Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy
Thanks! This looks very useful for me. I'm also interested in fleshing out the wrapper, (implementing all possible options, like bowtie's full parameter list), but this should fit my purposes for now. Best regards, Patrick Von: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Gesendet: Freitag, 18. Januar 2013 04:37 An: Sorn, Patrick Cc: 'galaxy-dev@lists.bx.psu.edu'; 'do...@cshl.edu' Betreff: Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy I have a very basic STAR wrapper that works: https://bitbucket.org/jgoecks/jeremys-code/src/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml?at=default For now, the wrapper does two things: maps RNA-seq reads and identifies chimeric reads/junctions. There are tons of options that aren't yet implemented, but the basics are there. Eventually I'll put the wrapper in the toolshed, but if you want to use it now, you'll need to create your own star_indexes.loc table (identical in structure to the bowtie_indexes.loc table) and add the appropriate entry to tool_data_table_conf.xml This page explains the details of these files: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup If you're interested in helping to flesh out the wrapper, pull requests or patches are welcome. Thanks, J. On Jan 16, 2013, at 7:05 AM, Sorn, Patrick wrote: Hi all, I want to integrate STAR Aligner v2.2.0c into Galaxy and I was wondering if anyone else is working on this? If nobody is, I would do this. Best regards, Patrick Sorn ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy
Do you know how I can read in gzipped FASTQ files in the STAR wrapper without writing an external Python script or the like? Thanks, Patrick Von: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Gesendet: Freitag, 18. Januar 2013 04:37 An: Sorn, Patrick Cc: 'galaxy-dev@lists.bx.psu.edu'; 'do...@cshl.edu' Betreff: Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy I have a very basic STAR wrapper that works: https://bitbucket.org/jgoecks/jeremys-code/src/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml?at=default For now, the wrapper does two things: maps RNA-seq reads and identifies chimeric reads/junctions. There are tons of options that aren't yet implemented, but the basics are there. Eventually I'll put the wrapper in the toolshed, but if you want to use it now, you'll need to create your own star_indexes.loc table (identical in structure to the bowtie_indexes.loc table) and add the appropriate entry to tool_data_table_conf.xml This page explains the details of these files: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup If you're interested in helping to flesh out the wrapper, pull requests or patches are welcome. Thanks, J. On Jan 16, 2013, at 7:05 AM, Sorn, Patrick wrote: Hi all, I want to integrate STAR Aligner v2.2.0c into Galaxy and I was wondering if anyone else is working on this? If nobody is, I would do this. Best regards, Patrick Sorn ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy
The wrapper isn't set up to support gzipped FASTQ because Galaxy unzips datasets when they are uploaded, so the wrapper won't ever see a gzipped FASTQ dataset. We plan to dataset gzip support to Galaxy in the future. J. On Jan 18, 2013, at 10:21 AM, Sorn, Patrick wrote: Do you know how I can read in gzipped FASTQ files in the STAR wrapper without writing an external Python script or the like? Thanks, Patrick Von: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Gesendet: Freitag, 18. Januar 2013 04:37 An: Sorn, Patrick Cc: 'galaxy-dev@lists.bx.psu.edu'; 'do...@cshl.edu' Betreff: Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy I have a very basic STAR wrapper that works: https://bitbucket.org/jgoecks/jeremys-code/src/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml?at=default For now, the wrapper does two things: maps RNA-seq reads and identifies chimeric reads/junctions. There are tons of options that aren't yet implemented, but the basics are there. Eventually I'll put the wrapper in the toolshed, but if you want to use it now, you'll need to create your own star_indexes.loc table (identical in structure to the bowtie_indexes.loc table) and add the appropriate entry to tool_data_table_conf.xml This page explains the details of these files: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup If you're interested in helping to flesh out the wrapper, pull requests or patches are welcome. Thanks, J. On Jan 16, 2013, at 7:05 AM, Sorn, Patrick wrote: Hi all, I want to integrate STAR Aligner v2.2.0c into Galaxy and I was wondering if anyone else is working on this? If nobody is, I would do this. Best regards, Patrick Sorn ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy
I have a very basic STAR wrapper that works: https://bitbucket.org/jgoecks/jeremys-code/src/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml?at=default For now, the wrapper does two things: maps RNA-seq reads and identifies chimeric reads/junctions. There are tons of options that aren't yet implemented, but the basics are there. Eventually I'll put the wrapper in the toolshed, but if you want to use it now, you'll need to create your own star_indexes.loc table (identical in structure to the bowtie_indexes.loc table) and add the appropriate entry to tool_data_table_conf.xml This page explains the details of these files: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup If you're interested in helping to flesh out the wrapper, pull requests or patches are welcome. Thanks, J. On Jan 16, 2013, at 7:05 AM, Sorn, Patrick wrote: Hi all, I want to integrate STAR Aligner v2.2.0c into Galaxy and I was wondering if anyone else is working on this? If nobody is, I would do this. Best regards, Patrick Sorn ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy
Hi all, I want to integrate STAR Aligner v2.2.0c into Galaxy and I was wondering if anyone else is working on this? If nobody is, I would do this. Best regards, Patrick Sorn ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
