Re: [galaxy-dev] question/bug with cuffcompare wrapper
Assaf, Thanks for the very helpful information. We largely sync our tool wrappers to the tool version used on our public server. We're currently running v1.0.1 of Cufflinks on main; hence, as you discovered, the wrappers are compatible with that version of Cufflinks but (sadly) incompatible with newer versions. If you modify the Cufflinks/compare/diff wrappers to be compatible with 1.0.2/3, please either put them in the toolshed or send them to me and I'll incorporate them into the Galaxy code base. Thanks, J. On Jun 6, 2011, at 2:42 PM, Assaf Gordon wrote: Hi, It seems the cuffcompare XML wrapper expects a file named cc_output to contain the transcript accuracy report. I guess it worked with versions 0.9.3 and 1.0.1, but at least in version 1.0.2, this file is now named cc_output.stats, and the transcript accuracy file is empty. so the XML wrapper is compatible with 1.0.1 but not really with 1.0.2/3 (Unless I missed something in the XML/python/cuffcompare execution chain). Also, Notice that starting version 1.0.2 they've added an option to normalize by either total number of reads or by number of reads that matched the given GTF file. To make matters worse, cufflinks defaults to normalizing to total reads, and cuffdiff defaults to normalizing by GTF-matching reads. The options are called --total-hits-norm and --compatible-hits-norm. There's no way for users to specify either of those in Galaxy, so running cufflinks/cuffdiff might give unexpected results (not that there are any expected results, but still...) Just something to think about when you work on the next version of cufflinks wrappers. -gordon ___ 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] question/bug with cuffcompare wrapper
Hi all, Jeremy Goecks wrote, On 06/07/2011 01:25 PM: If you modify the Cufflinks/compare/diff wrappers to be compatible with 1.0.2/3, please either put them in the toolshed or send them to me and I'll incorporate them into the Galaxy code base. We are actually working on customized version of those tools, with parameters which better suit our needs, I'm happy to share. They are far from stable, so no tool-shed yet. The XML's are here: http://cancan.cshl.edu/labmembers/gordon/files/cshl_rnaseq_tools_2011-06-07.tar.bz2 They use Cufflinks 1.0.3, but also require a small patch to Galaxy (included in the tarball), to add our $input.tag labeling hack. Without this patch, you'll need to modify the output labels and the --label parameter of cuffdiff (with this patch, it calculates the labels automatically). See the working interface go here: http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_cufflinks http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_cuffcompare http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_cuffdiff http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_cuffdiff_replicates Comments are always welcomed, -gordon ___ 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] question/bug with cuffcompare wrapper
Hi, It seems the cuffcompare XML wrapper expects a file named cc_output to contain the transcript accuracy report. I guess it worked with versions 0.9.3 and 1.0.1, but at least in version 1.0.2, this file is now named cc_output.stats, and the transcript accuracy file is empty. so the XML wrapper is compatible with 1.0.1 but not really with 1.0.2/3 (Unless I missed something in the XML/python/cuffcompare execution chain). Also, Notice that starting version 1.0.2 they've added an option to normalize by either total number of reads or by number of reads that matched the given GTF file. To make matters worse, cufflinks defaults to normalizing to total reads, and cuffdiff defaults to normalizing by GTF-matching reads. The options are called --total-hits-norm and --compatible-hits-norm. There's no way for users to specify either of those in Galaxy, so running cufflinks/cuffdiff might give unexpected results (not that there are any expected results, but still...) Just something to think about when you work on the next version of cufflinks wrappers. -gordon ___ 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/
