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 <jmchil...@gmail.com> 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 <f.debru...@vumc.nl> 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 [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
>> galaxy-dev-requ...@lists.galaxyproject.org 
>> [galaxy-dev-requ...@lists.galaxyproject.org]
>> Sent: Tuesday, December 16, 2014 18:00
>> To: galaxy-dev@lists.galaxyproject.org
>> Subject: galaxy-dev Digest, Vol 102, Issue 17
>>
>> Send galaxy-dev mailing list submissions to
>>         galaxy-dev@lists.galaxyproject.org
>>
>> 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
>>         galaxy-dev-requ...@lists.galaxyproject.org
>>
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>>
>> 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 <jmchil...@gmail.com>
>> To: Bongsoo Park <bx...@psu.edu>
>> Cc: galaxy-dev <galaxy-...@lists.bx.psu.edu>
>> Subject: Re: [galaxy-dev] How galaxy workflow work ?
>> Message-ID:
>>         <canwbokcggd3w7tkyd5fy-9d6qedlt+ta1gzzmkfe1apa2r8...@mail.gmail.com>
>> 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 <bx...@psu.edu> 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 <jmchil...@gmail.com>
>> To: Jelle Scholtalbers <j.scholtalb...@gmail.com>
>> Cc: galaxy-dev <galaxy-...@lists.bx.psu.edu>
>> Subject: Re: [galaxy-dev] Metadata error in uploading files to data
>>         libraries
>> Message-ID:
>>         <canwbokdzjumt4absen3b6rxokaxh+9fb23+_ohqmutfqnxb...@mail.gmail.com>
>> 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
>> <j.scholtalb...@gmail.com> 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: schol...@embl.de
>>> 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" <yu.w...@lrz.de>
>> To: John Chilton <jmchil...@gmail.com>
>> Cc: "Wang, Yu" <yu.w...@lrz.de>, "galaxy-dev@lists.galaxyproject.org"
>>         <galaxy-dev@lists.galaxyproject.org>
>> Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed
>> Message-ID:
>>         <f4c6170a-5f28-4871-971b-2881fc739...@badwlrz-sw13mb1.ads.mwn.de>
>> 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
>> w...@lrz.de<mailto:w...@lrz.de>
>>
>> On 15 Dec 2014, at 16:12, John Chilton 
>> <jmchil...@gmail.com<mailto:jmchil...@gmail.com>> 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 
>> <yu.w...@lrz.de<mailto:yu.w...@lrz.de>> 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
>> w...@lrz.de<mailto:w...@lrz.de>
>>
>>
>>
>>
>> ___________________________________________________________
>> 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" <yu.w...@lrz.de>
>> To: Peter Cock <p.j.a.c...@googlemail.com>
>> Cc: "Wang, Yu" <yu.w...@lrz.de>, "galaxy-dev@lists.galaxyproject.org"
>>         <galaxy-dev@lists.galaxyproject.org>
>> Subject: Re: [galaxy-dev] "join" produces an import error
>> Message-ID:
>>         <6d1d0da3-5aa2-4ab9-a104-7609fd0e7...@badwlrz-sw13mb4.ads.mwn.de>
>> 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
>> w...@lrz.de<mailto:w...@lrz.de>
>>
>> On 11 Dec 2014, at 17:24, Peter Cock 
>> <p.j.a.c...@googlemail.com<mailto:p.j.a.c...@googlemail.com>> wrote:
>>
>> On Wed, Dec 10, 2014 at 4:31 PM, Wang, Yu 
>> <yu.w...@lrz.de<mailto:yu.w...@lrz.de>> 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 <bjoern.gruen...@gmail.com>
>> To: "Wang, Yu" <yu.w...@lrz.de>
>> Cc: "galaxy-dev@lists.galaxyproject.org"
>>         <galaxy-dev@lists.galaxyproject.org>
>> Subject: Re: [galaxy-dev] package_numpy_1_7 can't be installed
>> Message-ID: <54900483.70...@gmail.com>
>> 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
>>> w...@lrz.de<mailto:w...@lrz.de>
>>>
>>> On 16 Dec 2014, at 04:07, Björn Grüning 
>>> <bjo...@gruenings.eu<mailto:bjo...@gruenings.eu>> 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
>>> w...@lrz.de<mailto:w...@lrz.de><mailto:w...@lrz.de>
>>>
>>> On 15 Dec 2014, at 16:12, John Chilton 
>>> <jmchil...@gmail.com<mailto:jmchil...@gmail.com><mailto:jmchil...@gmail.com>>
>>>  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 
>>> <yu.w...@lrz.de<mailto:yu.w...@lrz.de><mailto:yu.w...@lrz.de>> 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
>>> w...@lrz.de<mailto:w...@lrz.de><mailto:w...@lrz.de>
>>>
>>>
>>>
>>>
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