How galaxy workflow work ?

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How galaxy workflow work ?

shenwiyn
Hi ,
As we know galaxy tools work with the python,perl,and other tools script in galaxy-dist/tools,but are there any workflow scripts will be created when we edit or import it to run and where they saved? Are there some details about how galaxy workflow work? Thank you very much.


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Re: How galaxy workflow work ?

Peter Cock
Galaxy workflows are stored in the database, but can be exported
in JSON format (intended for importing into another Galaxy server).

Peter

On Wed, Dec 3, 2014 at 3:38 PM, Weiyan Shen <[hidden email]> wrote:

> Hi ,
> As we know galaxy tools work with the python,perl,and other tools script in
> galaxy-dist/tools,but are there any workflow scripts will be created when we
> edit or import it to run and where they saved? Are there some details about
> how galaxy workflow work? Thank you very much.
>
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: How galaxy workflow work ?

Bongsoo Park

Hi All,

I faced a problem after I tested the Bio-Blend API. I cannot access the history anymore with the below error messages. Although, I tried installation from the scratch, but I got the same error message. Please let me know how to fix this problem. Thanks! 

(GALAXY User Interface)

=======================================================

  "xhr": {

    "readyState": 4,

    "responseText": "{\"err_msg\": \"Uncaught exception in exposed API method:\", \"err_code\": 0}",

    "responseJSON": {

      "err_msg": "Uncaught exception in exposed API method:",

      "err_code": 0

    },

    "status": 500,

    "statusText": "Internal Server Error",

    "responseHeaders": {

      "Date": "Wed, 03 Dec 2014 15:50:02 GMT\r",

      "cache-control": "max-age=0,no-cache,no-store\r",

      "Server": "PasteWSGIServer/0.5 Python/2.7.8\r",

      "Connection": "close\r",

      "content-type": "application/json\r"

    }

=======================================================

I found the error message in the Galaxy instance shell interface.

=======================================================

galaxy.web.framework.decorators ERROR 2014-12-03 10:50:02,279 Uncaught exception in exposed API method:

Traceback (most recent call last):

  File "/home/bxp12/galaxy-dist/lib/galaxy/web/framework/decorators.py", line 244, in decorator

    rval = func( self, trans, *args, **kwargs)

  File "/home/bxp12/galaxy-ist/lib/galaxy/webapps/galaxy/api/history_contents.py", line 76, in index

    and ( history_id == trans.security.encode_id( trans.history.id ) ) ):

AttributeError: 'NoneType' object has no attribute 'id'

=======================================================

Best,

Bongsoo


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Re: How galaxy workflow work ?

John Chilton-4
Somehow your user object is not being set. Are you sure you have
initialized bioblend with the correct API key? Do other operations
work with that key?

-John

On Wed, Dec 3, 2014 at 11:00 AM, Bongsoo Park <[hidden email]> wrote:

> Hi All,
>
> I faced a problem after I tested the Bio-Blend API. I cannot access the
> history anymore with the below error messages. Although, I tried
> installation from the scratch, but I got the same error message. Please let
> me know how to fix this problem. Thanks!
>
> (GALAXY User Interface)
>
> =======================================================
>
>   "xhr": {
>
>     "readyState": 4,
>
>     "responseText": "{\"err_msg\": \"Uncaught exception in exposed API
> method:\", \"err_code\": 0}",
>
>     "responseJSON": {
>
>       "err_msg": "Uncaught exception in exposed API method:",
>
>       "err_code": 0
>
>     },
>
>     "status": 500,
>
>     "statusText": "Internal Server Error",
>
>     "responseHeaders": {
>
>       "Date": "Wed, 03 Dec 2014 15:50:02 GMT\r",
>
>       "cache-control": "max-age=0,no-cache,no-store\r",
>
>       "Server": "PasteWSGIServer/0.5 Python/2.7.8\r",
>
>       "Connection": "close\r",
>
>       "content-type": "application/json\r"
>
>     }
>
> =======================================================
>
> I found the error message in the Galaxy instance shell interface.
>
> =======================================================
>
> galaxy.web.framework.decorators ERROR 2014-12-03 10:50:02,279 Uncaught
> exception in exposed API method:
>
> Traceback (most recent call last):
>
>   File "/home/bxp12/galaxy-dist/lib/galaxy/web/framework/decorators.py",
> line 244, in decorator
>
>     rval = func( self, trans, *args, **kwargs)
>
>   File
> "/home/bxp12/galaxy-ist/lib/galaxy/webapps/galaxy/api/history_contents.py",
> line 76, in index
>
>     and ( history_id == trans.security.encode_id( trans.history.id ) ) ):
>
> AttributeError: 'NoneType' object has no attribute 'id'
>
> =======================================================
>
> Best,
>
> Bongsoo
>
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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[Spam:*****] Re: How galaxy workflow work ?

Freek de Bruijn-2
In reply to this post by shenwiyn
I am also having problems using the Galaxy API, with a similar error message to the one reported by Bongsoo Park a few weeks ago (Uncaught exception in exposed API method). We noticed it a few days ago and have not found the cause yet. What we do know:
- the problem occurs on several Galaxy servers, including the main instance at https://usegalaxy.org/;
- the problem seems to occur whilte using BioBlend, blend4j, and api Python scripts;
- even some of the blend4j unit tests are failing.

One of my colleagues noticed a lot of changes in for example workflows.py (in lib/galaxy/webapps/galaxy/api): https://bitbucket.org/galaxy/galaxy-dist/annotate/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb/lib/galaxy/webapps/galaxy/api/workflows.py#cl-117

Did something change in the Galaxy API? Should we adjust the libraries and the programs that use them?

Cheers, Freek


________________________________________
From: galaxy-dev [[hidden email]] on behalf of [hidden email] [[hidden email]]
Sent: Tuesday, December 16, 2014 18:00
To: [hidden email]
Subject: galaxy-dev Digest, Vol 102, Issue 17

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Today's Topics:

   1. Re: How galaxy workflow work ? (John Chilton)
   2. Re: Metadata error in uploading files to data libraries
      (John Chilton)
   3. Re: package_numpy_1_7 can't be installed (Wang, Yu)
   4. Re: "join" produces an import error (Wang, Yu)
   5. Re: package_numpy_1_7 can't be installed (Björn Grüning)


----------------------------------------------------------------------

Message: 1
Date: Mon, 15 Dec 2014 14:24:13 -0500
From: John Chilton <[hidden email]>
To: Bongsoo Park <[hidden email]>
Cc: galaxy-dev <[hidden email]>
Subject: Re: [galaxy-dev] How galaxy workflow work ?
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset=UTF-8

Somehow your user object is not being set. Are you sure you have
initialized bioblend with the correct API key? Do other operations
work with that key?

-John

On Wed, Dec 3, 2014 at 11:00 AM, Bongsoo Park <[hidden email]> wrote:

> Hi All,
>
> I faced a problem after I tested the Bio-Blend API. I cannot access the
> history anymore with the below error messages. Although, I tried
> installation from the scratch, but I got the same error message. Please let
> me know how to fix this problem. Thanks!
>
> (GALAXY User Interface)
>
> =======================================================
>
>   "xhr": {
>
>     "readyState": 4,
>
>     "responseText": "{\"err_msg\": \"Uncaught exception in exposed API
> method:\", \"err_code\": 0}",
>
>     "responseJSON": {
>
>       "err_msg": "Uncaught exception in exposed API method:",
>
>       "err_code": 0
>
>     },
>
>     "status": 500,
>
>     "statusText": "Internal Server Error",
>
>     "responseHeaders": {
>
>       "Date": "Wed, 03 Dec 2014 15:50:02 GMT\r",
>
>       "cache-control": "max-age=0,no-cache,no-store\r",
>
>       "Server": "PasteWSGIServer/0.5 Python/2.7.8\r",
>
>       "Connection": "close\r",
>
>       "content-type": "application/json\r"
>
>     }
>
> =======================================================
>
> I found the error message in the Galaxy instance shell interface.
>
> =======================================================
>
> galaxy.web.framework.decorators ERROR 2014-12-03 10:50:02,279 Uncaught
> exception in exposed API method:
>
> Traceback (most recent call last):
>
>   File "/home/bxp12/galaxy-dist/lib/galaxy/web/framework/decorators.py",
> line 244, in decorator
>
>     rval = func( self, trans, *args, **kwargs)
>
>   File
> "/home/bxp12/galaxy-ist/lib/galaxy/webapps/galaxy/api/history_contents.py",
> line 76, in index
>
>     and ( history_id == trans.security.encode_id( trans.history.id ) ) ):
>
> AttributeError: 'NoneType' object has no attribute 'id'
>
> =======================================================
>
> Best,
>
> Bongsoo
>
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/


------------------------------

Message: 2
Date: Mon, 15 Dec 2014 14:31:20 -0500
From: John Chilton <[hidden email]>
To: Jelle Scholtalbers <[hidden email]>
Cc: galaxy-dev <[hidden email]>
Subject: Re: [galaxy-dev] Metadata error in uploading files to data
        libraries
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset=UTF-8

Hello,

  Sorry we haven't made progress on this - and thanks for creating a
Trello card (https://trello.com/c/tw75nq1U).

  It looks like samtools is not on your path, can you use it from the
command-line? If not you should probably install it - I would suggest
install samtools 0.1.19 with homebrew (looks like you are a on Mac).
If you can run samtools from the command-line - can you do a which
`samtools` from your command-line and see where it is coming from and
then add that directory explicitly to your Galaxy PATH - say at the
top of run.sh in your Galaxy root (let me know if you need more
details on that).

-John

On Tue, Dec 9, 2014 at 3:02 AM, Jelle Scholtalbers
<[hidden email]> wrote:

> Hi all,
>
> after an update to the following changeset(14859:7ba05957588a, stable,
> 05.12.14), our bam files that are uploaded(linked) to a data library, are no
> longer indexed. The metadata_xxx.dat is created, but it stays empty.
> The following error message appears in the log, although the state of the
> dataset is 'ok':
>
> galaxy.jobs WARNING 2014-12-05 12:47:02,218 Error accessing /g/K/K27.bam,
> will retry: [Errno 1] Operation not permitted: '/g/K/K27.bam'
> galaxy.jobs WARNING 2014-12-08 13:38:57,045 Error accessing /g/K/K2.bam,
> will retry: [Errno 1] Operation not permitted: '/g/K/K2.bam'
>
> All file permissions are correct (i.e. galaxy owns them). Furthermore,
> executing samtools index, just works on those files:
> samtools index /g/K/K2.bam
> /g/galaxy/galaxy_data/files/_metadata_files/006/metadata_6598.dat
>
> When uploading the file - "copy files into galaxy" - the samtools index just
> works.
>
> ==============
>
> Now, on a clean local install(14874:885f940bff64, stable, 05.12.14) and
> samtools installed globally and with the bam file sorted, I get the
> following situation:
> When I try to upload this bam to a data library by linking the following
> error is shown on the dataset (note: here the dataset is set in error state,
> which does not happen on our server)
>
> Uploaded by: [hidden email]
> Date uploaded: Mon Dec 8 17:42:39 2014 (UTC)
> File size: 2.6 GB
> UUID: d23cf11a-0372-41cb-939a-7c8761d78b73
> Data type: auto
> Build: ?
> Miscellaneous information: Traceback (most recent call last): File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 407, in __main__() File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 396, in _
> Job Standard Error
>
> Traceback (most recent call last):
>   File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 407, in
>     __main__()
>   File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 396, in __main__
>     add_file( dataset, registry, json_file, output_path )
>   File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 294, in add_file
>     if datatype.dataset_content_needs_grooming( dataset.path ):
>   File
> "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
> line 147, in dataset_content_needs_grooming
>     version = self._get_samtools_version()
>   File
> "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
> line 129, in _get_samtools_version
>     output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
> stdout=subprocess.PIPE ).communicate()[1]
>   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
> line 711, in __init__
>     errread, errwrite)
>   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
> line 1308, in _execute_child
>     raise child_exception
> OSError: [Errno 2] No such file or directory
>
> error
> Database/Build: ?
> Number of data lines: None
> Disk file: /Users/scholtalbers/workspace/idr_data/WT1.sort.bam
>
> ===============================
> When uploading the bam without linking, I see the following processes:
> Upload->set meta->samtools index->'error state'
>
>  Miscellaneous information: uploaded bam file Traceback (most recent call
> last): File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 407, in __main__() File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.p
> Job Standard Error
>
> Traceback (most recent call last):
>   File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 407, in
>     __main__()
>   File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 396, in __main__
>     add_file( dataset, registry, json_file, output_path )
>   File
> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
> line 324, in add_file
>     if link_data_only == 'copy_files' and
> datatype.dataset_content_needs_grooming( output_path ):
>   File
> "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
> line 147, in dataset_content_needs_grooming
>     version = self._get_samtools_version()
>   File
> "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
> line 129, in _get_samtools_version
>     output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
> stdout=subprocess.PIPE ).communicate()[1]
>   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
> line 711, in __init__
>     errread, errwrite)
>   File
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
> line 1308, in _execute_child
>     raise child_exception
> OSError: [Errno 2] No such file or directory
>
> error
> Database/Build: ?
> Number of data lines: None
> Disk file:
> /Users/scholtalbers/workspace/galaxy-dist-new/database/files/000/dataset_6.dat
>
> =================================
>
> Although the error messages are different, it might be related?
>
> Cheers,
>
> Jelle
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/


------------------------------

Message: 3
Date: Mon, 15 Dec 2014 17:16:41 +0000
From: "Wang, Yu" <[hidden email]>
To: John Chilton <[hidden email]>
Cc: "Wang, Yu" <[hidden email]>, "[hidden email]"
        <[hidden email]>
Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="utf-8"

Hi, John,thanks for your answer. I installed svnversion, and compiled/installed ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not found.
I could install package_numpy_1_9 by using galaxy main tool shed. There is something wrong with package_numpy_1_7 on my environment.

Cheers,
Yu

di29her
[hidden email]<mailto:[hidden email]>

On 15 Dec 2014, at 16:12, John Chilton <[hidden email]<mailto:[hidden email]>> wrote:

Looks like this - https://github.com/clarete/curdling/issues/19

I think you somehow need to install the package svn on your machine - if you have root on that machine the command might be something like "sudo zypper install svn" or may it is "sudo zypper install subversion". If you don't have root on the machine I would ask the operating system maintainer or try to compile and install svn locally and make it available to Galaxy.

Hope this helps,

-John

On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu <[hidden email]<mailto:[hidden email]>> wrote:
Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I got the following error.
Can anyone point what goes wrong here?


Error   Running from numpy source directory.
/bin/sh: svnversion: command not found
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494: UserWarning:
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  warnings.warn(AtlasNotFoundError.__doc__)
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503: UserWarning:
    Blas (http://www.netlib.org/blas/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [blas]) or by setting
    the BLAS environment variable.
  warnings.warn(BlasNotFoundError.__doc__)
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506: UserWarning:
    Blas (http://www.netlib.org/blas/) sources not found.
    Directories to search for the sources can be specified in the
    numpy/distutils/site.cfg file (section [blas_src]) or by setting
    the BLAS_SRC environment variable.
  warnings.warn(BlasSrcNotFoundError.__doc__)
/bin/sh: svnversion: command not found
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408: UserWarning:
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  warnings.warn(AtlasNotFoundError.__doc__)
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419: UserWarning:
    Lapack (http://www.netlib.org/lapack/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [lapack]) or by setting
    the LAPACK environment variable.
  warnings.warn(LapackNotFoundError.__doc__)
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1422: UserWarning:
    Lapack (http://www.netlib.org/lapack/) sources not found.
    Directories to search for the sources can be specified in the
    numpy/distutils/site.cfg file (section [lapack_src]) or by setting
    the LAPACK_SRC environment variable.
  warnings.warn(LapackSrcNotFoundError.__doc__)
error: must supply either home or prefix/exec-prefix -- not both


Cheers,
Yu

di29her
[hidden email]<mailto:[hidden email]>




___________________________________________________________
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------------------------------

Message: 4
Date: Mon, 15 Dec 2014 17:20:07 +0000
From: "Wang, Yu" <[hidden email]>
To: Peter Cock <[hidden email]>
Cc: "Wang, Yu" <[hidden email]>, "[hidden email]"
        <[hidden email]>
Subject: Re: [galaxy-dev] "join" produces an import error
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="utf-8"

Hi, Peter, thanks for your answer. I found that package_numpy_1_7 can’t be installed by galaxy on my environment. Although I have installed ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not found.


Cheers,
Yu

di29her
[hidden email]<mailto:[hidden email]>

On 11 Dec 2014, at 17:24, Peter Cock <[hidden email]<mailto:[hidden email]>> wrote:

On Wed, Dec 10, 2014 at 4:31 PM, Wang, Yu <[hidden email]<mailto:[hidden email]>> wrote:
Hi, I am testing Basic Protocol 1 on my local galaxy instance. But Join
didn't work. What did I do wrong?
I installed join from galaxy main tool shed, bx_python_0_7 was installed but
with installation Status "missing tool dependencies".

...
Traceback (most recent call last):
File
"/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_join.py<http://toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_join.py>",
line 13, in <module>
  from bx.intervals import *
ImportError: No module named bx.intervals

It looks like the automated installation of bx python failed somehow.

Looking at the package, it will attempt to install NumPy 1.7.1
https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7

Galaxy dev team, why isn't this declaring a dependency on:
https://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7

Peter

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------------------------------

Message: 5
Date: Tue, 16 Dec 2014 11:08:03 +0100
From: Björn Grüning <[hidden email]>
To: "Wang, Yu" <[hidden email]>
Cc: "[hidden email]"
        <[hidden email]>
Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed
Message-ID: <[hidden email]>
Content-Type: text/plain; charset=utf-8

Hi,

Am 16.12.2014 um 10:39 schrieb Wang, Yu:
> Hi, Björn, my intention was to test a simple workflow (BASIC PROTOCOL 1 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418382/) on my local galaxy installation.
> By default, “join” function is not installed on galaxy. When I tried to install “join”, it reported error on the installation of bx_python_0_7 (Galaxy main tool shed).
> It looks like the automated installation of bx python failed somehow.
> Looking at the package, it will attempt to install NumPy 1.7.1
> https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7

I see, thanks for the information.
Unfortunately, this is a different package from what I was talking. Have
you compiled ATLAS or installed it with your package manager? Are you
running a Linux or OS-X.

The problem is that Galaxy tries to install:

pip install numpy

And this crashes because you don't have all requirements installed. If
possible try to install LAPACK and ATLAS with your package manager, you
need to set a lot of ENV variables if you compile it yourself.

Cheers,
Bjoern


> Then I tried to install NumPy 1.7.1 from Galaxy main tool shed, there were all these errors from LAPACK and ATLAS.
>
> Cheers,
> Yu
>
> di29her
> [hidden email]<mailto:[hidden email]>
>
> On 16 Dec 2014, at 04:07, Björn Grüning <[hidden email]<mailto:[hidden email]>> wrote:
>
> Hi Wang,
>
> can you point me to the exact version your try to install. There is an
> old numpy_1_7 package which should be deprecated. We had a lot of
> trouble installing ATLAS and LAPACK and decided to deprecate all
> packages which depends on LAPACK and ATLAS. Now we do not require both
> libraries anymore.
>
> Thanks,
> Bjoern
>
> Am 15.12.2014 um 18:16 schrieb Wang, Yu:
> Hi, John,thanks for your answer. I installed svnversion, and compiled/installed ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not found.
> I could install package_numpy_1_9 by using galaxy main tool shed. There is something wrong with package_numpy_1_7 on my environment.
>
> Cheers,
> Yu
>
> di29her
> [hidden email]<mailto:[hidden email]><mailto:[hidden email]>
>
> On 15 Dec 2014, at 16:12, John Chilton <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote:
>
> Looks like this - https://github.com/clarete/curdling/issues/19
>
> I think you somehow need to install the package svn on your machine - if you have root on that machine the command might be something like "sudo zypper install svn" or may it is "sudo zypper install subversion". If you don't have root on the machine I would ask the operating system maintainer or try to compile and install svn locally and make it available to Galaxy.
>
> Hope this helps,
>
> -John
>
> On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote:
> Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I got the following error.
> Can anyone point what goes wrong here?
>
>
> Error   Running from numpy source directory.
> /bin/sh: svnversion: command not found
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494: UserWarning:
>    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
>    Directories to search for the libraries can be specified in the
>    numpy/distutils/site.cfg file (section [atlas]) or by setting
>    the ATLAS environment variable.
>  warnings.warn(AtlasNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503: UserWarning:
>    Blas (http://www.netlib.org/blas/) libraries not found.
>    Directories to search for the libraries can be specified in the
>    numpy/distutils/site.cfg file (section [blas]) or by setting
>    the BLAS environment variable.
>  warnings.warn(BlasNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506: UserWarning:
>    Blas (http://www.netlib.org/blas/) sources not found.
>    Directories to search for the sources can be specified in the
>    numpy/distutils/site.cfg file (section [blas_src]) or by setting
>    the BLAS_SRC environment variable.
>  warnings.warn(BlasSrcNotFoundError.__doc__)
> /bin/sh: svnversion: command not found
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408: UserWarning:
>    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
>    Directories to search for the libraries can be specified in the
>    numpy/distutils/site.cfg file (section [atlas]) or by setting
>    the ATLAS environment variable.
>  warnings.warn(AtlasNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419: UserWarning:
>    Lapack (http://www.netlib.org/lapack/) libraries not found.
>    Directories to search for the libraries can be specified in the
>    numpy/distutils/site.cfg file (section [lapack]) or by setting
>    the LAPACK environment variable.
>  warnings.warn(LapackNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1422: UserWarning:
>    Lapack (http://www.netlib.org/lapack/) sources not found.
>    Directories to search for the sources can be specified in the
>    numpy/distutils/site.cfg file (section [lapack_src]) or by setting
>    the LAPACK_SRC environment variable.
>  warnings.warn(LapackSrcNotFoundError.__doc__)
> error: must supply either home or prefix/exec-prefix -- not both
>
>
> Cheers,
> Yu
>
> di29her
> [hidden email]<mailto:[hidden email]><mailto:[hidden email]>
>
>
>
>
> ___________________________________________________________
> 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:
>  https://lists.galaxyproject.org/
>
> 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:
>  https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/
>
>


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Re: [Spam:*****] Re: How galaxy workflow work ?

John Chilton-4
There have been a ton of changes to the workflow API - I have been
trying to preserve backward compatibility though - e.g. I have API
tests in Galaxy for a bunch of legacy/deprecated features related to
workflows now.

Do you have a stack trace on the Galaxy side for the "Uncaught
exception in exposed API method"?

I will run through the blend4j test cases and see they turn up.

-John

On Thu, Dec 18, 2014 at 9:44 AM, Bruijn, Freek de <[hidden email]> wrote:

> I am also having problems using the Galaxy API, with a similar error message to the one reported by Bongsoo Park a few weeks ago (Uncaught exception in exposed API method). We noticed it a few days ago and have not found the cause yet. What we do know:
> - the problem occurs on several Galaxy servers, including the main instance at https://usegalaxy.org/;
> - the problem seems to occur whilte using BioBlend, blend4j, and api Python scripts;
> - even some of the blend4j unit tests are failing.
>
> One of my colleagues noticed a lot of changes in for example workflows.py (in lib/galaxy/webapps/galaxy/api): https://bitbucket.org/galaxy/galaxy-dist/annotate/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb/lib/galaxy/webapps/galaxy/api/workflows.py#cl-117
>
> Did something change in the Galaxy API? Should we adjust the libraries and the programs that use them?
>
> Cheers, Freek
>
>
> ________________________________________
> From: galaxy-dev [[hidden email]] on behalf of [hidden email] [[hidden email]]
> Sent: Tuesday, December 16, 2014 18:00
> To: [hidden email]
> Subject: galaxy-dev Digest, Vol 102, Issue 17
>
> Send galaxy-dev mailing list submissions to
>         [hidden email]
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://lists.galaxyproject.org/listinfo/galaxy-dev
> or, via email, send a message with subject or body 'help' to
>         [hidden email]
>
> You can reach the person managing the list at
>         [hidden email]
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of galaxy-dev digest..."
>
>
> HEY!  This is important!  If you reply to a thread in a digest, please
> 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread.
> 2. Strip out everything else in the digest that is not part of the thread you are responding to.
>
> Why?
> 1. This will keep the subject meaningful.  People will have some idea from the subject line if they should read it or not.
> 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative.
>
> Today's Topics:
>
>    1. Re: How galaxy workflow work ? (John Chilton)
>    2. Re: Metadata error in uploading files to data libraries
>       (John Chilton)
>    3. Re: package_numpy_1_7 can't be installed (Wang, Yu)
>    4. Re: "join" produces an import error (Wang, Yu)
>    5. Re: package_numpy_1_7 can't be installed (Björn Grüning)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 15 Dec 2014 14:24:13 -0500
> From: John Chilton <[hidden email]>
> To: Bongsoo Park <[hidden email]>
> Cc: galaxy-dev <[hidden email]>
> Subject: Re: [galaxy-dev] How galaxy workflow work ?
> Message-ID:
>         <[hidden email]>
> Content-Type: text/plain; charset=UTF-8
>
> Somehow your user object is not being set. Are you sure you have
> initialized bioblend with the correct API key? Do other operations
> work with that key?
>
> -John
>
> On Wed, Dec 3, 2014 at 11:00 AM, Bongsoo Park <[hidden email]> wrote:
>> Hi All,
>>
>> I faced a problem after I tested the Bio-Blend API. I cannot access the
>> history anymore with the below error messages. Although, I tried
>> installation from the scratch, but I got the same error message. Please let
>> me know how to fix this problem. Thanks!
>>
>> (GALAXY User Interface)
>>
>> =======================================================
>>
>>   "xhr": {
>>
>>     "readyState": 4,
>>
>>     "responseText": "{\"err_msg\": \"Uncaught exception in exposed API
>> method:\", \"err_code\": 0}",
>>
>>     "responseJSON": {
>>
>>       "err_msg": "Uncaught exception in exposed API method:",
>>
>>       "err_code": 0
>>
>>     },
>>
>>     "status": 500,
>>
>>     "statusText": "Internal Server Error",
>>
>>     "responseHeaders": {
>>
>>       "Date": "Wed, 03 Dec 2014 15:50:02 GMT\r",
>>
>>       "cache-control": "max-age=0,no-cache,no-store\r",
>>
>>       "Server": "PasteWSGIServer/0.5 Python/2.7.8\r",
>>
>>       "Connection": "close\r",
>>
>>       "content-type": "application/json\r"
>>
>>     }
>>
>> =======================================================
>>
>> I found the error message in the Galaxy instance shell interface.
>>
>> =======================================================
>>
>> galaxy.web.framework.decorators ERROR 2014-12-03 10:50:02,279 Uncaught
>> exception in exposed API method:
>>
>> Traceback (most recent call last):
>>
>>   File "/home/bxp12/galaxy-dist/lib/galaxy/web/framework/decorators.py",
>> line 244, in decorator
>>
>>     rval = func( self, trans, *args, **kwargs)
>>
>>   File
>> "/home/bxp12/galaxy-ist/lib/galaxy/webapps/galaxy/api/history_contents.py",
>> line 76, in index
>>
>>     and ( history_id == trans.security.encode_id( trans.history.id ) ) ):
>>
>> AttributeError: 'NoneType' object has no attribute 'id'
>>
>> =======================================================
>>
>> Best,
>>
>> Bongsoo
>>
>>
>> ___________________________________________________________
>> 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:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 15 Dec 2014 14:31:20 -0500
> From: John Chilton <[hidden email]>
> To: Jelle Scholtalbers <[hidden email]>
> Cc: galaxy-dev <[hidden email]>
> Subject: Re: [galaxy-dev] Metadata error in uploading files to data
>         libraries
> Message-ID:
>         <[hidden email]>
> Content-Type: text/plain; charset=UTF-8
>
> Hello,
>
>   Sorry we haven't made progress on this - and thanks for creating a
> Trello card (https://trello.com/c/tw75nq1U).
>
>   It looks like samtools is not on your path, can you use it from the
> command-line? If not you should probably install it - I would suggest
> install samtools 0.1.19 with homebrew (looks like you are a on Mac).
> If you can run samtools from the command-line - can you do a which
> `samtools` from your command-line and see where it is coming from and
> then add that directory explicitly to your Galaxy PATH - say at the
> top of run.sh in your Galaxy root (let me know if you need more
> details on that).
>
> -John
>
> On Tue, Dec 9, 2014 at 3:02 AM, Jelle Scholtalbers
> <[hidden email]> wrote:
>> Hi all,
>>
>> after an update to the following changeset(14859:7ba05957588a, stable,
>> 05.12.14), our bam files that are uploaded(linked) to a data library, are no
>> longer indexed. The metadata_xxx.dat is created, but it stays empty.
>> The following error message appears in the log, although the state of the
>> dataset is 'ok':
>>
>> galaxy.jobs WARNING 2014-12-05 12:47:02,218 Error accessing /g/K/K27.bam,
>> will retry: [Errno 1] Operation not permitted: '/g/K/K27.bam'
>> galaxy.jobs WARNING 2014-12-08 13:38:57,045 Error accessing /g/K/K2.bam,
>> will retry: [Errno 1] Operation not permitted: '/g/K/K2.bam'
>>
>> All file permissions are correct (i.e. galaxy owns them). Furthermore,
>> executing samtools index, just works on those files:
>> samtools index /g/K/K2.bam
>> /g/galaxy/galaxy_data/files/_metadata_files/006/metadata_6598.dat
>>
>> When uploading the file - "copy files into galaxy" - the samtools index just
>> works.
>>
>> ==============
>>
>> Now, on a clean local install(14874:885f940bff64, stable, 05.12.14) and
>> samtools installed globally and with the bam file sorted, I get the
>> following situation:
>> When I try to upload this bam to a data library by linking the following
>> error is shown on the dataset (note: here the dataset is set in error state,
>> which does not happen on our server)
>>
>> Uploaded by: [hidden email]
>> Date uploaded: Mon Dec 8 17:42:39 2014 (UTC)
>> File size: 2.6 GB
>> UUID: d23cf11a-0372-41cb-939a-7c8761d78b73
>> Data type: auto
>> Build: ?
>> Miscellaneous information: Traceback (most recent call last): File
>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>> line 407, in __main__() File
>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>> line 396, in _
>> Job Standard Error
>>
>> Traceback (most recent call last):
>>   File
>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>> line 407, in
>>     __main__()
>>   File
>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>> line 396, in __main__
>>     add_file( dataset, registry, json_file, output_path )
>>   File
>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>> line 294, in add_file
>>     if datatype.dataset_content_needs_grooming( dataset.path ):
>>   File
>> "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
>> line 147, in dataset_content_needs_grooming
>>     version = self._get_samtools_version()
>>   File
>> "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
>> line 129, in _get_samtools_version
>>     output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
>> stdout=subprocess.PIPE ).communicate()[1]
>>   File
>> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
>> line 711, in __init__
>>     errread, errwrite)
>>   File
>> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
>> line 1308, in _execute_child
>>     raise child_exception
>> OSError: [Errno 2] No such file or directory
>>
>> error
>> Database/Build: ?
>> Number of data lines: None
>> Disk file: /Users/scholtalbers/workspace/idr_data/WT1.sort.bam
>>
>> ===============================
>> When uploading the bam without linking, I see the following processes:
>> Upload->set meta->samtools index->'error state'
>>
>>  Miscellaneous information: uploaded bam file Traceback (most recent call
>> last): File
>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>> line 407, in __main__() File
>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.p
>> Job Standard Error
>>
>> Traceback (most recent call last):
>>   File
>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>> line 407, in
>>     __main__()
>>   File
>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>> line 396, in __main__
>>     add_file( dataset, registry, json_file, output_path )
>>   File
>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>> line 324, in add_file
>>     if link_data_only == 'copy_files' and
>> datatype.dataset_content_needs_grooming( output_path ):
>>   File
>> "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
>> line 147, in dataset_content_needs_grooming
>>     version = self._get_samtools_version()
>>   File
>> "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
>> line 129, in _get_samtools_version
>>     output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
>> stdout=subprocess.PIPE ).communicate()[1]
>>   File
>> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
>> line 711, in __init__
>>     errread, errwrite)
>>   File
>> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
>> line 1308, in _execute_child
>>     raise child_exception
>> OSError: [Errno 2] No such file or directory
>>
>> error
>> Database/Build: ?
>> Number of data lines: None
>> Disk file:
>> /Users/scholtalbers/workspace/galaxy-dist-new/database/files/000/dataset_6.dat
>>
>> =================================
>>
>> Although the error messages are different, it might be related?
>>
>> Cheers,
>>
>> Jelle
>>
>> ___________________________________________________________
>> 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:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 15 Dec 2014 17:16:41 +0000
> From: "Wang, Yu" <[hidden email]>
> To: John Chilton <[hidden email]>
> Cc: "Wang, Yu" <[hidden email]>, "[hidden email]"
>         <[hidden email]>
> Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed
> Message-ID:
>         <[hidden email]>
> Content-Type: text/plain; charset="utf-8"
>
> Hi, John,thanks for your answer. I installed svnversion, and compiled/installed ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not found.
> I could install package_numpy_1_9 by using galaxy main tool shed. There is something wrong with package_numpy_1_7 on my environment.
>
> Cheers,
> Yu
>
> di29her
> [hidden email]<mailto:[hidden email]>
>
> On 15 Dec 2014, at 16:12, John Chilton <[hidden email]<mailto:[hidden email]>> wrote:
>
> Looks like this - https://github.com/clarete/curdling/issues/19
>
> I think you somehow need to install the package svn on your machine - if you have root on that machine the command might be something like "sudo zypper install svn" or may it is "sudo zypper install subversion". If you don't have root on the machine I would ask the operating system maintainer or try to compile and install svn locally and make it available to Galaxy.
>
> Hope this helps,
>
> -John
>
> On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu <[hidden email]<mailto:[hidden email]>> wrote:
> Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I got the following error.
> Can anyone point what goes wrong here?
>
>
> Error   Running from numpy source directory.
> /bin/sh: svnversion: command not found
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494: UserWarning:
>     Atlas (http://math-atlas.sourceforge.net/) libraries not found.
>     Directories to search for the libraries can be specified in the
>     numpy/distutils/site.cfg file (section [atlas]) or by setting
>     the ATLAS environment variable.
>   warnings.warn(AtlasNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503: UserWarning:
>     Blas (http://www.netlib.org/blas/) libraries not found.
>     Directories to search for the libraries can be specified in the
>     numpy/distutils/site.cfg file (section [blas]) or by setting
>     the BLAS environment variable.
>   warnings.warn(BlasNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506: UserWarning:
>     Blas (http://www.netlib.org/blas/) sources not found.
>     Directories to search for the sources can be specified in the
>     numpy/distutils/site.cfg file (section [blas_src]) or by setting
>     the BLAS_SRC environment variable.
>   warnings.warn(BlasSrcNotFoundError.__doc__)
> /bin/sh: svnversion: command not found
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408: UserWarning:
>     Atlas (http://math-atlas.sourceforge.net/) libraries not found.
>     Directories to search for the libraries can be specified in the
>     numpy/distutils/site.cfg file (section [atlas]) or by setting
>     the ATLAS environment variable.
>   warnings.warn(AtlasNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419: UserWarning:
>     Lapack (http://www.netlib.org/lapack/) libraries not found.
>     Directories to search for the libraries can be specified in the
>     numpy/distutils/site.cfg file (section [lapack]) or by setting
>     the LAPACK environment variable.
>   warnings.warn(LapackNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1422: UserWarning:
>     Lapack (http://www.netlib.org/lapack/) sources not found.
>     Directories to search for the sources can be specified in the
>     numpy/distutils/site.cfg file (section [lapack_src]) or by setting
>     the LAPACK_SRC environment variable.
>   warnings.warn(LapackSrcNotFoundError.__doc__)
> error: must supply either home or prefix/exec-prefix -- not both
>
>
> Cheers,
> Yu
>
> di29her
> [hidden email]<mailto:[hidden email]>
>
>
>
>
> ___________________________________________________________
> 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:
>   https://lists.galaxyproject.org/
>
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>   http://galaxyproject.org/search/mailinglists/
>
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>
> ------------------------------
>
> Message: 4
> Date: Mon, 15 Dec 2014 17:20:07 +0000
> From: "Wang, Yu" <[hidden email]>
> To: Peter Cock <[hidden email]>
> Cc: "Wang, Yu" <[hidden email]>, "[hidden email]"
>         <[hidden email]>
> Subject: Re: [galaxy-dev] "join" produces an import error
> Message-ID:
>         <[hidden email]>
> Content-Type: text/plain; charset="utf-8"
>
> Hi, Peter, thanks for your answer. I found that package_numpy_1_7 can’t be installed by galaxy on my environment. Although I have installed ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not found.
>
>
> Cheers,
> Yu
>
> di29her
> [hidden email]<mailto:[hidden email]>
>
> On 11 Dec 2014, at 17:24, Peter Cock <[hidden email]<mailto:[hidden email]>> wrote:
>
> On Wed, Dec 10, 2014 at 4:31 PM, Wang, Yu <[hidden email]<mailto:[hidden email]>> wrote:
> Hi, I am testing Basic Protocol 1 on my local galaxy instance. But Join
> didn't work. What did I do wrong?
> I installed join from galaxy main tool shed, bx_python_0_7 was installed but
> with installation Status "missing tool dependencies".
>
> ...
> Traceback (most recent call last):
> File
> "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_join.py<http://toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_join.py>",
> line 13, in <module>
>   from bx.intervals import *
> ImportError: No module named bx.intervals
>
> It looks like the automated installation of bx python failed somehow.
>
> Looking at the package, it will attempt to install NumPy 1.7.1
> https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7
>
> Galaxy dev team, why isn't this declaring a dependency on:
> https://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7
>
> Peter
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
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>
> ------------------------------
>
> Message: 5
> Date: Tue, 16 Dec 2014 11:08:03 +0100
> From: Björn Grüning <[hidden email]>
> To: "Wang, Yu" <[hidden email]>
> Cc: "[hidden email]"
>         <[hidden email]>
> Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset=utf-8
>
> Hi,
>
> Am 16.12.2014 um 10:39 schrieb Wang, Yu:
>> Hi, Björn, my intention was to test a simple workflow (BASIC PROTOCOL 1 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418382/) on my local galaxy installation.
>> By default, “join” function is not installed on galaxy. When I tried to install “join”, it reported error on the installation of bx_python_0_7 (Galaxy main tool shed).
>> It looks like the automated installation of bx python failed somehow.
>> Looking at the package, it will attempt to install NumPy 1.7.1
>> https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7
>
> I see, thanks for the information.
> Unfortunately, this is a different package from what I was talking. Have
> you compiled ATLAS or installed it with your package manager? Are you
> running a Linux or OS-X.
>
> The problem is that Galaxy tries to install:
>
> pip install numpy
>
> And this crashes because you don't have all requirements installed. If
> possible try to install LAPACK and ATLAS with your package manager, you
> need to set a lot of ENV variables if you compile it yourself.
>
> Cheers,
> Bjoern
>
>
>> Then I tried to install NumPy 1.7.1 from Galaxy main tool shed, there were all these errors from LAPACK and ATLAS.
>>
>> Cheers,
>> Yu
>>
>> di29her
>> [hidden email]<mailto:[hidden email]>
>>
>> On 16 Dec 2014, at 04:07, Björn Grüning <[hidden email]<mailto:[hidden email]>> wrote:
>>
>> Hi Wang,
>>
>> can you point me to the exact version your try to install. There is an
>> old numpy_1_7 package which should be deprecated. We had a lot of
>> trouble installing ATLAS and LAPACK and decided to deprecate all
>> packages which depends on LAPACK and ATLAS. Now we do not require both
>> libraries anymore.
>>
>> Thanks,
>> Bjoern
>>
>> Am 15.12.2014 um 18:16 schrieb Wang, Yu:
>> Hi, John,thanks for your answer. I installed svnversion, and compiled/installed ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not found.
>> I could install package_numpy_1_9 by using galaxy main tool shed. There is something wrong with package_numpy_1_7 on my environment.
>>
>> Cheers,
>> Yu
>>
>> di29her
>> [hidden email]<mailto:[hidden email]><mailto:[hidden email]>
>>
>> On 15 Dec 2014, at 16:12, John Chilton <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote:
>>
>> Looks like this - https://github.com/clarete/curdling/issues/19
>>
>> I think you somehow need to install the package svn on your machine - if you have root on that machine the command might be something like "sudo zypper install svn" or may it is "sudo zypper install subversion". If you don't have root on the machine I would ask the operating system maintainer or try to compile and install svn locally and make it available to Galaxy.
>>
>> Hope this helps,
>>
>> -John
>>
>> On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote:
>> Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I got the following error.
>> Can anyone point what goes wrong here?
>>
>>
>> Error   Running from numpy source directory.
>> /bin/sh: svnversion: command not found
>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494: UserWarning:
>>    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
>>    Directories to search for the libraries can be specified in the
>>    numpy/distutils/site.cfg file (section [atlas]) or by setting
>>    the ATLAS environment variable.
>>  warnings.warn(AtlasNotFoundError.__doc__)
>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503: UserWarning:
>>    Blas (http://www.netlib.org/blas/) libraries not found.
>>    Directories to search for the libraries can be specified in the
>>    numpy/distutils/site.cfg file (section [blas]) or by setting
>>    the BLAS environment variable.
>>  warnings.warn(BlasNotFoundError.__doc__)
>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506: UserWarning:
>>    Blas (http://www.netlib.org/blas/) sources not found.
>>    Directories to search for the sources can be specified in the
>>    numpy/distutils/site.cfg file (section [blas_src]) or by setting
>>    the BLAS_SRC environment variable.
>>  warnings.warn(BlasSrcNotFoundError.__doc__)
>> /bin/sh: svnversion: command not found
>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408: UserWarning:
>>    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
>>    Directories to search for the libraries can be specified in the
>>    numpy/distutils/site.cfg file (section [atlas]) or by setting
>>    the ATLAS environment variable.
>>  warnings.warn(AtlasNotFoundError.__doc__)
>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419: UserWarning:
>>    Lapack (http://www.netlib.org/lapack/) libraries not found.
>>    Directories to search for the libraries can be specified in the
>>    numpy/distutils/site.cfg file (section [lapack]) or by setting
>>    the LAPACK environment variable.
>>  warnings.warn(LapackNotFoundError.__doc__)
>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1422: UserWarning:
>>    Lapack (http://www.netlib.org/lapack/) sources not found.
>>    Directories to search for the sources can be specified in the
>>    numpy/distutils/site.cfg file (section [lapack_src]) or by setting
>>    the LAPACK_SRC environment variable.
>>  warnings.warn(LapackSrcNotFoundError.__doc__)
>> error: must supply either home or prefix/exec-prefix -- not both
>>
>>
>> Cheers,
>> Yu
>>
>> di29her
>> [hidden email]<mailto:[hidden email]><mailto:[hidden email]>
>>
>>
>>
>>
>> ___________________________________________________________
>> 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:
>>  https://lists.galaxyproject.org/
>>
>> 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:
>>  https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>  http://galaxyproject.org/search/mailinglists/
>>
>>
>
>
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> Please keep all replies on the list by using "reply all"
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Re: [Spam:*****] Re: How galaxy workflow work ?

John Chilton-4
There was definitely a bug where I broke backward compatibility on
workflows in central a couple nights ago - I have patched that and
blend4j's test cases for running workflows now actually cause the
workflows to run again.

There are still some problems with blend4j where it is very particular
about what is in the response - these are blend4j specific issues that
I will try to clear up - I have created a github issue here:

https://github.com/jmchilton/blend4j/issues/26

Sorry about the problems.

-John


On Thu, Dec 18, 2014 at 9:59 AM, John Chilton <[hidden email]> wrote:

> There have been a ton of changes to the workflow API - I have been
> trying to preserve backward compatibility though - e.g. I have API
> tests in Galaxy for a bunch of legacy/deprecated features related to
> workflows now.
>
> Do you have a stack trace on the Galaxy side for the "Uncaught
> exception in exposed API method"?
>
> I will run through the blend4j test cases and see they turn up.
>
> -John
>
> On Thu, Dec 18, 2014 at 9:44 AM, Bruijn, Freek de <[hidden email]> wrote:
>> I am also having problems using the Galaxy API, with a similar error message to the one reported by Bongsoo Park a few weeks ago (Uncaught exception in exposed API method). We noticed it a few days ago and have not found the cause yet. What we do know:
>> - the problem occurs on several Galaxy servers, including the main instance at https://usegalaxy.org/;
>> - the problem seems to occur whilte using BioBlend, blend4j, and api Python scripts;
>> - even some of the blend4j unit tests are failing.
>>
>> One of my colleagues noticed a lot of changes in for example workflows.py (in lib/galaxy/webapps/galaxy/api): https://bitbucket.org/galaxy/galaxy-dist/annotate/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb/lib/galaxy/webapps/galaxy/api/workflows.py#cl-117
>>
>> Did something change in the Galaxy API? Should we adjust the libraries and the programs that use them?
>>
>> Cheers, Freek
>>
>>
>> ________________________________________
>> From: galaxy-dev [[hidden email]] on behalf of [hidden email] [[hidden email]]
>> Sent: Tuesday, December 16, 2014 18:00
>> To: [hidden email]
>> Subject: galaxy-dev Digest, Vol 102, Issue 17
>>
>> Send galaxy-dev mailing list submissions to
>>         [hidden email]
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>>         https://lists.galaxyproject.org/listinfo/galaxy-dev
>> or, via email, send a message with subject or body 'help' to
>>         [hidden email]
>>
>> You can reach the person managing the list at
>>         [hidden email]
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of galaxy-dev digest..."
>>
>>
>> HEY!  This is important!  If you reply to a thread in a digest, please
>> 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread.
>> 2. Strip out everything else in the digest that is not part of the thread you are responding to.
>>
>> Why?
>> 1. This will keep the subject meaningful.  People will have some idea from the subject line if they should read it or not.
>> 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative.
>>
>> Today's Topics:
>>
>>    1. Re: How galaxy workflow work ? (John Chilton)
>>    2. Re: Metadata error in uploading files to data libraries
>>       (John Chilton)
>>    3. Re: package_numpy_1_7 can't be installed (Wang, Yu)
>>    4. Re: "join" produces an import error (Wang, Yu)
>>    5. Re: package_numpy_1_7 can't be installed (Björn Grüning)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 15 Dec 2014 14:24:13 -0500
>> From: John Chilton <[hidden email]>
>> To: Bongsoo Park <[hidden email]>
>> Cc: galaxy-dev <[hidden email]>
>> Subject: Re: [galaxy-dev] How galaxy workflow work ?
>> Message-ID:
>>         <[hidden email]>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Somehow your user object is not being set. Are you sure you have
>> initialized bioblend with the correct API key? Do other operations
>> work with that key?
>>
>> -John
>>
>> On Wed, Dec 3, 2014 at 11:00 AM, Bongsoo Park <[hidden email]> wrote:
>>> Hi All,
>>>
>>> I faced a problem after I tested the Bio-Blend API. I cannot access the
>>> history anymore with the below error messages. Although, I tried
>>> installation from the scratch, but I got the same error message. Please let
>>> me know how to fix this problem. Thanks!
>>>
>>> (GALAXY User Interface)
>>>
>>> =======================================================
>>>
>>>   "xhr": {
>>>
>>>     "readyState": 4,
>>>
>>>     "responseText": "{\"err_msg\": \"Uncaught exception in exposed API
>>> method:\", \"err_code\": 0}",
>>>
>>>     "responseJSON": {
>>>
>>>       "err_msg": "Uncaught exception in exposed API method:",
>>>
>>>       "err_code": 0
>>>
>>>     },
>>>
>>>     "status": 500,
>>>
>>>     "statusText": "Internal Server Error",
>>>
>>>     "responseHeaders": {
>>>
>>>       "Date": "Wed, 03 Dec 2014 15:50:02 GMT\r",
>>>
>>>       "cache-control": "max-age=0,no-cache,no-store\r",
>>>
>>>       "Server": "PasteWSGIServer/0.5 Python/2.7.8\r",
>>>
>>>       "Connection": "close\r",
>>>
>>>       "content-type": "application/json\r"
>>>
>>>     }
>>>
>>> =======================================================
>>>
>>> I found the error message in the Galaxy instance shell interface.
>>>
>>> =======================================================
>>>
>>> galaxy.web.framework.decorators ERROR 2014-12-03 10:50:02,279 Uncaught
>>> exception in exposed API method:
>>>
>>> Traceback (most recent call last):
>>>
>>>   File "/home/bxp12/galaxy-dist/lib/galaxy/web/framework/decorators.py",
>>> line 244, in decorator
>>>
>>>     rval = func( self, trans, *args, **kwargs)
>>>
>>>   File
>>> "/home/bxp12/galaxy-ist/lib/galaxy/webapps/galaxy/api/history_contents.py",
>>> line 76, in index
>>>
>>>     and ( history_id == trans.security.encode_id( trans.history.id ) ) ):
>>>
>>> AttributeError: 'NoneType' object has no attribute 'id'
>>>
>>> =======================================================
>>>
>>> Best,
>>>
>>> Bongsoo
>>>
>>>
>>> ___________________________________________________________
>>> 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:
>>>   https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/mailinglists/
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Mon, 15 Dec 2014 14:31:20 -0500
>> From: John Chilton <[hidden email]>
>> To: Jelle Scholtalbers <[hidden email]>
>> Cc: galaxy-dev <[hidden email]>
>> Subject: Re: [galaxy-dev] Metadata error in uploading files to data
>>         libraries
>> Message-ID:
>>         <[hidden email]>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Hello,
>>
>>   Sorry we haven't made progress on this - and thanks for creating a
>> Trello card (https://trello.com/c/tw75nq1U).
>>
>>   It looks like samtools is not on your path, can you use it from the
>> command-line? If not you should probably install it - I would suggest
>> install samtools 0.1.19 with homebrew (looks like you are a on Mac).
>> If you can run samtools from the command-line - can you do a which
>> `samtools` from your command-line and see where it is coming from and
>> then add that directory explicitly to your Galaxy PATH - say at the
>> top of run.sh in your Galaxy root (let me know if you need more
>> details on that).
>>
>> -John
>>
>> On Tue, Dec 9, 2014 at 3:02 AM, Jelle Scholtalbers
>> <[hidden email]> wrote:
>>> Hi all,
>>>
>>> after an update to the following changeset(14859:7ba05957588a, stable,
>>> 05.12.14), our bam files that are uploaded(linked) to a data library, are no
>>> longer indexed. The metadata_xxx.dat is created, but it stays empty.
>>> The following error message appears in the log, although the state of the
>>> dataset is 'ok':
>>>
>>> galaxy.jobs WARNING 2014-12-05 12:47:02,218 Error accessing /g/K/K27.bam,
>>> will retry: [Errno 1] Operation not permitted: '/g/K/K27.bam'
>>> galaxy.jobs WARNING 2014-12-08 13:38:57,045 Error accessing /g/K/K2.bam,
>>> will retry: [Errno 1] Operation not permitted: '/g/K/K2.bam'
>>>
>>> All file permissions are correct (i.e. galaxy owns them). Furthermore,
>>> executing samtools index, just works on those files:
>>> samtools index /g/K/K2.bam
>>> /g/galaxy/galaxy_data/files/_metadata_files/006/metadata_6598.dat
>>>
>>> When uploading the file - "copy files into galaxy" - the samtools index just
>>> works.
>>>
>>> ==============
>>>
>>> Now, on a clean local install(14874:885f940bff64, stable, 05.12.14) and
>>> samtools installed globally and with the bam file sorted, I get the
>>> following situation:
>>> When I try to upload this bam to a data library by linking the following
>>> error is shown on the dataset (note: here the dataset is set in error state,
>>> which does not happen on our server)
>>>
>>> Uploaded by: [hidden email]
>>> Date uploaded: Mon Dec 8 17:42:39 2014 (UTC)
>>> File size: 2.6 GB
>>> UUID: d23cf11a-0372-41cb-939a-7c8761d78b73
>>> Data type: auto
>>> Build: ?
>>> Miscellaneous information: Traceback (most recent call last): File
>>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>>> line 407, in __main__() File
>>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>>> line 396, in _
>>> Job Standard Error
>>>
>>> Traceback (most recent call last):
>>>   File
>>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>>> line 407, in
>>>     __main__()
>>>   File
>>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>>> line 396, in __main__
>>>     add_file( dataset, registry, json_file, output_path )
>>>   File
>>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>>> line 294, in add_file
>>>     if datatype.dataset_content_needs_grooming( dataset.path ):
>>>   File
>>> "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
>>> line 147, in dataset_content_needs_grooming
>>>     version = self._get_samtools_version()
>>>   File
>>> "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
>>> line 129, in _get_samtools_version
>>>     output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
>>> stdout=subprocess.PIPE ).communicate()[1]
>>>   File
>>> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
>>> line 711, in __init__
>>>     errread, errwrite)
>>>   File
>>> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
>>> line 1308, in _execute_child
>>>     raise child_exception
>>> OSError: [Errno 2] No such file or directory
>>>
>>> error
>>> Database/Build: ?
>>> Number of data lines: None
>>> Disk file: /Users/scholtalbers/workspace/idr_data/WT1.sort.bam
>>>
>>> ===============================
>>> When uploading the bam without linking, I see the following processes:
>>> Upload->set meta->samtools index->'error state'
>>>
>>>  Miscellaneous information: uploaded bam file Traceback (most recent call
>>> last): File
>>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>>> line 407, in __main__() File
>>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.p
>>> Job Standard Error
>>>
>>> Traceback (most recent call last):
>>>   File
>>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>>> line 407, in
>>>     __main__()
>>>   File
>>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>>> line 396, in __main__
>>>     add_file( dataset, registry, json_file, output_path )
>>>   File
>>> "/Users/scholtalbers/workspace/galaxy-dist-new/tools/data_source/upload.py",
>>> line 324, in add_file
>>>     if link_data_only == 'copy_files' and
>>> datatype.dataset_content_needs_grooming( output_path ):
>>>   File
>>> "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
>>> line 147, in dataset_content_needs_grooming
>>>     version = self._get_samtools_version()
>>>   File
>>> "/Users/scholtalbers/workspace/galaxy-dist-new/lib/galaxy/datatypes/binary.py",
>>> line 129, in _get_samtools_version
>>>     output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
>>> stdout=subprocess.PIPE ).communicate()[1]
>>>   File
>>> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
>>> line 711, in __init__
>>>     errread, errwrite)
>>>   File
>>> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
>>> line 1308, in _execute_child
>>>     raise child_exception
>>> OSError: [Errno 2] No such file or directory
>>>
>>> error
>>> Database/Build: ?
>>> Number of data lines: None
>>> Disk file:
>>> /Users/scholtalbers/workspace/galaxy-dist-new/database/files/000/dataset_6.dat
>>>
>>> =================================
>>>
>>> Although the error messages are different, it might be related?
>>>
>>> Cheers,
>>>
>>> Jelle
>>>
>>> ___________________________________________________________
>>> 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:
>>>   https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/mailinglists/
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Mon, 15 Dec 2014 17:16:41 +0000
>> From: "Wang, Yu" <[hidden email]>
>> To: John Chilton <[hidden email]>
>> Cc: "Wang, Yu" <[hidden email]>, "[hidden email]"
>>         <[hidden email]>
>> Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed
>> Message-ID:
>>         <[hidden email]>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi, John,thanks for your answer. I installed svnversion, and compiled/installed ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not found.
>> I could install package_numpy_1_9 by using galaxy main tool shed. There is something wrong with package_numpy_1_7 on my environment.
>>
>> Cheers,
>> Yu
>>
>> di29her
>> [hidden email]<mailto:[hidden email]>
>>
>> On 15 Dec 2014, at 16:12, John Chilton <[hidden email]<mailto:[hidden email]>> wrote:
>>
>> Looks like this - https://github.com/clarete/curdling/issues/19
>>
>> I think you somehow need to install the package svn on your machine - if you have root on that machine the command might be something like "sudo zypper install svn" or may it is "sudo zypper install subversion". If you don't have root on the machine I would ask the operating system maintainer or try to compile and install svn locally and make it available to Galaxy.
>>
>> Hope this helps,
>>
>> -John
>>
>> On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu <[hidden email]<mailto:[hidden email]>> wrote:
>> Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I got the following error.
>> Can anyone point what goes wrong here?
>>
>>
>> Error   Running from numpy source directory.
>> /bin/sh: svnversion: command not found
>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494: UserWarning:
>>     Atlas (http://math-atlas.sourceforge.net/) libraries not found.
>>     Directories to search for the libraries can be specified in the
>>     numpy/distutils/site.cfg file (section [atlas]) or by setting
>>     the ATLAS environment variable.
>>   warnings.warn(AtlasNotFoundError.__doc__)
>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503: UserWarning:
>>     Blas (http://www.netlib.org/blas/) libraries not found.
>>     Directories to search for the libraries can be specified in the
>>     numpy/distutils/site.cfg file (section [blas]) or by setting
>>     the BLAS environment variable.
>>   warnings.warn(BlasNotFoundError.__doc__)
>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506: UserWarning:
>>     Blas (http://www.netlib.org/blas/) sources not found.
>>     Directories to search for the sources can be specified in the
>>     numpy/distutils/site.cfg file (section [blas_src]) or by setting
>>     the BLAS_SRC environment variable.
>>   warnings.warn(BlasSrcNotFoundError.__doc__)
>> /bin/sh: svnversion: command not found
>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408: UserWarning:
>>     Atlas (http://math-atlas.sourceforge.net/) libraries not found.
>>     Directories to search for the libraries can be specified in the
>>     numpy/distutils/site.cfg file (section [atlas]) or by setting
>>     the ATLAS environment variable.
>>   warnings.warn(AtlasNotFoundError.__doc__)
>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419: UserWarning:
>>     Lapack (http://www.netlib.org/lapack/) libraries not found.
>>     Directories to search for the libraries can be specified in the
>>     numpy/distutils/site.cfg file (section [lapack]) or by setting
>>     the LAPACK environment variable.
>>   warnings.warn(LapackNotFoundError.__doc__)
>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1422: UserWarning:
>>     Lapack (http://www.netlib.org/lapack/) sources not found.
>>     Directories to search for the sources can be specified in the
>>     numpy/distutils/site.cfg file (section [lapack_src]) or by setting
>>     the LAPACK_SRC environment variable.
>>   warnings.warn(LapackSrcNotFoundError.__doc__)
>> error: must supply either home or prefix/exec-prefix -- not both
>>
>>
>> Cheers,
>> Yu
>>
>> di29her
>> [hidden email]<mailto:[hidden email]>
>>
>>
>>
>>
>> ___________________________________________________________
>> 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:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20141215/0071cfef/attachment-0001.html>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Mon, 15 Dec 2014 17:20:07 +0000
>> From: "Wang, Yu" <[hidden email]>
>> To: Peter Cock <[hidden email]>
>> Cc: "Wang, Yu" <[hidden email]>, "[hidden email]"
>>         <[hidden email]>
>> Subject: Re: [galaxy-dev] "join" produces an import error
>> Message-ID:
>>         <[hidden email]>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi, Peter, thanks for your answer. I found that package_numpy_1_7 can’t be installed by galaxy on my environment. Although I have installed ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not found.
>>
>>
>> Cheers,
>> Yu
>>
>> di29her
>> [hidden email]<mailto:[hidden email]>
>>
>> On 11 Dec 2014, at 17:24, Peter Cock <[hidden email]<mailto:[hidden email]>> wrote:
>>
>> On Wed, Dec 10, 2014 at 4:31 PM, Wang, Yu <[hidden email]<mailto:[hidden email]>> wrote:
>> Hi, I am testing Basic Protocol 1 on my local galaxy instance. But Join
>> didn't work. What did I do wrong?
>> I installed join from galaxy main tool shed, bx_python_0_7 was installed but
>> with installation Status "missing tool dependencies".
>>
>> ...
>> Traceback (most recent call last):
>> File
>> "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_join.py<http://toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_join.py>",
>> line 13, in <module>
>>   from bx.intervals import *
>> ImportError: No module named bx.intervals
>>
>> It looks like the automated installation of bx python failed somehow.
>>
>> Looking at the package, it will attempt to install NumPy 1.7.1
>> https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7
>>
>> Galaxy dev team, why isn't this declaring a dependency on:
>> https://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7
>>
>> Peter
>>
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20141215/2fae439b/attachment-0001.html>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Tue, 16 Dec 2014 11:08:03 +0100
>> From: Björn Grüning <[hidden email]>
>> To: "Wang, Yu" <[hidden email]>
>> Cc: "[hidden email]"
>>         <[hidden email]>
>> Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed
>> Message-ID: <[hidden email]>
>> Content-Type: text/plain; charset=utf-8
>>
>> Hi,
>>
>> Am 16.12.2014 um 10:39 schrieb Wang, Yu:
>>> Hi, Björn, my intention was to test a simple workflow (BASIC PROTOCOL 1 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418382/) on my local galaxy installation.
>>> By default, “join” function is not installed on galaxy. When I tried to install “join”, it reported error on the installation of bx_python_0_7 (Galaxy main tool shed).
>>> It looks like the automated installation of bx python failed somehow.
>>> Looking at the package, it will attempt to install NumPy 1.7.1
>>> https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7
>>
>> I see, thanks for the information.
>> Unfortunately, this is a different package from what I was talking. Have
>> you compiled ATLAS or installed it with your package manager? Are you
>> running a Linux or OS-X.
>>
>> The problem is that Galaxy tries to install:
>>
>> pip install numpy
>>
>> And this crashes because you don't have all requirements installed. If
>> possible try to install LAPACK and ATLAS with your package manager, you
>> need to set a lot of ENV variables if you compile it yourself.
>>
>> Cheers,
>> Bjoern
>>
>>
>>> Then I tried to install NumPy 1.7.1 from Galaxy main tool shed, there were all these errors from LAPACK and ATLAS.
>>>
>>> Cheers,
>>> Yu
>>>
>>> di29her
>>> [hidden email]<mailto:[hidden email]>
>>>
>>> On 16 Dec 2014, at 04:07, Björn Grüning <[hidden email]<mailto:[hidden email]>> wrote:
>>>
>>> Hi Wang,
>>>
>>> can you point me to the exact version your try to install. There is an
>>> old numpy_1_7 package which should be deprecated. We had a lot of
>>> trouble installing ATLAS and LAPACK and decided to deprecate all
>>> packages which depends on LAPACK and ATLAS. Now we do not require both
>>> libraries anymore.
>>>
>>> Thanks,
>>> Bjoern
>>>
>>> Am 15.12.2014 um 18:16 schrieb Wang, Yu:
>>> Hi, John,thanks for your answer. I installed svnversion, and compiled/installed ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not found.
>>> I could install package_numpy_1_9 by using galaxy main tool shed. There is something wrong with package_numpy_1_7 on my environment.
>>>
>>> Cheers,
>>> Yu
>>>
>>> di29her
>>> [hidden email]<mailto:[hidden email]><mailto:[hidden email]>
>>>
>>> On 15 Dec 2014, at 16:12, John Chilton <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote:
>>>
>>> Looks like this - https://github.com/clarete/curdling/issues/19
>>>
>>> I think you somehow need to install the package svn on your machine - if you have root on that machine the command might be something like "sudo zypper install svn" or may it is "sudo zypper install subversion". If you don't have root on the machine I would ask the operating system maintainer or try to compile and install svn locally and make it available to Galaxy.
>>>
>>> Hope this helps,
>>>
>>> -John
>>>
>>> On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote:
>>> Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I got the following error.
>>> Can anyone point what goes wrong here?
>>>
>>>
>>> Error   Running from numpy source directory.
>>> /bin/sh: svnversion: command not found
>>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494: UserWarning:
>>>    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
>>>    Directories to search for the libraries can be specified in the
>>>    numpy/distutils/site.cfg file (section [atlas]) or by setting
>>>    the ATLAS environment variable.
>>>  warnings.warn(AtlasNotFoundError.__doc__)
>>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503: UserWarning:
>>>    Blas (http://www.netlib.org/blas/) libraries not found.
>>>    Directories to search for the libraries can be specified in the
>>>    numpy/distutils/site.cfg file (section [blas]) or by setting
>>>    the BLAS environment variable.
>>>  warnings.warn(BlasNotFoundError.__doc__)
>>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506: UserWarning:
>>>    Blas (http://www.netlib.org/blas/) sources not found.
>>>    Directories to search for the sources can be specified in the
>>>    numpy/distutils/site.cfg file (section [blas_src]) or by setting
>>>    the BLAS_SRC environment variable.
>>>  warnings.warn(BlasSrcNotFoundError.__doc__)
>>> /bin/sh: svnversion: command not found
>>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408: UserWarning:
>>>    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
>>>    Directories to search for the libraries can be specified in the
>>>    numpy/distutils/site.cfg file (section [atlas]) or by setting
>>>    the ATLAS environment variable.
>>>  warnings.warn(AtlasNotFoundError.__doc__)
>>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419: UserWarning:
>>>    Lapack (http://www.netlib.org/lapack/) libraries not found.
>>>    Directories to search for the libraries can be specified in the
>>>    numpy/distutils/site.cfg file (section [lapack]) or by setting
>>>    the LAPACK environment variable.
>>>  warnings.warn(LapackNotFoundError.__doc__)
>>> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1422: UserWarning:
>>>    Lapack (http://www.netlib.org/lapack/) sources not found.
>>>    Directories to search for the sources can be specified in the
>>>    numpy/distutils/site.cfg file (section [lapack_src]) or by setting
>>>    the LAPACK_SRC environment variable.
>>>  warnings.warn(LapackSrcNotFoundError.__doc__)
>>> error: must supply either home or prefix/exec-prefix -- not both
>>>
>>>
>>> Cheers,
>>> Yu
>>>
>>> di29her
>>> [hidden email]<mailto:[hidden email]><mailto:[hidden email]>
>>>
>>>
>>>
>>>
>>> ___________________________________________________________
>>> 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:
>>>  https://lists.galaxyproject.org/
>>>
>>> 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:
>>>  https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>  http://galaxyproject.org/search/mailinglists/
>>>
>>>
>>
>>
>> ------------------------------
>>
>> Subject: Digest Footer
>>
>> _______________________________________________
>> galaxy-dev mailing list
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>> https://lists.galaxyproject.org/listinfo/galaxy-dev
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>> ------------------------------
>>
>> End of galaxy-dev Digest, Vol 102, Issue 17
>> *******************************************
>> ___________________________________________________________
>> 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:
>>   https://lists.galaxyproject.org/
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Re: [Spam:*****] Re: How galaxy workflow work ?

Ruslan
In reply to this post by shenwiyn
galaxy.web.framework.decorators ERROR 2014-12-18 12:22:04,760 Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py", line 244, in decorator
    rval = func( self, trans, *args, **kwargs)
  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/workflows.py", line 231, in create
    populate_state=True,
  File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/run.py", line 18, in invoke
    modules.populate_module_and_state( trans, workflow, workflow_run_config.param_map )
  File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line 843, in populate_module_and_state
    step_errors = module_injector.inject( step, step_args=step_args )
  File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line 830, in inject
    state, step_errors = module.compute_runtime_state( trans, step_args )
  File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line 264, in compute_runtime_state
    state = self.decode_runtime_state( trans, step_updates.pop( "tool_state" ) )
KeyError: 'tool_state'

Cheers,
Ruslan Forostianov


___________________________________________________________
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Re: [Spam:*****] Re: How galaxy workflow work ?

John Chilton-4
That is odd. Does that workflow run through the UI? It looks like it
was missing a tool during import. Certainly the API should indicate
that overtly instead of failing in this fashion.

If it does run, can you export it to JSON and send it to me?

-John

On Thu, Dec 18, 2014 at 10:55 AM, Ruslan Forostianov <[hidden email]> wrote:

> galaxy.web.framework.decorators ERROR 2014-12-18 12:22:04,760 Uncaught
> exception in exposed API method:
> Traceback (most recent call last):
>   File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py",
> line 244, in decorator
>     rval = func( self, trans, *args, **kwargs)
>   File
> "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/workflows.py", line
> 231, in create
>     populate_state=True,
>   File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/run.py", line 18, in
> invoke
>     modules.populate_module_and_state( trans, workflow,
> workflow_run_config.param_map )
>   File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line 843,
> in populate_module_and_state
>     step_errors = module_injector.inject( step, step_args=step_args )
>   File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line 830,
> in inject
>     state, step_errors = module.compute_runtime_state( trans, step_args )
>   File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line 264,
> in compute_runtime_state
>     state = self.decode_runtime_state( trans, step_updates.pop( "tool_state"
> ) )
> KeyError: 'tool_state'
>
> Cheers,
> Ruslan Forostianov
>
___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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Re: [Spam:*****] Re: How galaxy workflow work ?

Ruslan
Hi John,

I did some investigation. 
I added logging statement to line 843 of lib/galaxy/workflow/modules.py file:

for step in workflow.steps:
        step_args = param_map.get( step.id, {} )
        log.info('step.id=' + str(step.id) + ', step_args=' + str(step_args))
        step_errors = module_injector.inject( step, step_args=step_args )

It gives:
galaxy.workflow.modules INFO 2014-12-18 13:39:31,464 step.id=21, step_args={'contrast': u'Female-Male'}

See http post below. It looks like somehow runtime parameter appears among steps.

4 * Client out-bound request
4 > Content-Type: application/json
4 > Accept: application/json
{"parameters":{"21":{"contrast":"Female-Male"}},"workflow_id":"d4bec7f9d7e8cf4d","history":"hist_id=59bd7ef52a8ce0e8","ds_map":{"21":{"id":"fb94345e0a2a5a2c","src":"hda"},"22":{"id":"9384bb69863b3f9e","src":"hda"}},"no_add_to_history":"true"}


On Fri, Dec 19, 2014 at 7:47 PM, John Chilton <[hidden email]> wrote:
That is odd. Does that workflow run through the UI? It looks like it
was missing a tool during import. Certainly the API should indicate
that overtly instead of failing in this fashion.

If it does run, can you export it to JSON and send it to me?

-John

On Thu, Dec 18, 2014 at 10:55 AM, Ruslan Forostianov <[hidden email]> wrote:
> galaxy.web.framework.decorators ERROR 2014-12-18 12:22:04,760 Uncaught
> exception in exposed API method:
> Traceback (most recent call last):
>   File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py",
> line 244, in decorator
>     rval = func( self, trans, *args, **kwargs)
>   File
> "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/workflows.py", line
> 231, in create
>     populate_state=True,
>   File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/run.py", line 18, in
> invoke
>     modules.populate_module_and_state( trans, workflow,
> workflow_run_config.param_map )
>   File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line 843,
> in populate_module_and_state
>     step_errors = module_injector.inject( step, step_args=step_args )
>   File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line 830,
> in inject
>     state, step_errors = module.compute_runtime_state( trans, step_args )
>   File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line 264,
> in compute_runtime_state
>     state = self.decode_runtime_state( trans, step_updates.pop( "tool_state"
> ) )
> KeyError: 'tool_state'
>
> Cheers,
> Ruslan Forostianov
>



--
Ruslan Forostianov,
Software Developer
www.thehyve.nl
E [hidden email]
M +31(0)6 83 51 30 81
Skype foro.ru

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Re: [Spam:*****] Re: How galaxy workflow work ?

John Chilton-4
That post looks like it might be wrong. If 21 is the step id of the
tool (edgeR) then ds_map should probably reference steps 19 and 20
right?

Also - I will see what I can do about improving these workflow API
error messages - it is never exactly clear to me what is wrong when
there are problems.

-John

On Fri, Dec 19, 2014 at 4:21 PM, Ruslan Forostianov <[hidden email]> wrote:

> Hi John,
>
> I did some investigation.
> I added logging statement to line 843 of lib/galaxy/workflow/modules.py
> file:
>
> for step in workflow.steps:
>         step_args = param_map.get( step.id, {} )
>         log.info('step.id=' + str(step.id) + ', step_args=' +
> str(step_args))
>         step_errors = module_injector.inject( step, step_args=step_args )
>
> It gives:
> galaxy.workflow.modules INFO 2014-12-18 13:39:31,464 step.id=21,
> step_args={'contrast': u'Female-Male'}
>
> See http post below. It looks like somehow runtime parameter appears among
> steps.
>
> 4 * Client out-bound request
> 4 > POST
> http://galaxy.thehyve.net/api/workflows?key=5c4f870bc0108a60dc7435a000fb7874
> 4 > Content-Type: application/json
> 4 > Accept: application/json
> {"parameters":{"21":{"contrast":"Female-Male"}},"workflow_id":"d4bec7f9d7e8cf4d","history":"hist_id=59bd7ef52a8ce0e8","ds_map":{"21":{"id":"fb94345e0a2a5a2c","src":"hda"},"22":{"id":"9384bb69863b3f9e","src":"hda"}},"no_add_to_history":"true"}
>
> Here is link to ga file for completeness:
> https://github.com/thehyve/trait_workflow_runner/blob/master/src/main/resources/nl/vumc/biomedbridges/galaxy/rna-seq-dge.ga
>
> On Fri, Dec 19, 2014 at 7:47 PM, John Chilton <[hidden email]> wrote:
>>
>> That is odd. Does that workflow run through the UI? It looks like it
>> was missing a tool during import. Certainly the API should indicate
>> that overtly instead of failing in this fashion.
>>
>> If it does run, can you export it to JSON and send it to me?
>>
>> -John
>>
>> On Thu, Dec 18, 2014 at 10:55 AM, Ruslan Forostianov <[hidden email]>
>> wrote:
>> > galaxy.web.framework.decorators ERROR 2014-12-18 12:22:04,760 Uncaught
>> > exception in exposed API method:
>> > Traceback (most recent call last):
>> >   File
>> > "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py",
>> > line 244, in decorator
>> >     rval = func( self, trans, *args, **kwargs)
>> >   File
>> > "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/workflows.py",
>> > line
>> > 231, in create
>> >     populate_state=True,
>> >   File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/run.py", line 18,
>> > in
>> > invoke
>> >     modules.populate_module_and_state( trans, workflow,
>> > workflow_run_config.param_map )
>> >   File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line
>> > 843,
>> > in populate_module_and_state
>> >     step_errors = module_injector.inject( step, step_args=step_args )
>> >   File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line
>> > 830,
>> > in inject
>> >     state, step_errors = module.compute_runtime_state( trans, step_args
>> > )
>> >   File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line
>> > 264,
>> > in compute_runtime_state
>> >     state = self.decode_runtime_state( trans, step_updates.pop(
>> > "tool_state"
>> > ) )
>> > KeyError: 'tool_state'
>> >
>> > Cheers,
>> > Ruslan Forostianov
>> >
>
>
>
>
> --
> Ruslan Forostianov,
> Software Developer
> www.thehyve.nl
> E [hidden email]
> M +31(0)6 83 51 30 81
> Skype foro.ru
___________________________________________________________
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