[galaxy-dev] wrapper accepts fastqcssanger when it shouldn't
Hi all, So in my wrapper for my trimming tool, sickle, I only allow fastq, fastqsanger, fastqillumina, or fastqsolexa input data. However, if a fastqsanger file's datatype has been erroneously changed to fastqcssanger, my tool will still show that file in the dropdown for the possible inputs. Why does this happen? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] value_from_basic - KeyError: 'base_name', was: Tests not being run on toolsheds?
On Mon, Mar 23, 2015 at 12:27 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Dave, Now that you've fixed some of the test back log, the bad news is this issue I reported last week appears to be a major regression affecting multiple tools on the Test Tool Shed: https://testtoolshed.g2.bx.psu.edu/view/peterjc/align_back_trans https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr https://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod ... https://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus ... https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs ... https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id These are all recent test runs from 2015-03-18. Note that some tool tests from the same date are passing, e.g. https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_composition https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer Hi Dave, These tools do not seem to have been tested on the TestToolShed since 2015-03-18. Does something need resetting/unblocking again? Regards, 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] wrapper accepts fastqcssanger when it shouldn't
On Thu, Apr 2, 2015 at 10:02 AM, Nikhil Joshi najo...@ucdavis.edu wrote: Hi all, So in my wrapper for my trimming tool, sickle, I only allow fastq, fastqsanger, fastqillumina, or fastqsolexa input data. However, if a fastqsanger file's datatype has been erroneously changed to fastqcssanger, my tool will still show that file in the dropdown for the possible inputs. Why does this happen? - Nik. Because you allowed fastq, this includes all the subclasses of fastq which (unfortunately in this case) includes fastqcssanger. 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] using DataManager to add custom genomes
Hi all, Is it possible to use a DataManager (or anything) to allow a user (or admin) to upload their genome of choice and have it be indexed and be used as a built-in/cached genome *without* having to go on the command-line? I.e., only using the Galaxy interface? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] NGINX uWSGI with require_login needs uwsgi_param SCRIPT_NAME '';
Dannon, thanks, This is on dev at commit 43a94ada37124dde5759b0c94bf25a97ff4da17a Am running nginx 1.6.2 on RedHat EL 6.6 Python 2.7.8 with uWSGI 2.0.10 I can send my galaxy.ini and nginx.conf to you separately off list. DT -- David Trudgian Ph.D., Computational Scientist UT Southwestern BioHPC From: Dannon Baker [dannon.ba...@gmail.com] Sent: Thursday, April 02, 2015 3:52 PM To: David Trudgian Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] NGINX uWSGI with require_login needs uwsgi_param SCRIPT_NAME ''; Hey David, What version of galaxy are you using? I'm not able to reproduce this with the current release, but maybe I don't have all the information here. Previously, this SCRIPT_NAME issue was observed when static_enabled was true, but I've never seen it otherwise. Any information you might be able to share to help me reproduce this would be valuable -- we shouldn't have to inject meaningless parameters into the environment to make things work. -Dannon On Thu, Apr 2, 2015 at 3:23 PM, David Trudgian david.trudg...@utsouthwestern.edumailto:david.trudg...@utsouthwestern.edu wrote: Hi, When I enabled 'require_login = True' on a galaxy instance running with NGINX+uWSGI I receive internal server error pages due to a Key error for File 'lib/galaxy/web/framework/base.py', line 356 in path return self.environ['SCRIPT_NAME'] + self.environ['PATH_INFO'] KeyError: 'SCRIPT_NAME' Works fine with 'require_login = False' - I'm not sure why require_login makes it take a code path which needs SCRIPT_NAME. Anyway - the addition of... uwsgi_param SCRIPT_NAME ''; ... to the nginx.conf prevents this error. Should I try and add this to the uWSGI config snippets on the wiki? Thanks, -- David Trudgian Ph.D., Computational Scientist UT Southwestern BioHPC -- David Trudgian Ph.D., Computational Scientist UT Southwestern BioHPC UT Southwestern Medical Center The future of medicine, today. ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] NGINX uWSGI with require_login needs uwsgi_param SCRIPT_NAME '';
Hi, When I enabled 'require_login = True' on a galaxy instance running with NGINX+uWSGI I receive internal server error pages due to a Key error for File 'lib/galaxy/web/framework/base.py', line 356 in path return self.environ['SCRIPT_NAME'] + self.environ['PATH_INFO'] KeyError: 'SCRIPT_NAME' Works fine with 'require_login = False' - I'm not sure why require_login makes it take a code path which needs SCRIPT_NAME. Anyway - the addition of... uwsgi_param SCRIPT_NAME ''; ... to the nginx.conf prevents this error. Should I try and add this to the uWSGI config snippets on the wiki? Thanks, -- David Trudgian Ph.D., Computational Scientist UT Southwestern BioHPC -- David Trudgian Ph.D., Computational Scientist UT Southwestern BioHPC UT Southwestern Medical Center The future of medicine, today. ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] using DataManager to add custom genomes
Hi Nikhil, Have a look at https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_fetch_genome_dbkeys_all_fasta to add a new genome/fasta. Once you have the genome entry, then you can use additional Data Manager to make tool specific (bwa, samtools, etc) indexes. Thanks for using Galaxy, Dan On Apr 2, 2015, at 5:41 AM, Nikhil Joshi najo...@ucdavis.edu wrote: Of course this would be for a local install of galaxy. On Thu, Apr 2, 2015 at 2:29 AM, Nikhil Joshi najo...@ucdavis.edu wrote: Hi all, Is it possible to use a DataManager (or anything) to allow a user (or admin) to upload their genome of choice and have it be indexed and be used as a built-in/cached genome *without* having to go on the command-line? I.e., only using the Galaxy interface? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Workflow bug when *.loc entries are missing
On Wed, Apr 1, 2015 at 6:50 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Apr 1, 2015 at 11:29 AM, Saket Choudhary sake...@gmail.com wrote: On 1 April 2015 at 02:06, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Mar 31, 2015 at 6:12 PM, John Chilton jmchil...@gmail.com wrote: I think it is probably a pair of bugs you are seeing: ... The fix unfortunately is messy and will likely break stuff. -John Running tools anyway where the expected example.loc entry is missing is bad, but most tools would fail cleanly when given an empty path - so this is less critical than the first half of the bug. i.e. Can we address the side effects of Saket's commit?: https://github.com/galaxyproject/galaxy/commit/667c04844e35e76a698161fff6c88cb03be8396a https://bitbucket.org/galaxy/galaxy-central/commits/757412c63654ff16f6cd6a0b6ff776b25e0b5b03 Hi Peter, Sorry, this really is a major bug. I agree this was pushed without much testing. In fact, I did not at all consider the use case you just pointed out. I can send a PR that simply reverts the change, since I am not sure I will have enough time to look into it deeper. Looks like I have broken more things than what I have contributed. Saket Thanks Saket, I didn't mean to criticize - only to ensure you were aware of this (in case you had any insight about how to fix it). Galaxy is amazingly complicated, so subtle side-effects like this can be hard to avoid - especially on the interactive side where testing is harder. [We don't yet have a proper test framework for workflows - although John has been working on that.] I don't understand this area of Galaxy at all (mako templates etc), so I think we'll need to defer to the full time developers who know this bit best. Definitely - I will definitely take a crack at fixing it - though I cannot do it this week. Monday I will set aside some to try to tweak it so the fix for radio buttons will still work without actually resubmitting every workflow parameter - if I cannot fix it I will revert the commit. -John P.S. I am with Peter on this Saket - I wouldn't feel bad - this is a really subtle bug. I do know that feeling of being worried the bugs I have added to Galaxy greatly out number the features though. I know that you have not actually done this - but I have added so many more bugs than you that I am less sure about myself. Regards, 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
