Problems running functional tests

classic Classic list List threaded Threaded
9 messages Options
| Threaded
Open this post in threaded view
|

Problems running functional tests

iracooke
Hi All,

I'm starting to add functional tests to my tools but I've found that I can't get the test framework to work well with tool dependencies.

The tool I'm considering is xtandem

http://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem

When I install this tool on my local galaxy instance (on a clean install) the tool runs fine and if I look in the handler logs I see

executing: PACKAGE_BASE=/home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab/env.sh; PACKAGE_BASE=/home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab/env.sh; rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /home/iracooke/galaxy-central/database/files/000/dataset_1.dat   --var-mods=' 57.021464__at__C '   --fix-mods=' 15.994915__at__M '   /home/iracooke/galaxy-central/database/files/000/dataset_2.dat -o /home/iracooke/galaxy-central/database/files/000/dataset_4.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
galaxy.jobs DEBUG 2013-04-27 06:53:35,586 (4) Persisting job destination (destination id: local:///)


Note that in this case the tool environments from my tool dependencies are loaded ... and the tool runs fine.

When running functional tests however the tests are executed without first loading the environments from tool dependencies ... and naturally the tool fails.  On my local machine I get the following when running the tests (Note that no loading of dependency shel environments occurs).  (This seems to be the same issue on the testtoolshed.g2.bx.psu.edu ).

Job dispatched
galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,564 (3) executing: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat   --var-mods=' 15.994915__at__M , '   --fix-mods=' 57.021464__at__C '   /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
galaxy.jobs DEBUG 2013-04-27 06:55:19,730 (3) Persisting job destination (destination id: local:///)
galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,889 execution finished: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat   --var-mods=' 15.994915__at__M ,'   --fix-mods=' 57.021464__at__C '   /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
...
galaxy.jobs DEBUG 2013-04-27 06:55:24,277 setting dataset state to ERROR


Is there something wrong with the way I've defined my tool dependencies for this tool?  Or perhaps it's a bug in the testing framework.

Cheers
Ira






___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: Problems running functional tests

Dave Bouvier
Ira,

There is a known issue with resolving tool dependencies when running
functional tests. One workaround is to set the
GALAXY_TOOL_DEPENDENCY_DIR environment variable to the path configured
in your universe_wsgi.ini.

This issue is documented in https://trello.com/c/eVT3QWJF

    --Dave B.

On 5/8/13 20:08:08.000, Ira Cooke wrote:

> Hi All,
>
> I'm starting to add functional tests to my tools but I've found that I can't get the test framework to work well with tool dependencies.
>
> The tool I'm considering is xtandem
>
> http://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem
>
> When I install this tool on my local galaxy instance (on a clean install) the tool runs fine and if I look in the handler logs I see
>
> executing: PACKAGE_BASE=/home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab/env.sh; PACKAGE_BASE=/home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab/env.sh; rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /home/iracooke/galaxy-central/database/files/000/dataset_1.dat   --var-mods=' 57.021464__at__C '   --fix-mods=' 15.994915__at__M '   /home/iracooke/galaxy-central/database/files/000/dataset_2.dat -o /home/iracooke/galaxy-central/database/files/000/dataset_4.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
> galaxy.jobs DEBUG 2013-04-27 06:53:35,586 (4) Persisting job destination (destination id: local:///)
>
>
> Note that in this case the tool environments from my tool dependencies are loaded ... and the tool runs fine.
>
> When running functional tests however the tests are executed without first loading the environments from tool dependencies ... and naturally the tool fails.  On my local machine I get the following when running the tests (Note that no loading of dependency shel environments occurs).  (This seems to be the same issue on the testtoolshed.g2.bx.psu.edu ).
>
> Job dispatched
> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,564 (3) executing: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat   --var-mods=' 15.994915__at__M , '   --fix-mods=' 57.021464__at__C '   /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
> galaxy.jobs DEBUG 2013-04-27 06:55:19,730 (3) Persisting job destination (destination id: local:///)
> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,889 execution finished: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat   --var-mods=' 15.994915__at__M ,'   --fix-mods=' 57.021464__at__C '   /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
> ...
> galaxy.jobs DEBUG 2013-04-27 06:55:24,277 setting dataset state to ERROR
>
>
> Is there something wrong with the way I've defined my tool dependencies for this tool?  Or perhaps it's a bug in the testing framework.
>
> Cheers
> Ira
>
>
>
>
>
>
> ___________________________________________________________
> 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/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: Problems running functional tests

Peter Cock
> On 5/8/13 20:08:08.000, Ira Cooke wrote:
>>
>> Hi All,
>>
>> I'm starting to add functional tests to my tools but I've found that I
>> can't get the test framework to work well with tool dependencies.
>>
>> The tool I'm considering is xtandem
>>
>> http://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem
>>
>> When I install this tool on my local galaxy instance (on a clean install)
>> the tool runs fine and if I look in the handler logs I see
>>
>> executing:
>> PACKAGE_BASE=/home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab;
>> export PACKAGE_BASE; .
>> /home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab/env.sh;
>> PACKAGE_BASE=/home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab;
>> export PACKAGE_BASE; .
>> /home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab/env.sh;
>> rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d
>> /home/iracooke/galaxy-central/database/files/000/dataset_1.dat
>> --var-mods='            57.021464__at__C                '       --fix-mods='
>> 15.994915__at__M                '
>> /home/iracooke/galaxy-central/database/files/000/dataset_2.dat -o
>> /home/iracooke/galaxy-central/database/files/000/dataset_4.dat -r
>> --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0
>> --strict-monoisotopic-mass --keep-params-files
>> galaxy.jobs DEBUG 2013-04-27 06:53:35,586 (4) Persisting job destination
>> (destination id: local:///)
>>
>>
>> Note that in this case the tool environments from my tool dependencies are
>> loaded ... and the tool runs fine.
>>
>> When running functional tests however the tests are executed without first
>> loading the environments from tool dependencies ... and naturally the tool
>> fails.  On my local machine I get the following when running the tests (Note
>> that no loading of dependency shel environments occurs).  (This seems to be
>> the same issue on the testtoolshed.g2.bx.psu.edu ).
>>
>> Job dispatched
>> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,564 (3) executing: rvm
>> 1.9.3@protk-1.2.0 do tandem_search.rb -d
>> /tmp/tmp3I8GgN/database/files/000/dataset_1.dat             --var-mods='
>> 15.994915__at__M                ,               '               --fix-mods='
>> 57.021464__at__C                '
>> /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o
>> /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin
>> --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0
>> --strict-monoisotopic-mass --keep-params-files
>> galaxy.jobs DEBUG 2013-04-27 06:55:19,730 (3) Persisting job destination
>> (destination id: local:///)
>> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,889 execution
>> finished: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d
>> /tmp/tmp3I8GgN/database/files/000/dataset_1.dat                --var-mods='
>> 15.994915__at__M                ,'              --fix-mods='
>> 57.021464__at__C                '
>> /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o
>> /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin
>> --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0
>> --strict-monoisotopic-mass --keep-params-files
>> ...
>> galaxy.jobs DEBUG 2013-04-27 06:55:24,277 setting dataset state to ERROR
>>
>>
>> Is there something wrong with the way I've defined my tool dependencies
>> for this tool?  Or perhaps it's a bug in the testing framework.
>>
>> Cheers
>> Ira

On Thu, May 9, 2013 at 3:10 PM, Dave Bouvier <[hidden email]> wrote:
> Ira,
>
> There is a known issue with resolving tool dependencies when running
> functional tests. One workaround is to set the GALAXY_TOOL_DEPENDENCY_DIR
> environment variable to the path configured in your universe_wsgi.ini.
>
> This issue is documented in https://trello.com/c/eVT3QWJF
>
>    --Dave B.

Does this issue affect the Tool Shed tests as well, or just when run
via run_functional_test.sh? (I'm working though a couple of test
failures related to the dependency installation breaking somehow).

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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: Problems running functional tests

Dave Bouvier
This only affects tests that are run manually, the automated testing
framework correctly resolves tool dependencies.

    --Dave B.

On 5/9/13 10:41:22.000, Peter Cock wrote:

>> On 5/8/13 20:08:08.000, Ira Cooke wrote:
>>>
>>> Hi All,
>>>
>>> I'm starting to add functional tests to my tools but I've found that I
>>> can't get the test framework to work well with tool dependencies.
>>>
>>> The tool I'm considering is xtandem
>>>
>>> http://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem
>>>
>>> When I install this tool on my local galaxy instance (on a clean install)
>>> the tool runs fine and if I look in the handler logs I see
>>>
>>> executing:
>>> PACKAGE_BASE=/home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab;
>>> export PACKAGE_BASE; .
>>> /home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab/env.sh;
>>> PACKAGE_BASE=/home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab;
>>> export PACKAGE_BASE; .
>>> /home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab/env.sh;
>>> rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d
>>> /home/iracooke/galaxy-central/database/files/000/dataset_1.dat
>>> --var-mods='            57.021464__at__C                '       --fix-mods='
>>> 15.994915__at__M                '
>>> /home/iracooke/galaxy-central/database/files/000/dataset_2.dat -o
>>> /home/iracooke/galaxy-central/database/files/000/dataset_4.dat -r
>>> --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0
>>> --strict-monoisotopic-mass --keep-params-files
>>> galaxy.jobs DEBUG 2013-04-27 06:53:35,586 (4) Persisting job destination
>>> (destination id: local:///)
>>>
>>>
>>> Note that in this case the tool environments from my tool dependencies are
>>> loaded ... and the tool runs fine.
>>>
>>> When running functional tests however the tests are executed without first
>>> loading the environments from tool dependencies ... and naturally the tool
>>> fails.  On my local machine I get the following when running the tests (Note
>>> that no loading of dependency shel environments occurs).  (This seems to be
>>> the same issue on the testtoolshed.g2.bx.psu.edu ).
>>>
>>> Job dispatched
>>> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,564 (3) executing: rvm
>>> 1.9.3@protk-1.2.0 do tandem_search.rb -d
>>> /tmp/tmp3I8GgN/database/files/000/dataset_1.dat             --var-mods='
>>> 15.994915__at__M                ,               '               --fix-mods='
>>> 57.021464__at__C                '
>>> /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o
>>> /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin
>>> --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0
>>> --strict-monoisotopic-mass --keep-params-files
>>> galaxy.jobs DEBUG 2013-04-27 06:55:19,730 (3) Persisting job destination
>>> (destination id: local:///)
>>> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,889 execution
>>> finished: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d
>>> /tmp/tmp3I8GgN/database/files/000/dataset_1.dat                --var-mods='
>>> 15.994915__at__M                ,'              --fix-mods='
>>> 57.021464__at__C                '
>>> /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o
>>> /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin
>>> --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0
>>> --strict-monoisotopic-mass --keep-params-files
>>> ...
>>> galaxy.jobs DEBUG 2013-04-27 06:55:24,277 setting dataset state to ERROR
>>>
>>>
>>> Is there something wrong with the way I've defined my tool dependencies
>>> for this tool?  Or perhaps it's a bug in the testing framework.
>>>
>>> Cheers
>>> Ira
>
> On Thu, May 9, 2013 at 3:10 PM, Dave Bouvier <[hidden email]> wrote:
>> Ira,
>>
>> There is a known issue with resolving tool dependencies when running
>> functional tests. One workaround is to set the GALAXY_TOOL_DEPENDENCY_DIR
>> environment variable to the path configured in your universe_wsgi.ini.
>>
>> This issue is documented in https://trello.com/c/eVT3QWJF
>>
>>     --Dave B.
>
> Does this issue affect the Tool Shed tests as well, or just when run
> via run_functional_test.sh? (I'm working though a couple of test
> failures related to the dependency installation breaking somehow).
>
> 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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: [galaxy-iuc] Problems running functional tests

iracooke
Yes I agree that gnuplot should be removed from the list ... to tell the truth I think my dependency should build without it.

I'm also wondering if the other packages have been added to the build-bot yet?  My tool comes up as failing tests ... but no test result is shown, and last I saw it was failing due to a missing package dependency.

Ira


On 14/05/2013, at 12:12 AM, Nate Coraor <[hidden email]> wrote:

> On May 10, 2013, at 10:16 AM, Dave Bouvier wrote:
>
>> Ira,
>>
>> I've created a trello card (https://trello.com/c/7VTlX9rD) with the current list of recommended packages for tool dependency installation, based on this email and the galaxy-iuc thread. If there are further packages that are determined to be required, let me know and I'll update the list.
>>
>>  --Dave B.
>>
>> On 5/10/13 07:02:50.000, Ira Cooke wrote:
>>> Hi Dave,
>>>
>>> Thanks for the info and workaround.  Actually now when I look at my test results on the test toolshed I can see that the error is most likely due to one of my dependencies failing installation.    My guess is that one of the system packages required by my dependency is not installed on the build-bot.
>>>
>>> I'm not sure how best to approach this ... perhaps I need a setup similar to the build-bot myself for testing.  I'm not sure how far you've got towards deciding on the package lists you would have on the build-bot ... but FYI the packages I need on a fresh install of ubuntu are below.
>>>
>>> build-essential mercurial libreadline6-dev zlib1g-dev libssl-dev libyaml-dev libsqlite3-dev sqlite3 libxml2-dev libxslt1-dev autoconf libgdbm-dev libncurses5-dev automake libtool bison pkg-config libffi-dev subversion libbz2-dev swig expat libpng12-dev gawk gnuplot libperl-dev libfuse-dev libcurl4-openssl-dev libxml2-dev libgd2-xpm-dev liblocal-lib-perl cpanminus unzip
>
> Just a thought, but some of these may be best to place in the toolshed.  The version control systems and build tools are fine, as are (probably) the -dev versions of core system libraries like png, ssl, zlib, etc.  But gnuplot should be a repository.
>
> --nate
>
>>>
>>> Cheers
>>> Ira
>>>
>>>
>>> On 10/05/2013, at 12:51 AM, Dave Bouvier <[hidden email]> wrote:
>>>
>>>> This only affects tests that are run manually, the automated testing framework correctly resolves tool dependencies.
>>>>
>>>>  --Dave B.
>>>>
>>>> On 5/9/13 10:41:22.000, Peter Cock wrote:
>>>>>> On 5/8/13 20:08:08.000, Ira Cooke wrote:
>>>>>>>
>>>>>>> Hi All,
>>>>>>>
>>>>>>> I'm starting to add functional tests to my tools but I've found that I
>>>>>>> can't get the test framework to work well with tool dependencies.
>>>>>>>
>>>>>>> The tool I'm considering is xtandem
>>>>>>>
>>>>>>> http://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem
>>>>>>>
>>>>>>> When I install this tool on my local galaxy instance (on a clean install)
>>>>>>> the tool runs fine and if I look in the handler logs I see
>>>>>>>
>>>>>>> executing:
>>>>>>> PACKAGE_BASE=/home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab;
>>>>>>> export PACKAGE_BASE; .
>>>>>>> /home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab/env.sh;
>>>>>>> PACKAGE_BASE=/home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab;
>>>>>>> export PACKAGE_BASE; .
>>>>>>> /home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab/env.sh;
>>>>>>> rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d
>>>>>>> /home/iracooke/galaxy-central/database/files/000/dataset_1.dat
>>>>>>> --var-mods='            57.021464__at__C                '       --fix-mods='
>>>>>>> 15.994915__at__M                '
>>>>>>> /home/iracooke/galaxy-central/database/files/000/dataset_2.dat -o
>>>>>>> /home/iracooke/galaxy-central/database/files/000/dataset_4.dat -r
>>>>>>> --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0
>>>>>>> --strict-monoisotopic-mass --keep-params-files
>>>>>>> galaxy.jobs DEBUG 2013-04-27 06:53:35,586 (4) Persisting job destination
>>>>>>> (destination id: local:///)
>>>>>>>
>>>>>>>
>>>>>>> Note that in this case the tool environments from my tool dependencies are
>>>>>>> loaded ... and the tool runs fine.
>>>>>>>
>>>>>>> When running functional tests however the tests are executed without first
>>>>>>> loading the environments from tool dependencies ... and naturally the tool
>>>>>>> fails.  On my local machine I get the following when running the tests (Note
>>>>>>> that no loading of dependency shel environments occurs).  (This seems to be
>>>>>>> the same issue on the testtoolshed.g2.bx.psu.edu ).
>>>>>>>
>>>>>>> Job dispatched
>>>>>>> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,564 (3) executing: rvm
>>>>>>> 1.9.3@protk-1.2.0 do tandem_search.rb -d
>>>>>>> /tmp/tmp3I8GgN/database/files/000/dataset_1.dat             --var-mods='
>>>>>>> 15.994915__at__M                ,               '               --fix-mods='
>>>>>>> 57.021464__at__C                '
>>>>>>> /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o
>>>>>>> /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin
>>>>>>> --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0
>>>>>>> --strict-monoisotopic-mass --keep-params-files
>>>>>>> galaxy.jobs DEBUG 2013-04-27 06:55:19,730 (3) Persisting job destination
>>>>>>> (destination id: local:///)
>>>>>>> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,889 execution
>>>>>>> finished: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d
>>>>>>> /tmp/tmp3I8GgN/database/files/000/dataset_1.dat                --var-mods='
>>>>>>> 15.994915__at__M                ,'              --fix-mods='
>>>>>>> 57.021464__at__C                '
>>>>>>> /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o
>>>>>>> /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin
>>>>>>> --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0
>>>>>>> --strict-monoisotopic-mass --keep-params-files
>>>>>>> ...
>>>>>>> galaxy.jobs DEBUG 2013-04-27 06:55:24,277 setting dataset state to ERROR
>>>>>>>
>>>>>>>
>>>>>>> Is there something wrong with the way I've defined my tool dependencies
>>>>>>> for this tool?  Or perhaps it's a bug in the testing framework.
>>>>>>>
>>>>>>> Cheers
>>>>>>> Ira
>>>>>
>>>>> On Thu, May 9, 2013 at 3:10 PM, Dave Bouvier <[hidden email]> wrote:
>>>>>> Ira,
>>>>>>
>>>>>> There is a known issue with resolving tool dependencies when running
>>>>>> functional tests. One workaround is to set the GALAXY_TOOL_DEPENDENCY_DIR
>>>>>> environment variable to the path configured in your universe_wsgi.ini.
>>>>>>
>>>>>> This issue is documented in https://trello.com/c/eVT3QWJF
>>>>>>
>>>>>>   --Dave B.
>>>>>
>>>>> Does this issue affect the Tool Shed tests as well, or just when run
>>>>> via run_functional_test.sh? (I'm working though a couple of test
>>>>> failures related to the dependency installation breaking somehow).
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Peter
>>>>>
>>>
>>>
>> _______________________________________________
>> galaxy-iuc mailing list
>> [hidden email]
>> http://lists.bx.psu.edu/listinfo/galaxy-iuc
>


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: Problems running functional tests

iracooke
In reply to this post by Dave Bouvier
Hi Dave,

Just following up on this (now quite a bit later sorry).  

I can't seem to get things to work using your suggested workaround.

Using a fresh checkout of galaxy-central 9931:716f29e4c77d

I run

GALAXY_TOOL_DEPENDENCY_DIR=/home/iracooke/tool_dependencies sh run_functional_tests.sh -installed

In my universe_wsgi.ini I have

tool_dependency_dir = /home/iracooke/tool_dependencies

When running tests I find that the dependencies fail to be resolved (ie ... I get errors like the following).

galaxy.jobs.handler INFO 2013-04-28 11:01:17,955 (3) Job dispatched
galaxy.tools DEBUG 2013-04-28 11:01:18,594 Building dependency shell command for dependency 'galaxy_protk'
galaxy.tools WARNING 2013-04-28 11:01:18,595 Failed to resolve dependency on 'galaxy_protk', ignoring
galaxy.tools DEBUG 2013-04-28 11:01:18,596 Building dependency shell command for dependency 'trans_proteomic_pipeline'
galaxy.tools WARNING 2013-04-28 11:01:18,596 Failed to resolve dependency on 'trans_proteomic_pipeline', ignoring


When I run the tool myself (ie from galaxy ui not from the test script) it resolves the dependencies just fine.

Any idea what am I doing wrong?

Thanks

Ira



On 10/05/2013, at 12:10 AM, Dave Bouvier <[hidden email]> wrote:

> Ira,
>
> There is a known issue with resolving tool dependencies when running functional tests. One workaround is to set the GALAXY_TOOL_DEPENDENCY_DIR environment variable to the path configured in your universe_wsgi.ini.
>
> This issue is documented in https://trello.com/c/eVT3QWJF
>
>   --Dave B.
>
> On 5/8/13 20:08:08.000, Ira Cooke wrote:
>> Hi All,
>>
>> I'm starting to add functional tests to my tools but I've found that I can't get the test framework to work well with tool dependencies.
>>
>> The tool I'm considering is xtandem
>>
>> http://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem
>>
>> When I install this tool on my local galaxy instance (on a clean install) the tool runs fine and if I look in the handler logs I see
>>
>> executing: PACKAGE_BASE=/home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab/env.sh; PACKAGE_BASE=/home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab/env.sh; rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /home/iracooke/galaxy-central/database/files/000/dataset_1.dat   --var-mods=' 57.021464__at__C '   --fix-mods=' 15.994915__at__M '   /home/iracooke/galaxy-central/database/files/000/dataset_2.dat -o /home/iracooke/galaxy-central/database/files/000/dataset_4.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
>> galaxy.jobs DEBUG 2013-04-27 06:53:35,586 (4) Persisting job destination (destination id: local:///)
>>
>>
>> Note that in this case the tool environments from my tool dependencies are loaded ... and the tool runs fine.
>>
>> When running functional tests however the tests are executed without first loading the environments from tool dependencies ... and naturally the tool fails.  On my local machine I get the following when running the tests (Note that no loading of dependency shel environments occurs).  (This seems to be the same issue on the testtoolshed.g2.bx.psu.edu ).
>>
>> Job dispatched
>> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,564 (3) executing: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat   --var-mods=' 15.994915__at__M , '   --fix-mods=' 57.021464__at__C '   /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
>> galaxy.jobs DEBUG 2013-04-27 06:55:19,730 (3) Persisting job destination (destination id: local:///)
>> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,889 execution finished: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat   --var-mods=' 15.994915__at__M ,'   --fix-mods=' 57.021464__at__C '   /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
>> ...
>> galaxy.jobs DEBUG 2013-04-27 06:55:24,277 setting dataset state to ERROR
>>
>>
>> Is there something wrong with the way I've defined my tool dependencies for this tool?  Or perhaps it's a bug in the testing framework.
>>
>> Cheers
>> Ira
>>
>>
>>
>>
>>
>>
>> ___________________________________________________________
>> 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/
>>
>> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: Problems running functional tests

Dave Bouvier
Ira,

Yes, I should have mentioned that due to the way functional tests are
executed, an environment variable needs to be explicitly exported before
the functional test framework will recognize it. The syntax is very
nearly the same:

export GALAXY_TOOL_DEPENDENCY_DIR=/home/iracooke/tool_dependencies ; sh
run_functional_tests.sh -installed

    --Dave B.

On 6/3/13 00:25:53.000, Ira Cooke wrote:

> Hi Dave,
>
> Just following up on this (now quite a bit later sorry).
>
> I can't seem to get things to work using your suggested workaround.
>
> Using a fresh checkout of galaxy-central 9931:716f29e4c77d
>
> I run
>
> GALAXY_TOOL_DEPENDENCY_DIR=/home/iracooke/tool_dependencies sh run_functional_tests.sh -installed
>
> In my universe_wsgi.ini I have
>
> tool_dependency_dir = /home/iracooke/tool_dependencies
>
> When running tests I find that the dependencies fail to be resolved (ie ... I get errors like the following).
>
> galaxy.jobs.handler INFO 2013-04-28 11:01:17,955 (3) Job dispatched
> galaxy.tools DEBUG 2013-04-28 11:01:18,594 Building dependency shell command for dependency 'galaxy_protk'
> galaxy.tools WARNING 2013-04-28 11:01:18,595 Failed to resolve dependency on 'galaxy_protk', ignoring
> galaxy.tools DEBUG 2013-04-28 11:01:18,596 Building dependency shell command for dependency 'trans_proteomic_pipeline'
> galaxy.tools WARNING 2013-04-28 11:01:18,596 Failed to resolve dependency on 'trans_proteomic_pipeline', ignoring
>
>
> When I run the tool myself (ie from galaxy ui not from the test script) it resolves the dependencies just fine.
>
> Any idea what am I doing wrong?
>
> Thanks
>
> Ira
>
>
>
> On 10/05/2013, at 12:10 AM, Dave Bouvier <[hidden email]> wrote:
>
>> Ira,
>>
>> There is a known issue with resolving tool dependencies when running functional tests. One workaround is to set the GALAXY_TOOL_DEPENDENCY_DIR environment variable to the path configured in your universe_wsgi.ini.
>>
>> This issue is documented in https://trello.com/c/eVT3QWJF
>>
>>    --Dave B.
>>
>> On 5/8/13 20:08:08.000, Ira Cooke wrote:
>>> Hi All,
>>>
>>> I'm starting to add functional tests to my tools but I've found that I can't get the test framework to work well with tool dependencies.
>>>
>>> The tool I'm considering is xtandem
>>>
>>> http://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem
>>>
>>> When I install this tool on my local galaxy instance (on a clean install) the tool runs fine and if I look in the handler logs I see
>>>
>>> executing: PACKAGE_BASE=/home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab/env.sh; PACKAGE_BASE=/home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab/env.sh; rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /home/iracooke/galaxy-central/database/files/000/dataset_1.dat   --var-mods=' 57.021464__at__C '   --fix-mods=' 15.994915__at__M '   /home/iracooke/galaxy-central/database/files/000/dataset_2.dat -o /home/iracooke/galaxy-central/database/files/000/dataset_4.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
>>> galaxy.jobs DEBUG 2013-04-27 06:53:35,586 (4) Persisting job destination (destination id: local:///)
>>>
>>>
>>> Note that in this case the tool environments from my tool dependencies are loaded ... and the tool runs fine.
>>>
>>> When running functional tests however the tests are executed without first loading the environments from tool dependencies ... and naturally the tool fails.  On my local machine I get the following when running the tests (Note that no loading of dependency shel environments occurs).  (This seems to be the same issue on the testtoolshed.g2.bx.psu.edu ).
>>>
>>> Job dispatched
>>> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,564 (3) executing: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat   --var-mods=' 15.994915__at__M , '   --fix-mods=' 57.021464__at__C '   /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
>>> galaxy.jobs DEBUG 2013-04-27 06:55:19,730 (3) Persisting job destination (destination id: local:///)
>>> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,889 execution finished: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat   --var-mods=' 15.994915__at__M ,'   --fix-mods=' 57.021464__at__C '   /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
>>> ...
>>> galaxy.jobs DEBUG 2013-04-27 06:55:24,277 setting dataset state to ERROR
>>>
>>>
>>> Is there something wrong with the way I've defined my tool dependencies for this tool?  Or perhaps it's a bug in the testing framework.
>>>
>>> Cheers
>>> Ira
>>>
>>>
>>>
>>>
>>>
>>>
>>> ___________________________________________________________
>>> 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/
>>>
>>> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: Problems running functional tests

iracooke
Oops ... I should have thought of that

Thanks .. it works now.

Ira


On 04/06/2013, at 11:20 PM, Dave Bouvier <[hidden email]> wrote:

> Ira,
>
> Yes, I should have mentioned that due to the way functional tests are executed, an environment variable needs to be explicitly exported before the functional test framework will recognize it. The syntax is very nearly the same:
>
> export GALAXY_TOOL_DEPENDENCY_DIR=/home/iracooke/tool_dependencies ; sh run_functional_tests.sh -installed
>
>   --Dave B.
>
> On 6/3/13 00:25:53.000, Ira Cooke wrote:
>> Hi Dave,
>>
>> Just following up on this (now quite a bit later sorry).
>>
>> I can't seem to get things to work using your suggested workaround.
>>
>> Using a fresh checkout of galaxy-central 9931:716f29e4c77d
>>
>> I run
>>
>> GALAXY_TOOL_DEPENDENCY_DIR=/home/iracooke/tool_dependencies sh run_functional_tests.sh -installed
>>
>> In my universe_wsgi.ini I have
>>
>> tool_dependency_dir = /home/iracooke/tool_dependencies
>>
>> When running tests I find that the dependencies fail to be resolved (ie ... I get errors like the following).
>>
>> galaxy.jobs.handler INFO 2013-04-28 11:01:17,955 (3) Job dispatched
>> galaxy.tools DEBUG 2013-04-28 11:01:18,594 Building dependency shell command for dependency 'galaxy_protk'
>> galaxy.tools WARNING 2013-04-28 11:01:18,595 Failed to resolve dependency on 'galaxy_protk', ignoring
>> galaxy.tools DEBUG 2013-04-28 11:01:18,596 Building dependency shell command for dependency 'trans_proteomic_pipeline'
>> galaxy.tools WARNING 2013-04-28 11:01:18,596 Failed to resolve dependency on 'trans_proteomic_pipeline', ignoring
>>
>>
>> When I run the tool myself (ie from galaxy ui not from the test script) it resolves the dependencies just fine.
>>
>> Any idea what am I doing wrong?
>>
>> Thanks
>>
>> Ira
>>
>>
>>
>> On 10/05/2013, at 12:10 AM, Dave Bouvier <[hidden email]> wrote:
>>
>>> Ira,
>>>
>>> There is a known issue with resolving tool dependencies when running functional tests. One workaround is to set the GALAXY_TOOL_DEPENDENCY_DIR environment variable to the path configured in your universe_wsgi.ini.
>>>
>>> This issue is documented in https://trello.com/c/eVT3QWJF
>>>
>>>   --Dave B.
>>>
>>> On 5/8/13 20:08:08.000, Ira Cooke wrote:
>>>> Hi All,
>>>>
>>>> I'm starting to add functional tests to my tools but I've found that I can't get the test framework to work well with tool dependencies.
>>>>
>>>> The tool I'm considering is xtandem
>>>>
>>>> http://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem
>>>>
>>>> When I install this tool on my local galaxy instance (on a clean install) the tool runs fine and if I look in the handler logs I see
>>>>
>>>> executing: PACKAGE_BASE=/home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab/env.sh; PACKAGE_BASE=/home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab/env.sh; rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /home/iracooke/galaxy-central/database/files/000/dataset_1.dat   --var-mods=' 57.021464__at__C '   --fix-mods=' 15.994915__at__M '   /home/iracooke/galaxy-central/database/files/000/dataset_2.dat -o /home/iracooke/galaxy-central/database/files/000/dataset_4.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
>>>> galaxy.jobs DEBUG 2013-04-27 06:53:35,586 (4) Persisting job destination (destination id: local:///)
>>>>
>>>>
>>>> Note that in this case the tool environments from my tool dependencies are loaded ... and the tool runs fine.
>>>>
>>>> When running functional tests however the tests are executed without first loading the environments from tool dependencies ... and naturally the tool fails.  On my local machine I get the following when running the tests (Note that no loading of dependency shel environments occurs).  (This seems to be the same issue on the testtoolshed.g2.bx.psu.edu ).
>>>>
>>>> Job dispatched
>>>> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,564 (3) executing: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat   --var-mods=' 15.994915__at__M , '   --fix-mods=' 57.021464__at__C '   /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
>>>> galaxy.jobs DEBUG 2013-04-27 06:55:19,730 (3) Persisting job destination (destination id: local:///)
>>>> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,889 execution finished: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat   --var-mods=' 15.994915__at__M ,'   --fix-mods=' 57.021464__at__C '   /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
>>>> ...
>>>> galaxy.jobs DEBUG 2013-04-27 06:55:24,277 setting dataset state to ERROR
>>>>
>>>>
>>>> Is there something wrong with the way I've defined my tool dependencies for this tool?  Or perhaps it's a bug in the testing framework.
>>>>
>>>> Cheers
>>>> Ira
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ___________________________________________________________
>>>> 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/
>>>>
>>>> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
| Threaded
Open this post in threaded view
|

Re: Problems running functional tests

Björn Grüning
Hi Ira,

is it still working for you?

I installed one repository in a fresh installation and executed:

export
GALAXY_TOOL_DEPENDENCY_DIR=/home/bag/projects/galaxy/galaxy-central/tool_deps/ ; sh run_functional_tests.sh -installed

It failed with:
Failed to resolve dependency on 'SCRIPT_PATH', ignoring

Any ideas?
Bjoern



> Oops ... I should have thought of that
>
> Thanks .. it works now.
>
> Ira
>
>
> On 04/06/2013, at 11:20 PM, Dave Bouvier <[hidden email]> wrote:
>
> > Ira,
> >
> > Yes, I should have mentioned that due to the way functional tests are executed, an environment variable needs to be explicitly exported before the functional test framework will recognize it. The syntax is very nearly the same:
> >
> > export GALAXY_TOOL_DEPENDENCY_DIR=/home/iracooke/tool_dependencies ; sh run_functional_tests.sh -installed
> >
> >   --Dave B.
> >
> > On 6/3/13 00:25:53.000, Ira Cooke wrote:
> >> Hi Dave,
> >>
> >> Just following up on this (now quite a bit later sorry).
> >>
> >> I can't seem to get things to work using your suggested workaround.
> >>
> >> Using a fresh checkout of galaxy-central 9931:716f29e4c77d
> >>
> >> I run
> >>
> >> GALAXY_TOOL_DEPENDENCY_DIR=/home/iracooke/tool_dependencies sh run_functional_tests.sh -installed
> >>
> >> In my universe_wsgi.ini I have
> >>
> >> tool_dependency_dir = /home/iracooke/tool_dependencies
> >>
> >> When running tests I find that the dependencies fail to be resolved (ie ... I get errors like the following).
> >>
> >> galaxy.jobs.handler INFO 2013-04-28 11:01:17,955 (3) Job dispatched
> >> galaxy.tools DEBUG 2013-04-28 11:01:18,594 Building dependency shell command for dependency 'galaxy_protk'
> >> galaxy.tools WARNING 2013-04-28 11:01:18,595 Failed to resolve dependency on 'galaxy_protk', ignoring
> >> galaxy.tools DEBUG 2013-04-28 11:01:18,596 Building dependency shell command for dependency 'trans_proteomic_pipeline'
> >> galaxy.tools WARNING 2013-04-28 11:01:18,596 Failed to resolve dependency on 'trans_proteomic_pipeline', ignoring
> >>
> >>
> >> When I run the tool myself (ie from galaxy ui not from the test script) it resolves the dependencies just fine.
> >>
> >> Any idea what am I doing wrong?
> >>
> >> Thanks
> >>
> >> Ira
> >>
> >>
> >>
> >> On 10/05/2013, at 12:10 AM, Dave Bouvier <[hidden email]> wrote:
> >>
> >>> Ira,
> >>>
> >>> There is a known issue with resolving tool dependencies when running functional tests. One workaround is to set the GALAXY_TOOL_DEPENDENCY_DIR environment variable to the path configured in your universe_wsgi.ini.
> >>>
> >>> This issue is documented in https://trello.com/c/eVT3QWJF
> >>>
> >>>   --Dave B.
> >>>
> >>> On 5/8/13 20:08:08.000, Ira Cooke wrote:
> >>>> Hi All,
> >>>>
> >>>> I'm starting to add functional tests to my tools but I've found that I can't get the test framework to work well with tool dependencies.
> >>>>
> >>>> The tool I'm considering is xtandem
> >>>>
> >>>> http://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem
> >>>>
> >>>> When I install this tool on my local galaxy instance (on a clean install) the tool runs fine and if I look in the handler logs I see
> >>>>
> >>>> executing: PACKAGE_BASE=/home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab/env.sh; PACKAGE_BASE=/home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab/env.sh; rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /home/iracooke/galaxy-central/database/files/000/dataset_1.dat   --var-mods=' 57.021464__at__C '   --fix-mods=' 15.994915__at__M '   /home/iracooke/galaxy-central/database/files/000/dataset_2.dat -o /home/iracooke/galaxy-central/database/files/000/dataset_4.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
> >>>> galaxy.jobs DEBUG 2013-04-27 06:53:35,586 (4) Persisting job destination (destination id: local:///)
> >>>>
> >>>>
> >>>> Note that in this case the tool environments from my tool dependencies are loaded ... and the tool runs fine.
> >>>>
> >>>> When running functional tests however the tests are executed without first loading the environments from tool dependencies ... and naturally the tool fails.  On my local machine I get the following when running the tests (Note that no loading of dependency shel environments occurs).  (This seems to be the same issue on the testtoolshed.g2.bx.psu.edu ).
> >>>>
> >>>> Job dispatched
> >>>> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,564 (3) executing: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat   --var-mods=' 15.994915__at__M , '   --fix-mods=' 57.021464__at__C '   /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
> >>>> galaxy.jobs DEBUG 2013-04-27 06:55:19,730 (3) Persisting job destination (destination id: local:///)
> >>>> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,889 execution finished: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat   --var-mods=' 15.994915__at__M ,'   --fix-mods=' 57.021464__at__C '   /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files
> >>>> ...
> >>>> galaxy.jobs DEBUG 2013-04-27 06:55:24,277 setting dataset state to ERROR
> >>>>
> >>>>
> >>>> Is there something wrong with the way I've defined my tool dependencies for this tool?  Or perhaps it's a bug in the testing framework.
> >>>>
> >>>> Cheers
> >>>> Ira
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> ___________________________________________________________
> >>>> 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/
> >>>>
> >>>> 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:
>   http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/