On Mon, Apr 4, 2011 at 12:19 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Fri, Apr 1, 2011 at 12:01 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: >> On Thu, Mar 31, 2011 at 6:28 PM, Peter Cock <p.j.a.c...@googlemail.com> >> wrote: >>> Hi all, >>> >>> The NCBI have just released BLAST 2.2.25+ which includes some >>> interesting new stuff of interest to the tabular output, ... >> >> One reason why I want to move to BLAST 2.2.25+ on our local >> machine is they fixed the subject IDs in tabular output, ... > > Hi Kanwei, > > Could you transplant or merge this commit please? > https://bitbucket.org/peterjc/galaxy-central/changeset/ab40f95393ec > > It updates the test output files to work with BLAST 2.2.25+, which I > will be using locally due to several important bug fixes. As you don't > offer BLAST+ on the Penn State server I don't expect this to cause > you any problems. > > Also (and unrelated to this change), do you see this from the test suite? > > $ ./run_functional_tests.sh -id ncbi_blastp_wrapper > ... > ====================================================================== > ERROR: NCBI BLAST+ blastp ( ncbi_blastp_wrapper ) > Test-1 > ---------------------------------------------------------------------- > Traceback (most recent call last): > File > "/home/pjcock/repositories/galaxy-central/test/functional/test_toolbox.py", > line 155, in test_tool > self.do_it( td ) > File > "/home/pjcock/repositories/galaxy-central/test/functional/test_toolbox.py", > line 71, in do_it > page_inputs = > self.__expand_grouping(testdef.tool.inputs_by_page[0], all_inputs) > File > "/home/pjcock/repositories/galaxy-central/test/functional/test_toolbox.py", > line 122, in __expand_grouping > elif isinstance(declared_inputs[value.name], str): > KeyError: 'blast_type'
Solved, it seems I can't omit any parameters in the <test> and expect the defaults to be used. This doesn't seem desirable (new bug?), but the quick fix is to add a few lines to the test. Could you commit this too: https://bitbucket.org/peterjc/galaxy-central/changeset/124e4556f3c5 Thanks, 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/
