[galaxy-dev] checkboxes bug fix
Hi, Since I haven't updated Galaxy for a while now I don't know if it was actually fixed but I had issues with my default-selected checkboxes: When I deselected them, the value sent in the query remained as if they were still selected. Even when I re-ran the job, all the checkboxes were selected as if I never deselected them. Therefore, in lib/galaxy/web/form_builder.py I changed: 105return 'input type=checkbox id=%s name=%s value=true%s%sinput type=hidden name=%s%s value=true%s' \ for: 105return 'input type=checkbox id=%s name=%s value=true%s%sinput type=hidden name=%s%s value=false%s' \ And it works fine now :) Cheers, L-A ___ 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] Defining new file formats in Galaxy (for new tool wrappers)
On Thu, Jun 2, 2011 at 6:39 PM, Greg Von Kuster g...@bx.psu.edu wrote: We will certainly include support for new data formats into the Galaxy core. In case you haven't seen it, details for adding new formats is available in our wiki at https://bitbucket.org/galaxy/galaxy-central/wiki/AddingDatatypes. Hi Greg, Should that page talk about lib/galaxy/datatypes/registry.py as well? That seems to be where mime types are specified, and for some reason (a historical fall back?), there is another sniffer listing here too (as well as in datatypes_conf.xml). Peter ___ 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] Update of cufflinks
Thanks Assaf. A couple notes on Galaxy's Cufflinks' wrappers and update checks: *galaxy-central changeset 4557:eee0e1d344d2, which updated the Cufflinks/compare/diff wrappers to support v1.0.* disabled the update check for Cufflinks. *There is no --no-update-check option for for Cuffcompare; I haven't checked to see if Cuffcompare actually contacts cufflinks.cbcb.umd.edu before running or not. *galaxy-central changeset 5638:1ab3dfb5d929 disables the update check for Cuffdiff. Best, J. On Jun 2, 2011, at 3:33 PM, Assaf Gordon wrote: Just FYI, With the recent version of cufflinks (at least 1.0.2), the developers added a 'feature' of automatic version check. While the idea is nice, the implications are not: cufflinks,cuffcompare and cuffdiff will connect to host cufflinks.cbcb.umd.edu every time you run them. I'm sure the intentions were good, but I don't like programs calling home, basically reporting usage statistics and origins. The check_update code is also not written with security in mind, and might be exploited (buffer overruns and such) - it's best to disable it. This will also generate a message to STDERR, which is just annoying (and bad, with galaxy). To disable it on the command line, add --no-update-check to every invocation. If you compiled it from source code, edit the file ./src/common.cpp and change the line: bool no_update_check = false; to: bool no_update_check = true; Then recompile and re-install. -gordon Jeremy Goecks wrote, On 05/10/2011 09:02 AM: We recently updated the Cufflinks/compare/diff wrappers to be compatible with v1.0.* ; the wrappers are available in galaxy-central and should be available in galaxy-dist in the next couple weeks as we're planning another release soon. New features in v1.0.* have not been implemented in these updates (and, in fact, there are features from 0.9.* that are still not available); the changes we made were simply to ensure that the wrappers' current functionality works with the new versions. In the next couple months we plan to extend the current wrappers to include new functionality. However, community contributions that extend the current wrappers to include new functionality would be most welcome, and we can integrate them into the galaxy code base if/when they are available. Best, J. ___ 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] Components
Hi everyone, I'm new in galaxy and I want to create a component, so I have multiple questions. The component executes a script which takes different formats : fasta|fastq|sff. As output it takes a folder, to do so I used the extra_files_path attribute of an output data (--out='$output.extra_files_path'). The result file is stored in this folder with the log file and should be in the same format as the input one. I wrote the xml file and it works just fine, however as it's a folder there is no way to use the result file(s) for further analysis. How can I manage this ? Also it can happen that there is more than 1 file outputted, how can I manage multiple outputs ? An other question about the input format, I have an option to the script to specify the format. I saw there is auto-format detection routines in galaxy, there is a way so I can call them to automatically complete this option ? thx, Jerome ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Components
On Mon, Jun 6, 2011 at 2:45 PM, Mariette jmari...@toulouse.inra.fr wrote: Hi everyone, I'm new in galaxy and I want to create a component, so I have multiple questions. The component executes a script which takes different formats : fasta|fastq|sff. As output it takes a folder, to do so I used the extra_files_path attribute of an output data (--out='$output.extra_files_path'). The result file is stored in this folder with the log file and should be in the same format as the input one. I wrote the xml file and it works just fine, however as it's a folder there is no way to use the result file(s) for further analysis. How can I manage this ? I use a wrapper script which moves the output file from the sub-directory to the location Galaxy requested. Regarding the file format, if you only have one input file you can use format=input, otherwise use the change_format tag in the XML. Also it can happen that there is more than 1 file outputted, how can I manage multiple outputs ? An other question about the input format, I have an option to the script to specify the format. I saw there is auto-format detection routines in galaxy, there is a way so I can call them to automatically complete this option ? Normally the wrapper specifies the output format explicitly. Peter ___ 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] Color blindness and Galaxy UI
Peter, most of the current UI theme was designed by someone who is red- green colorblind (me), and we avoid using color alone for encoding information. The change has been reverted, thanks for brining it to our attention. On Jun 5, 2011, at 7:40 AM, Peter Cock wrote: Do you have any color blind developers or users testing Galaxy and any UI changes? Those of you with family members or close colleagues affected by this are probably well aware of the issue. If not, please keep in mind that red-green color blindness is fairly common, and that color alone should not be used to distinguish status changes. ___ 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] Color blindness and Galaxy UI
On Mon, Jun 6, 2011 at 11:18 AM, James Taylor ja...@jamestaylor.org wrote: Peter, most of the current UI theme was designed by someone who is red-green colorblind (me), and we avoid using color alone for encoding information. The change has been reverted, thanks for brining it to our attention. I expect you would have spotted this commit soon anyway then :) On Mon, Jun 6, 2011 at 4:30 PM, Kanwei Li kan...@gmail.com wrote: Maybe the background color for the error can be changed as well? I just got a colorblind tester and #FA for example provides a much better contrast than the current color. (ss attached) That sounds sensible - see what James thinks ;) Peter ___ 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/
[galaxy-dev] CuffDiff output mis-named ?
Hi,
In cuffdiff_wrapper.xml, there are three outputs associated with CDS:
data format=tabular name=cds_exp_fpkm_tracking label=${tool.name} on
${on_string}: CDS Expression FPKM Tracking/
data format=tabular name=cds_fpkm_tracking label=${tool.name} on
${on_string}: CDS FPKM tracking/
data format=tabular name=cds_diff label=${tool.name} on ${on_string}: CDS
diff/
Based on the naming convention of the other outputs (and the output files from
cuffdiff),
I think the label of the first one should be renamed to CDS Expression only
(assuming the relevant input file cds_exp.diff).
-gordon
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