2:37 p.m.
Hello,
I'm very new to Galaxy, and trying to use SOAPaligner/soap2 as a test
integration case.
soap2 includes two executables, 2bwt-builder and soap. 2bwt-builder
takes a FASTA files and generates a set of 13 different index files,
which soap needs in order to do it's alignment.
I have started by just creating the tool XML configuration for
2bwt-builder. The configuration follows:
<tool id="2bwt-builder" name="2bwt-Builder">
<description>build index files for the SOAPaligner/soap2</description>
<command>2bwt-builder $input</command>
<inputs>
<param type="data" format="fasta" name="input"
label="Source file"/>
</inputs>
<outputs>
<data format="tabular" name=".amb Index File"/>
<data format="tabular" name=".ann Index File"/>
<data format="tabular" name=".bwt Index File"/>
<data format="tabular" name=".fmv Index File"/>
<data format="tabular" name=".hot Index File"/>
<data format="tabular" name=".lkt Index File"/>
<data format="tabular" name=".pac Index File"/>
<data format="tabular" name=".rev.bwt Index File"/>
<data format="tabular" name=".rev.fmv Index File"/>
<data format="tabular" name=".rev.lkt Index File"/>
<data format="tabular" name=".rev.pac Index File"/>
<data format="tabular" name=".sa Index File"/>
<data format="tabular" name=".sai Index File"/>
</outputs>
</tool>
I've used the tabular data type for the output files, which I'm not sure
is correct. When the script runs, it generates 13 output files in my
history, but they are all empty according to galaxy. When I look at
galaxy_dist/database/files/.../, the output files have been generated
correctly and are non-empty.
Where am I going wrong? Thank you in advance for any advice.
--
Branden Timm
System Administrator
Great Lakes Bioenergy Research Center
University of Wisconsin
btimm(a)glbrc.wisc.edu
3:06 p.m.
Hi Branden
Hello,
I'm very new to Galaxy, and trying to use SOAPaligner/soap2 as a test
integration case.
soap2 includes two executables, 2bwt-builder and soap. 2bwt-builder
takes a FASTA files and generates a set of 13 different index files,
which soap needs in order to do it's alignment.
I have started by just creating the tool XML configuration for
2bwt-builder. The configuration follows:
<tool id="2bwt-builder" name="2bwt-Builder">
<description>build index files for the SOAPaligner/soap2</description>
<command>2bwt-builder $input</command>
the "command line" needs all output files listed, see:
http://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial
However, in your case: Do you really want to make an extra tool for the
indexing step? Wouldn't it make more sense to have the indices pre-built
for some genomes?
Your soap galaxy tool can then re-use the indices again and again. This
is also much more space efficient, as all the user share the same index
files.
Regards, Hans
<inputs>
<param type="data" format="fasta" name="input"
label="Source file"/>
</inputs>
<outputs>
<data format="tabular" name=".amb Index File"/>
<data format="tabular" name=".ann Index File"/>
<data format="tabular" name=".bwt Index File"/>
<data format="tabular" name=".fmv Index File"/>
<data format="tabular" name=".hot Index File"/>
<data format="tabular" name=".lkt Index File"/>
<data format="tabular" name=".pac Index File"/>
<data format="tabular" name=".rev.bwt Index File"/>
<data format="tabular" name=".rev.fmv Index File"/>
<data format="tabular" name=".rev.lkt Index File"/>
<data format="tabular" name=".rev.pac Index File"/>
<data format="tabular" name=".sa Index File"/>
<data format="tabular" name=".sai Index File"/>
</outputs>
</tool>
I've used the tabular data type for the output files, which I'm not sure
is correct. When the script runs, it generates 13 output files in my
history, but they are all empty according to galaxy. When I look at
galaxy_dist/database/files/.../, the output files have been generated
correctly and are non-empty.
Where am I going wrong? Thank you in advance for any advice.
--
Branden Timm
System Administrator
Great Lakes Bioenergy Research Center
University of Wisconsin
btimm(a)glbrc.wisc.edu
_______________________________________________
galaxy-dev mailing list
galaxy-dev(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
3:35 p.m.
Hi Hans,
Thanks for the advice. I agree it does make more sense to generate
the indexes once. Would I create those indexes in the same directory as
the FASTA and follow the DataIntegration document here?
http://bitbucket.org/galaxy/galaxy-central/wiki/DataIntegration
Cheers
--
Branden Timm
btimm(a)glbrc.wisc.edu
On 8/17/2010 10:06 AM, Hans-Rudolf Hotz wrote:
Hi Branden
> Hello,
> I'm very new to Galaxy, and trying to use SOAPaligner/soap2 as a test
> integration case.
>
> soap2 includes two executables, 2bwt-builder and soap. 2bwt-builder
> takes a FASTA files and generates a set of 13 different index files,
> which soap needs in order to do it's alignment.
>
> I have started by just creating the tool XML configuration for
> 2bwt-builder. The configuration follows:
>
> <tool id="2bwt-builder" name="2bwt-Builder">
> <description>build index files for the SOAPaligner/soap2</description>
> <command>2bwt-builder $input</command>
the "command line" needs all output files listed, see:
http://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial
However, in your case: Do you really want to make an extra tool for
the indexing step? Wouldn't it make more sense to have the indices
pre-built for some genomes?
Your soap galaxy tool can then re-use the indices again and again.
This is also much more space efficient, as all the user share the same
index files.
Regards, Hans
> <inputs>
> <param type="data" format="fasta" name="input"
label="Source file"/>
> </inputs>
>
> <outputs>
> <data format="tabular" name=".amb Index File"/>
> <data format="tabular" name=".ann Index File"/>
> <data format="tabular" name=".bwt Index File"/>
> <data format="tabular" name=".fmv Index File"/>
> <data format="tabular" name=".hot Index File"/>
> <data format="tabular" name=".lkt Index File"/>
> <data format="tabular" name=".pac Index File"/>
> <data format="tabular" name=".rev.bwt Index File"/>
> <data format="tabular" name=".rev.fmv Index File"/>
> <data format="tabular" name=".rev.lkt Index File"/>
> <data format="tabular" name=".rev.pac Index File"/>
> <data format="tabular" name=".sa Index File"/>
> <data format="tabular" name=".sai Index File"/>
> </outputs>
> </tool>
>
> I've used the tabular data type for the output files, which I'm not sure
> is correct. When the script runs, it generates 13 output files in my
> history, but they are all empty according to galaxy. When I look at
> galaxy_dist/database/files/.../, the output files have been generated
> correctly and are non-empty.
>
> Where am I going wrong? Thank you in advance for any advice.
>
> --
> Branden Timm
> System Administrator
> Great Lakes Bioenergy Research Center
> University of Wisconsin
> btimm(a)glbrc.wisc.edu
> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev(a)lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
4 p.m.
Hi Branden,
If you look at some of the NGS tools (see SAM-to-BAM for instance,
because it's simple) you can see the way we have handled this, which
is to offer several pre-built indexes but also give the user the
option to use a fasta file for which there is no pre-built index,
through the use of conditionals. So there is definitely no need to
make an entirely separate tool for the indexing. Also, note that
handling files used for input/output/indexes for external tools can
sometimes be tricky, if those tools expect the files to have
particular extensions. SAM-to-BAM also handles this situation with
some temp file renaming trickery.
For the pre-built indexes, once you have them built, have a look at
the DataIntegration wiki page, but
http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup
will also be helpful to you (start with the "Setting Up the
Reference Genomes for NGS Tools" section).
Let us know if you run into any more issues.
Regards,
Kelly
Galaxy Team
On Aug 17, 2010, at 11:35 AM, Branden Timm wrote:
Hi Hans,
Thanks for the advice. I agree it does make more sense to generate
the indexes once. Would I create those indexes in the same
directory as the FASTA and follow the DataIntegration document here?
http://bitbucket.org/galaxy/galaxy-central/wiki/DataIntegration
Cheers
--
Branden Timm
btimm(a)glbrc.wisc.edu
On 8/17/2010 10:06 AM, Hans-Rudolf Hotz wrote:
> Hi Branden
>
>> Hello,
>> I'm very new to Galaxy, and trying to use SOAPaligner/soap2 as a
>> test
>> integration case.
>>
>> soap2 includes two executables, 2bwt-builder and soap. 2bwt-builder
>> takes a FASTA files and generates a set of 13 different index files,
>> which soap needs in order to do it's alignment.
>>
>> I have started by just creating the tool XML configuration for
>> 2bwt-builder. The configuration follows:
>>
>> <tool id="2bwt-builder" name="2bwt-Builder">
>> <description>build index files for the SOAPaligner/soap2</
>> description>
>> <command>2bwt-builder $input</command>
>
> the "command line" needs all output files listed, see:
> http://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial
>
>
> However, in your case: Do you really want to make an extra tool for
> the indexing step? Wouldn't it make more sense to have the indices
> pre-built for some genomes?
>
> Your soap galaxy tool can then re-use the indices again and again.
> This is also much more space efficient, as all the user share the
> same index files.
>
> Regards, Hans
>
>
>> <inputs>
>> <param type="data" format="fasta" name="input"
label="Source file"/>
>> </inputs>
>>
>> <outputs>
>> <data format="tabular" name=".amb Index File"/>
>> <data format="tabular" name=".ann Index File"/>
>> <data format="tabular" name=".bwt Index File"/>
>> <data format="tabular" name=".fmv Index File"/>
>> <data format="tabular" name=".hot Index File"/>
>> <data format="tabular" name=".lkt Index File"/>
>> <data format="tabular" name=".pac Index File"/>
>> <data format="tabular" name=".rev.bwt Index File"/>
>> <data format="tabular" name=".rev.fmv Index File"/>
>> <data format="tabular" name=".rev.lkt Index File"/>
>> <data format="tabular" name=".rev.pac Index File"/>
>> <data format="tabular" name=".sa Index File"/>
>> <data format="tabular" name=".sai Index File"/>
>> </outputs>
>> </tool>
>>
>> I've used the tabular data type for the output files, which I'm
>> not sure
>> is correct. When the script runs, it generates 13 output files in my
>> history, but they are all empty according to galaxy. When I look at
>> galaxy_dist/database/files/.../, the output files have been
>> generated
>> correctly and are non-empty.
>>
>> Where am I going wrong? Thank you in advance for any advice.
>>
>> --
>> Branden Timm
>> System Administrator
>> Great Lakes Bioenergy Research Center
>> University of Wisconsin
>> btimm(a)glbrc.wisc.edu
>> _______________________________________________
>> galaxy-dev mailing list
>> galaxy-dev(a)lists.bx.psu.edu
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________
galaxy-dev mailing list
galaxy-dev(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
4:17 p.m.
On 08/17/2010 05:35 PM, Branden Timm wrote:
Hi Hans,
Thanks for the advice. I agree it does make more sense to generate the
indexes once. Would I create those indexes in the same directory as the
FASTA and follow the DataIntegration document here?
http://bitbucket.org/galaxy/galaxy-central/wiki/DataIntegration
As you write your own tool, you can put them wherever you want (as long
as the files are accessible to your Galaxy instance, and you provide the
correct path in the command line.
Eventually, once it is working, you might want to set up a
"soap_index.loc" file, listing all your genomes (ie indices for the
individual genomes) and write a wrapper for the soap binary. As an
example you might want to look at megablast_wrapper.py.
Hans
Cheers
--
Branden Timm
btimm(a)glbrc.wisc.edu
On 8/17/2010 10:06 AM, Hans-Rudolf Hotz wrote:
> Hi Branden
>
>> Hello,
>> I'm very new to Galaxy, and trying to use SOAPaligner/soap2 as a test
>> integration case.
>>
>> soap2 includes two executables, 2bwt-builder and soap. 2bwt-builder
>> takes a FASTA files and generates a set of 13 different index files,
>> which soap needs in order to do it's alignment.
>>
>> I have started by just creating the tool XML configuration for
>> 2bwt-builder. The configuration follows:
>>
>> <tool id="2bwt-builder" name="2bwt-Builder">
>> <description>build index files for the
SOAPaligner/soap2</description>
>> <command>2bwt-builder $input</command>
>
> the "command line" needs all output files listed, see:
> http://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial
>
>
> However, in your case: Do you really want to make an extra tool for
> the indexing step? Wouldn't it make more sense to have the indices
> pre-built for some genomes?
>
> Your soap galaxy tool can then re-use the indices again and again.
> This is also much more space efficient, as all the user share the same
> index files.
>
> Regards, Hans
>
>
>> <inputs>
>> <param type="data" format="fasta" name="input"
label="Source file"/>
>> </inputs>
>>
>> <outputs>
>> <data format="tabular" name=".amb Index File"/>
>> <data format="tabular" name=".ann Index File"/>
>> <data format="tabular" name=".bwt Index File"/>
>> <data format="tabular" name=".fmv Index File"/>
>> <data format="tabular" name=".hot Index File"/>
>> <data format="tabular" name=".lkt Index File"/>
>> <data format="tabular" name=".pac Index File"/>
>> <data format="tabular" name=".rev.bwt Index File"/>
>> <data format="tabular" name=".rev.fmv Index File"/>
>> <data format="tabular" name=".rev.lkt Index File"/>
>> <data format="tabular" name=".rev.pac Index File"/>
>> <data format="tabular" name=".sa Index File"/>
>> <data format="tabular" name=".sai Index File"/>
>> </outputs>
>> </tool>
>>
>> I've used the tabular data type for the output files, which I'm not sure
>> is correct. When the script runs, it generates 13 output files in my
>> history, but they are all empty according to galaxy. When I look at
>> galaxy_dist/database/files/.../, the output files have been generated
>> correctly and are non-empty.
>>
>> Where am I going wrong? Thank you in advance for any advice.
>>
>> --
>> Branden Timm
>> System Administrator
>> Great Lakes Bioenergy Research Center
>> University of Wisconsin
>> btimm(a)glbrc.wisc.edu
>> _______________________________________________
>> galaxy-dev mailing list
>> galaxy-dev(a)lists.bx.psu.edu
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
5:21 p.m.
Just a follow up here ... if the <command> tag needs to list all output files, but
the tool itself does not specify output files on the command line, does that mean I need
to write a wrapper for my tool that accepts each output file as a command-line parameter?
Currently I've tried specifying all of the output files on the <command> line,
where each variable corresponds to a <data> line under outputs, but then
SOAPaligner/soap2 tries to read those non-existent files as FASTA files.
As a more general question, is there a way to see the exact command(s) that Galaxy is
dispatching on my behalf when I execute a tool? I checked paster.log but it wasn't
there. It seems like that would be a great debugging feature.
Branden
On Aug 17, 2010, at 10:06 AM, Hans-Rudolf Hotz wrote:
Hi Branden
> Hello,
> I'm very new to Galaxy, and trying to use SOAPaligner/soap2 as a test
> integration case.
>
> soap2 includes two executables, 2bwt-builder and soap. 2bwt-builder
> takes a FASTA files and generates a set of 13 different index files,
> which soap needs in order to do it's alignment.
>
> I have started by just creating the tool XML configuration for
> 2bwt-builder. The configuration follows:
>
> <tool id="2bwt-builder" name="2bwt-Builder">
> <description>build index files for the SOAPaligner/soap2</description>
> <command>2bwt-builder $input</command>
the "command line" needs all output files listed, see:
http://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial
However, in your case: Do you really want to make an extra tool for the indexing step?
Wouldn't it make more sense to have the indices pre-built for some genomes?
Your soap galaxy tool can then re-use the indices again and again. This is also much more
space efficient, as all the user share the same index files.
Regards, Hans
> <inputs>
> <param type="data" format="fasta" name="input"
label="Source file"/>
> </inputs>
>
> <outputs>
> <data format="tabular" name=".amb Index File"/>
> <data format="tabular" name=".ann Index File"/>
> <data format="tabular" name=".bwt Index File"/>
> <data format="tabular" name=".fmv Index File"/>
> <data format="tabular" name=".hot Index File"/>
> <data format="tabular" name=".lkt Index File"/>
> <data format="tabular" name=".pac Index File"/>
> <data format="tabular" name=".rev.bwt Index File"/>
> <data format="tabular" name=".rev.fmv Index File"/>
> <data format="tabular" name=".rev.lkt Index File"/>
> <data format="tabular" name=".rev.pac Index File"/>
> <data format="tabular" name=".sa Index File"/>
> <data format="tabular" name=".sai Index File"/>
> </outputs>
> </tool>
>
> I've used the tabular data type for the output files, which I'm not sure
> is correct. When the script runs, it generates 13 output files in my
> history, but they are all empty according to galaxy. When I look at
> galaxy_dist/database/files/.../, the output files have been generated
> correctly and are non-empty.
>
> Where am I going wrong? Thank you in advance for any advice.
>
> --
> Branden Timm
> System Administrator
> Great Lakes Bioenergy Research Center
> University of Wisconsin
> btimm(a)glbrc.wisc.edu
> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev(a)lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
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5 comments
3 participants
participants (3)
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Branden Timm -
Hans-Rudolf Hotz -
Kelly Vincent