013 at 5:20 PM, Joachim Jacob |VIB| <
>>> joachim.ja...@vib.be <mailto:joachim.ja...@vib.be>> wrote:
>>>
>>>     Hi Hagai,
>>>
>>>     Actually, using a workflow, you are able to select multiple input
>>>     files, and let the workflow run separately on all input files.
>>>
>>>     I would proceed by creating a data library for all your fastq
>>>     files, which you can upload via FTP, or via a system directory.
>>>     You can use a sample of your fastq files to create the steps in a
>>>     history you want to perform, and extract a workflow out of it.
>>>     Next, copy all fastq files from a data library in a new history,
>>>     and run your workflow on the all input files.
>>>
>>>     I hope this helps you further,
>>>     Joachim
>>>
>>>
>>>     Joachim Jacob
>>>
>>>     Rijvisschestraat 120, 9052 Zwijnaarde
>>>     Tel: +32 9 244.66.34 <tel:%2B32%209%20244.66.34>
>>>
>>>     Bioinformatics Training and Services (BITS)
>>>     http://www.bits.vib.be
>>>     @bitsatvib
>>>
>>>
>>>     On 02/12/2013 04:02 PM, Hagai Cohen wrote:
>>>
>>>         Hi,
>>>         I'm looking for a preferred way of running Bowtie (or any
>>>         other tool) on multiple input files and run statistics on the
>>>         Bowtie output afterwards.
>>>
>>>         The input is a directory of files fastq1..fastq100
>>>         The bowtie output should be bed1...bed100
>>>         The statistics tool should run on bed1...bed100 and return
>>>         xls1..xls100
>>>         Then I will write a tool which will get xls1..xls100 and merge
>>>         them to one final output.
>>>
>>>         I searched for a smiliar cases, and I couldn't figure anyone
>>>         which had this problem before.
>>>         Can't use the parallelism tag, because what will be the input
>>>         for each tool? it should be a fastq file not a directory of
>>>         fastq files.
>>>         Neither I would like to run each fastq file in a different
>>>         workflow - creating a mess.
>>>
>>>         I thought only on two solutions:
>>>         1. Implement new datatypes: bed_dir & fastq_dir and implements
>>>         new tool wrappers which will get a folder instead of a file.
>>>         2. merge the input files before sending to bowtie, and use
>>>         parallelism tag to make them be splitted & merged again on
>>>         each tool.
>>>
>>>         Does anyone has any better suggestion?
>>>
>>>         Thanks,
>>>         Hagai
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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>>>
>>>
>>>
>>>
>>
>
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