On Thu, Oct 17, 2013 at 5:04 PM, John Chilton wrote:
> On Thu, Oct 17, 2013 at 5:49 AM, Peter Cock wrote:
>> On Thu, Oct 17, 2013 at 11:36 AM, John Chilton wrote:
>>
>> (And with the job splitting not being enabled by default, I am
>> aware that I am in a relatively small group of Galaxy admins
On Thu, Oct 17, 2013 at 5:49 AM, Peter Cock wrote:
> On Thu, Oct 17, 2013 at 11:36 AM, John Chilton wrote:
>> I broke the TaskWrapper last week with my exit code handling "fix",
>> the double semi-colon thing you are seeing there. Your fix would break
>> non-task split jobs so that is probably th
On Thu, Oct 17, 2013 at 11:36 AM, John Chilton wrote:
> I broke the TaskWrapper last week with my exit code handling "fix",
> the double semi-colon thing you are seeing there. Your fix would break
> non-task split jobs so that is probably the problem(?) Hopefully? Want
> to revert 8e001dc9675c and
I broke the TaskWrapper last week with my exit code handling "fix",
the double semi-colon thing you are seeing there. Your fix would break
non-task split jobs so that is probably the problem(?) Hopefully? Want
to revert 8e001dc9675c and pull in the changeset I just pushed out.
Otherwise, I will te
On Thu, Oct 17, 2013 at 10:53 AM, Peter Cock wrote:
> Hi John,
>
> Is all your semi-colon fixing on the trunk? I've found another bug in
> this area (patch below), which is showing up with task splitting under
> SGE.
>
> ...
>
> Note the repeated semi-colon, which causes the child jobs to fail (pa
Hi John,
Is all your semi-colon fixing on the trunk? I've found another bug in
this area (patch below), which is showing up with task splitting under
SGE.
e.g. this job is meant to be running and merging 5 BLAST XML files, stderr:
nothing to merge for
/mnt/galaxy/galaxy-central/database/files/00
Hey All,
Patch available with test case, let me know what I broke :).
https://bitbucket.org/jmchilton/galaxy-central-multi-input-tool-fixes-2/commits/e0016057e1648d7f4d29fbaf14252cbefff6d0bd
-John
On Fri, Oct 11, 2013 at 10:37 AM, Björn Grüning
wrote:
> Am Freitag, den 11.10.2013, 09:18 -0500
Am Freitag, den 11.10.2013, 09:18 -0500 schrieb John Chilton:
> My plan is to refactor build_command_line out of
> lib/galaxy/jobs/runners/__init__.py, into its own module and add unit
> tests for this functionality. I'll issue a pull request and let people
> test it. I am also testing Nicola's PR,
I already fixed it one week ago:
https://bitbucket.org/nsoranzo/galaxy-central-tools/commits/74b5fd2318d33b76382b052eae6a28b035dc075f
but then Ross committed a similar fix to galaxy-central, I merged it in
my pull request and then Ross reverted the fix!
This is the reason for rebasing pull req
Hi Nate,
> Hi Björn,
>
> Are you certain that SGE is responsible? I ran in to the same thing with
> bowtie2 with other runners.
> The double semicolon is invalid syntax in Bourne-compatible shells and so the
> tool ought to be fixed not to produce them (it happens under certain
> combinatio
My plan is to refactor build_command_line out of
lib/galaxy/jobs/runners/__init__.py, into its own module and add unit
tests for this functionality. I'll issue a pull request and let people
test it. I am also testing Nicola's PR, I will approve it shortly.
Nate yelled at me for committing code yes
Ah now I got it ... there are two build_command_line functions.
lib/galaxy/tools/__init__.py and lib/galaxy/jobs/runners/__init__.py.
And one is adding a trailing ';'
So either stripping the trailing semicolon, right after creating the
command line from cheetah (patch was attached) or adding more
If the tool produces a trailing semi-colon (and without Nicola's patch
the bowtie 2 tool definitely could), then I bet build_command_line()
is going to be what is adding the second semi-colon. It has not check
that there isn't a semi-colon at the end of the command before adding
one and extending t
Hi Nicola,
interesting you fixed bowtie in the same way than we did. But somehow I
would like to strip a trailing ';' by default in Galaxy, when it does
not break anything else.
Thanks for sharing!
Bjoern
> Il giorno ven, 11/10/2013 alle 01.10 +0200, Björn Grüning ha scritto:
> > Dear all,
> >
Il giorno ven, 11/10/2013 alle 01.10 +0200, Björn Grüning ha scritto:
> Dear all,
>
> some SGE instances will add automatically an semicolon add the end of
> each command, resulting in a disrupted job, because ';;' are not
> allowed.
>
> The latest changes to the Bowtie2 wrapper resulting in suc
Opps, sent that last e-mail before I meant to, gmail is acting very
buggy for me this morning. I just meant to say I would modify
build_command_line in lib/galaxy/jobs/runners/__init__.py instead. It
seems like there is a lot of logic in there for this kind of thing
already. I will create a Trello
Hi Björn,
Are you certain that SGE is responsible? I ran in to the same thing with
bowtie2 with other runners. The double semicolon is invalid syntax in
Bourne-compatible shells and so the tool ought to be fixed not to produce them
(it happens under certain combinations of options). Have you
This sounds like a good way to solve the problem, I guess I would modify
On Thu, Oct 10, 2013 at 6:10 PM, Björn Grüning
wrote:
>
> Dear all,
>
> some SGE instances will add automatically an semicolon add the end of
> each command, resulting in a disrupted job, because ';;' are not
> allowed.
>
>
Dear all,
some SGE instances will add automatically an semicolon add the end of
each command, resulting in a disrupted job, because ';;' are not
allowed.
The latest changes to the Bowtie2 wrapper resulting in such a case and a
crash in our instance. An easy solution would be to fix the wrapper a
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