Re: [galaxy-dev] [galaxy-user] why is ./tools/sr_mapping/bowtie_color_wrapper.xml not implemented by default?
Kevin, Some of the tools in Galaxy are wrappers of external tools, and Bowtie is one such example. These underlying tools must be installed in addition to the standard Galaxy distribution, and then some extra configuration and data preparation is necessary, before the Galaxy tool can be used. There is a wiki page dedicated to installing the NGS tools (http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup) which details how to set these up. Let us know if you need further information. (Note that this topic is better suited to galaxy-dev instead of galaxy- user since it's about local installations.) Regards, Kelly Galaxy Team On Aug 20, 2010, at 12:08 AM, Kevin Lam wrote:
Hi, I see that the public galaxy at usegalaxy.org has a few differences with a local installation in that some tools are not implemented as well. for e.g. ./tools/sr_mapping/bowtie_color_wrapper.xml
May I know if there's a reason for this?
Cheers Kevin _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Hi Kelly, Apologies for the mispost. I do understand the dependencies and why you cannot distribute bowtie together with galaxy. I have bowtie on my system. and I saw that Map with Bowtie for Illumina<http://node03:8080/tool_runner?tool_id=bowtie_wrapper> is implemented by default. So I do not understand why Map with Bowtie for SOLiD<http://main.g2.bx.psu.edu/tool_runner?tool_id=bowtie_color_wrapper> isn't, since it (I presume) has the same underlying dependencies? I am reading http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup and http://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial But there's no relevant instructions on how to implement bowtie-color. Am I looking in the wrong place? Thanks Kevin On Fri, Aug 20, 2010 at 1:32 PM, Kelly Vincent <kpvincent@bx.psu.edu> wrote:
Kevin,
Some of the tools in Galaxy are wrappers of external tools, and Bowtie is one such example. These underlying tools must be installed in addition to the standard Galaxy distribution, and then some extra configuration and data preparation is necessary, before the Galaxy tool can be used. There is a wiki page dedicated to installing the NGS tools ( http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup) which details how to set these up. Let us know if you need further information.
(Note that this topic is better suited to galaxy-dev instead of galaxy-user since it's about local installations.)
Regards, Kelly Galaxy Team
On Aug 20, 2010, at 12:08 AM, Kevin Lam wrote:
Hi, I see that the public galaxy at usegalaxy.org has a few differences with a local installation in that some tools are not implemented as well. for e.g. ./tools/sr_mapping/bowtie_color_wrapper.xml
May I know if there's a reason for this?
Cheers Kevin _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Hi, Bowtie for SOLiD is actually enabled as much as Bowtie for Illumina is (both are in the tool_conf.xml.sample file and both rely on the same Python file, bowtie_wrapper.py). If the tool is not loading, the most common cause is that the loc file (bowtie_indices_color.loc, which is different from the one for the Illumina version) isn't in place. If the loc file is there, then something else is wrong--check the traceback in the paster.log to see why it wouldn't load, and let us know if you have trouble fixing it. The NGSLocalSetup wiki page does address the two different loc files under the Bowtie section, though it does discuss them together because they are so similar (I also just added a column in the table showing the tool with its associated loc files to include the XML name). Regards, Kelly On Aug 20, 2010, at 4:09 AM, Kevin Lam wrote:
Hi Kelly, Apologies for the mispost. I do understand the dependencies and why you cannot distribute bowtie together with galaxy. I have bowtie on my system. and I saw that Map with Bowtie for Illumina is implemented by default. So I do not understand why Map with Bowtie for SOLiD isn't, since it (I presume) has the same underlying dependencies?
I am reading http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup and http://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial
But there's no relevant instructions on how to implement bowtie- color. Am I looking in the wrong place?
Thanks Kevin
On Fri, Aug 20, 2010 at 1:32 PM, Kelly Vincent <kpvincent@bx.psu.edu> wrote: Kevin,
Some of the tools in Galaxy are wrappers of external tools, and Bowtie is one such example. These underlying tools must be installed in addition to the standard Galaxy distribution, and then some extra configuration and data preparation is necessary, before the Galaxy tool can be used. There is a wiki page dedicated to installing the NGS tools (http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup ) which details how to set these up. Let us know if you need further information.
(Note that this topic is better suited to galaxy-dev instead of galaxy-user since it's about local installations.)
Regards, Kelly Galaxy Team
On Aug 20, 2010, at 12:08 AM, Kevin Lam wrote:
Hi, I see that the public galaxy at usegalaxy.org has a few differences with a local installation in that some tools are not implemented as well. for e.g. ./tools/sr_mapping/bowtie_color_wrapper.xml
May I know if there's a reason for this?
Cheers Kevin _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Kevin, Actually, one of my colleagues just pointed out that the loc file for SOLiD isn't in the setup.sh file. This was just an oversight and I've added it with rev 4177:d9e099daa827. Kelly On Aug 20, 2010, at 4:09 AM, Kevin Lam wrote:
Hi Kelly, Apologies for the mispost. I do understand the dependencies and why you cannot distribute bowtie together with galaxy. I have bowtie on my system. and I saw that Map with Bowtie for Illumina is implemented by default. So I do not understand why Map with Bowtie for SOLiD isn't, since it (I presume) has the same underlying dependencies?
I am reading http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup and http://bitbucket.org/galaxy/galaxy-central/wiki/AddToolTutorial
But there's no relevant instructions on how to implement bowtie- color. Am I looking in the wrong place?
Thanks Kevin
On Fri, Aug 20, 2010 at 1:32 PM, Kelly Vincent <kpvincent@bx.psu.edu> wrote: Kevin,
Some of the tools in Galaxy are wrappers of external tools, and Bowtie is one such example. These underlying tools must be installed in addition to the standard Galaxy distribution, and then some extra configuration and data preparation is necessary, before the Galaxy tool can be used. There is a wiki page dedicated to installing the NGS tools (http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup ) which details how to set these up. Let us know if you need further information.
(Note that this topic is better suited to galaxy-dev instead of galaxy-user since it's about local installations.)
Regards, Kelly Galaxy Team
On Aug 20, 2010, at 12:08 AM, Kevin Lam wrote:
Hi, I see that the public galaxy at usegalaxy.org has a few differences with a local installation in that some tools are not implemented as well. for e.g. ./tools/sr_mapping/bowtie_color_wrapper.xml
May I know if there's a reason for this?
Cheers Kevin _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
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