Re: [galaxy-dev] bowtie2: no stderr output
Dear John Thank you for responding. Not too sure why I can't see your link unfortunately, but did you mean this? http://dev.list.galaxyproject.org/bowtie-wrapper-td4658698.html I've tried modifying the command but doesn't seem to work either. And I can't use the wrapper too? I've just updated galaxy as well but doesn't fix it. Any ideas? Many thanks! Liz On Mon, Nov 3, 2014 at 6:59 AM, John Chilton jmchil...@gmail.com wrote: It looks like this was a problem for awhile but isn't anymore on main https://trello.com/c/yFeXvhUg. It doesn't look like there has been any changes to the bowtie2 wrapper since it was migrated to the tool shed so I am not sure why it isn't working for you? As an admin can you open a successful bowtie2 dataset and see what the standard error and standard output are saved as - maybe copying them into pastebin or gist. It might help illuminate the problem. -John On Mon, Oct 27, 2014 at 4:31 AM, Elizabeth Chia elc...@gmail.com wrote: Dear all Usually the alignment statistics from bowtie2 will be printed to the stderr file, however, on the local instance, the stderr file is empty after alignment. It still does the alignment, but the statistics are not printed out. This is my hg summary: parent: 13802:f7dd0060c296 latest_2014.06.02 Merged in dannon/galaxy-central-prmaker/stable (pull request #404) branch: stable commit: 288 modified, 357 added, 18 unknown (new branch head) update: 27 new changesets (update) Will updating to the latest version help? Or are there any patches available? Thanks. Regards liz ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] tools version (eg: cufflinks) and bowtie indices file
Hi there 1. Why is it that even after installing cufflinks 2.1.1 from the toolshed, it doesn't get reflected when I clicked on the tool from the side panel? It still shows 0.0.5 and 0.0.7. Think it's the same with others too (eg: bowtie) 2. I've modified the bowtie_indices.loc file under tool-data but the entries doesn't get reflected on the Map with Bowtie for Illumina (select a reference genome). I did the same for the bowtie2_indices.loc file and this one got reflected under Bowtie2. Been a little frustrating. Can anyone please advise? Many thanks. Best regards liz ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tools version (eg: cufflinks) and bowtie indices file
Hi Elizabeth, Am 09.11.2014 um 20:26 schrieb Elizabeth Chia: Hi there 1. Why is it that even after installing cufflinks 2.1.1 from the toolshed, it doesn't get reflected when I clicked on the tool from the side panel? It still shows 0.0.5 and 0.0.7. Think it's the same with others too (eg: bowtie) The Galaxy tool versions do not correspond to the cufflinks program version. I think 0.0.7 is the most recent version. 2. I've modified the bowtie_indices.loc file under tool-data but the entries doesn't get reflected on the Map with Bowtie for Illumina (select a reference genome). I did the same for the bowtie2_indices.loc file and this one got reflected under Bowtie2. Have you installed data_managers? Please have also a look at: https://wiki.galaxyproject.org/Admin/DataIntegration Hope this helps a little bit, Bjoern Been a little frustrating. Can anyone please advise? Many thanks. Best regards liz ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
