Hello- I'm about to embark on an effort to try and roll Illumina's CASAVA pipeline software--demultiplex.pl, GERALD.pl, run.pl and other scripts, into a local Galaxy install. I'd prefer not to reinvent the wheel, so I'd like to hear from anyone that's already done part or all of what I'm going to attempt. Any advice is greatly appreciated. Alternatively, if this is something that other developers are interested in, maybe it could be considered for a coding sprint during the breakout session at the developers' conference or during one of the BEER sessions? Thanks! Glen
Hi Glen, I am very interested in such a development. AFAIK, there isn't (yet) a Galaxy tool(s) that such pipeline. I am pretty sure this will be of great interest within the NGS/Galaxy community. Please keep us updated about its progress (maybe via the bitbucket wiki?). cheers, Erick On 30 March 2010 09:30, Glen Otero <gotero@linuxprophet.com> wrote:
Hello-
I'm about to embark on an effort to try and roll Illumina's CASAVA pipeline software--demultiplex.pl, GERALD.pl, run.pl and other scripts, into a local Galaxy install. I'd prefer not to reinvent the wheel, so I'd like to hear from anyone that's already done part or all of what I'm going to attempt. Any advice is greatly appreciated.
Alternatively, if this is something that other developers are interested in, maybe it could be considered for a coding sprint during the breakout session at the developers' conference or during one of the BEER sessions?
Thanks!
Glen
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Glen, I forgot to mention an wiki page I came across last month (CASAVA is considered as a possible tool) : https://wiki.nbic.nl/index.php/Next_Generation_Sequencing:_Generic_pipeline cheers, Erick On 30 March 2010 11:46, Erick Antezana <erick.antezana@gmail.com> wrote:
Hi Glen,
I am very interested in such a development. AFAIK, there isn't (yet) a Galaxy tool(s) that such pipeline. I am pretty sure this will be of great interest within the NGS/Galaxy community. Please keep us updated about its progress (maybe via the bitbucket wiki?).
cheers, Erick
On 30 March 2010 09:30, Glen Otero <gotero@linuxprophet.com> wrote:
Hello-
I'm about to embark on an effort to try and roll Illumina's CASAVA pipeline software--demultiplex.pl, GERALD.pl, run.pl and other scripts, into a local Galaxy install. I'd prefer not to reinvent the wheel, so I'd like to hear from anyone that's already done part or all of what I'm going to attempt. Any advice is greatly appreciated.
Alternatively, if this is something that other developers are interested in, maybe it could be considered for a coding sprint during the breakout session at the developers' conference or during one of the BEER sessions?
Thanks!
Glen
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Hi Erick- I'll try to keep the community posted on my progress, although that is likely to be unpredictable, just like my foreseeable development efforts. I'd like to hear from anyone that has incorporated a perl script into Galaxy and any advice they might have. Glen On Mar 30, 2010, at 2:46 AM, Erick Antezana wrote:
Hi Glen,
I am very interested in such a development. AFAIK, there isn't (yet) a Galaxy tool(s) that such pipeline. I am pretty sure this will be of great interest within the NGS/Galaxy community. Please keep us updated about its progress (maybe via the bitbucket wiki?).
cheers, Erick
On 30 March 2010 09:30, Glen Otero <gotero@linuxprophet.com> wrote:
Hello-
I'm about to embark on an effort to try and roll Illumina's CASAVA pipeline software--demultiplex.pl, GERALD.pl, run.pl and other scripts, into a local Galaxy install. I'd prefer not to reinvent the wheel, so I'd like to hear from anyone that's already done part or all of what I'm going to attempt. Any advice is greatly appreciated.
Alternatively, if this is something that other developers are interested in, maybe it could be considered for a coding sprint during the breakout session at the developers' conference or during one of the BEER sessions?
Thanks!
Glen
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Hi Glen & Erick, FYI, we have a pipeline running on our site, which works for Illumina reads (starting with FASTQ files) and covers some parts of the described pipeline. It allows you to align reads with a few read mappers, to quantitate transcripts, and also to predict novel transcripts. Some of these tools are not fully integrated into galaxy yet, but others should be fully functional. We are currently work on improving their interaction and to get bugs fixed. The underlying methods are described in the slides of a recent talk (http://www.fml.tuebingen.mpg.de/raetsch/lectures/NGS-Bioinformatics-Paris-Ma... starting with slide 10) and the galaxy instance is available here http://galaxy.fml.mpg.de. Some of the tools have not been released/published yet, but will be hopefully soon. In this case we will also provide the galaxy bindings. Cheers, Gunnar
I am very interested in such a development. AFAIK, there isn't (yet) a Galaxy tool(s) that such pipeline. I am pretty sure this will be of great interest within the NGS/Galaxy community. Please keep us updated about its progress (maybe via the bitbucket wiki?).
cheers, Erick
On 30 March 2010 09:30, Glen Otero <gotero@linuxprophet.com> wrote:
Hello-
I'm about to embark on an effort to try and roll Illumina's CASAVA pipeline software--demultiplex.pl, GERALD.pl, run.pl and other scripts, into a local Galaxy install. I'd prefer not to reinvent the wheel, so I'd like to hear from anyone that's already done part or all of what I'm going to attempt. Any advice is greatly appreciated.
Alternatively, if this is something that other developers are interested in, maybe it could be considered for a coding sprint during the breakout session at the developers' conference or during one of the BEER sessions?
Thanks!
Glen
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
participants (3)
-
Erick Antezana -
Glen Otero -
Gunnar Raetsch