Hi Peter, I think you need to merge your commits as I cannot seem to transplant or import the patches properly. K On Mon, Apr 4, 2011 at 9:46 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Mon, Apr 4, 2011 at 12:19 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Fri, Apr 1, 2011 at 12:01 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, Mar 31, 2011 at 6:28 PM, Peter Cock <p.j.a.cock@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