Re: [galaxy-dev] Updating BLAST+ wrapper
On Mon, Apr 4, 2011 at 6:07 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Apr 4, 2011 at 5:55 PM, Kanwei Li kan...@gmail.com wrote: Done the manual way Thanks. I was hoping to have finished this today, but it turns out there are some subtle but annoying changes to how BLAST records the hit id/name/description in their XML file which make the script to convert from XML to tabular unhappy. Hi Kanwei, I think I'm nearly done now, but I am still working on the blast25 branch you had trouble merging/transplanting from. I guess I will need to make a new clean branch from the galaxy tip for submission. Do you prefer several small atomic commits (which I understand is the recommend practice in git), or a few large commits (which seems quite common on the Galaxy hg history)? 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/
Re: [galaxy-dev] Updating BLAST+ wrapper
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/
Re: [galaxy-dev] Updating BLAST+ wrapper
On Mon, Apr 4, 2011 at 4:03 PM, Kanwei Li kan...@gmail.com wrote: I tried both ways, no dice (you can try yourself with a clean galaxy-central base) I'm a bit puzzled and not an hg expert. Was there an error message? And for plan (B), what went wrong with using patch and the raw changes? Surely that should work? https://bitbucket.org/peterjc/galaxy-central/changeset/ab40f95393ec/raw/galaxy-central-ab40f95393ec.diff https://bitbucket.org/peterjc/galaxy-central/changeset/124e4556f3c5/raw/galaxy-central-124e4556f3c5.diff 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] Updating BLAST+ wrapper
On Mon, Apr 4, 2011 at 4:36 PM, Kanwei Li kan...@gmail.com wrote: dhcp243253:galaxy-central kanwei$ hg transplant -s ~/peter/galaxy-central/ -b blast25 searching for changes changeset: 5585:ab40f95393ec branch: blast25 parent: 5583:086c9c2c52b9 user: peterjc p.j.a.c...@googlemail.com date: Mon Apr 04 12:12:11 2011 +0100 summary: Update tests for NCBI BLAST 2.2.25+ which fixed subject ID in tabular output apply changeset? [ynmpcq?]: y changeset: 5586:124e4556f3c5 branch: blast25 user: peterjc p.j.a.c...@googlemail.com date: Mon Apr 04 14:44:52 2011 +0100 summary: Include optional parameters in BLASTP test to avoid KeyError apply changeset? [ynmpcq?]: y searching for changes adding changesets adding manifests adding file changes added 2 changesets with 4 changes to 4 files dhcp243253:galaxy-central kanwei$ hg tip changeset: 5338:124e4556f3c5 branch: blast25 tag: tip user: peterjc p.j.a.c...@googlemail.com date: Mon Apr 04 14:44:52 2011 +0100 summary: Include optional parameters in BLASTP test to avoid KeyError The above is strange - why have you got a blast25 branch? Maybe the transplant isn't working as expected... dhcp243253:galaxy-central kanwei$ hg push pushing to https://kan...@bitbucket.org/galaxy/galaxy-central/ searching for changes abort: push creates new remote branches: blast25! (use 'hg push --new-branch' to create new remote branches) dhcp243253:galaxy-central kanwei$ hg merge blast25 abort: merging with a working directory ancestor has no effect It looks like you are on the blast25 branch, try checking out default then merging the new blast25 branch. It should be a fast-forward merge (just the two commits). Then you can push default back to galaxy-central on bitbucket. I think. Importing the diffs gives merge error Are you using a hg command here? What I meant for the Plan B was just using the Unix command patch to apply my changes by hand to the default branch. Then commit it under your name. It won't be associated with my bitbucket account, but it should just work. 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] Updating BLAST+ wrapper
Done the manual way ___ 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] Updating BLAST+ wrapper
Hi all, The NCBI have just released BLAST 2.2.25+ which includes some interesting new stuff of interest to the tabular output, i.e. Added support for query and subject length to tabular output I would therefore like to update my BLAST+ wrappers in Galaxy to add these two columns to the 'extended tabular' output option. They are going to be very helpful as you can now calculate things like the percentage identity (or similarity) compared to the query or sequence. If there are no objections I propose to add these as columns 23 and 24 (i.e. at the end), so minimise disruption to anyone already using the tabular output. I would hope to have a branch ready for merging next week... 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/
