Re: [galaxy-dev] Python script can't can't import BioPython modules in Galaxy 16.01

[Makis Ladoukakis]

Yeah Linda, this was the case for me. When I started the virtual environment I 
reinstalled BioPython and everything worked again. I suggest you do the same to 
any packages you need for your tools.

Makis

To: galaxy-dev@lists.galaxyproject.org
From: linda.bak...@wur.nl
Date: Thu, 3 Mar 2016 14:10:44 +0100
Subject: Re: [galaxy-dev] Python script can't can't import BioPython modules in 
Galaxy 16.01


  

  
  
I guess this relates directly to my
  question as well...

  

  

  

  On 03/03/2016 01:06 PM, Makis Ladoukakis wrote:



  
  
  Hello everyone,



I've recently upgraded to Galaxy 16.01 and i have some issues
with a python wrapper from a tool. When I run it via Galaxy I
get the following error:



Traceback (most recent call last):
  File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", 
line 12, in 
from Bio import SeqIO
ImportError: No module named Bio


However when I click on the "view details" icon to copy the
command from the tool and run it on my command line the tool
works perfectly. In addition this issue occurs while I already
have installed BioPython.



When I type Python and write  "from Bio import SeqIO" I get no
error.



Can this be an issue related to the virtual environment that is
initialized each time Galaxy starts?



Thank you in advance,

Makis Ladoukakis





  
  

  
  

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-- 
Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: +31-317-480756
email: linda.bak...@wur.nl
  


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[galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

[William Ge]

Hi, all,

Sorry to bother you again. I am trying to install tools using the script. I 
have downloaded the playbook, but stuck here:


[galaxy@Pegasus ansible-galaxy-tools]$ ansible-playbook tasks/tools.yml -i 
"localhost," --extra-vars galaxy_tools_api_key=xcd2Glx

ERROR: pip is not a legal parameter of an Ansible Play



I did not find anything related on the Galaxy search either. Any help will be 
appreciated.



The web Admin interface only allows tool installation one by one. I wish it 
allows batch installation there.



Thanks,

Bill



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Re: [galaxy-dev] playbook download error

[William Ge]

It worked! Thank you very much, Bjoern!
However, another error came up during the next step:

[galaxy@Pegasus ansible-galaxy-tools]$ ansible-playbook tasks/tools.yml -i 
"localhost," --extra-vars galaxy_tools_api_key=xcd2Glx
ERROR: pip is not a legal parameter of an Ansible Play

I did not find anything related on the Galaxy search either. Any help will be 
appreciated. 

The web Admin interface only allows tool installation one by one. I wish it 
allows batch installation there. 

Thanks,
Bill


-Original Message-
From: Björn Grüning [mailto:bjoern.gruen...@gmail.com] 
Sent: Thursday, March 3, 2016 10:59 AM
To: William Ge ; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] playbook download error

Hi,

try git clone --recursive
https://github.com/galaxyproject/ansible-galaxy-tools.git

Cheers,
Bjoern

Am 03.03.2016 um 19:54 schrieb William Ge:
> Hi, all,
> 
>  
> 
> I tried to download the playbook for automatic installation of Galaxy 
> tools, but encountered the following error:
> 
>  
> 
> [galaxy@Pegasus galaxy]$ git clone --recursive 
> g...@github.com:afgane/galaxy-tools-playbook.git
> 
> Initialized empty Git repository in
> /home/galaxy/galaxy/galaxy-tools-playbook/.git/
> 
> Permission denied (publickey).
> 
> fatal: The remote end hung up unexpectedly
> 
>  
> 
> Is this repository still open to public download?
> 
>  
> 
> I’m new and not quite familiar with the playbook application. Any step 
> by step guide will be helpful.
> 
>  
> 
> Thanks,
> 
> Bill
> 
> 
> 
> ___
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Re: [galaxy-dev] playbook download error

[Björn Grüning]

Hi,

try git clone --recursive
https://github.com/galaxyproject/ansible-galaxy-tools.git

Cheers,
Bjoern

Am 03.03.2016 um 19:54 schrieb William Ge:
> Hi, all,
> 
>  
> 
> I tried to download the playbook for automatic installation of Galaxy
> tools, but encountered the following error:
> 
>  
> 
> [galaxy@Pegasus galaxy]$ git clone --recursive
> g...@github.com:afgane/galaxy-tools-playbook.git
> 
> Initialized empty Git repository in
> /home/galaxy/galaxy/galaxy-tools-playbook/.git/
> 
> Permission denied (publickey).
> 
> fatal: The remote end hung up unexpectedly
> 
>  
> 
> Is this repository still open to public download?
> 
>  
> 
> I’m new and not quite familiar with the playbook application. Any step
> by step guide will be helpful.
> 
>  
> 
> Thanks,
> 
> Bill
> 
> 
> 
> ___
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[galaxy-dev] playbook download error

[William Ge]

Hi, all,

I tried to download the playbook for automatic installation of Galaxy tools, 
but encountered the following error:

[galaxy@Pegasus galaxy]$ git clone --recursive 
g...@github.com:afgane/galaxy-tools-playbook.git
Initialized empty Git repository in 
/home/galaxy/galaxy/galaxy-tools-playbook/.git/
Permission denied (publickey).
fatal: The remote end hung up unexpectedly

Is this repository still open to public download?

I'm new and not quite familiar with the playbook application. Any step by step 
guide will be helpful.

Thanks,
Bill
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Re: [galaxy-dev] Galaxy 15.10 Jobs not running

[Ryan G]

Hi Nate - Thanks.  Our galaxy.ini shows:

job_config_file = config/job_conf.xml

Our job_conf.xml is (which is the same as job_conf.xml.sample_basic) :














Hmmm, ok weird.  We just restart Galaxy for the 5th or 6th time to get a
clean log file to send and it works now.   Hmmm.   I will consider this
issue closed.   Is there any documention that talks about how the job
runner and manager, all work together?  I'd like to add some debugging
statements in the code so there is more info in the log file.



On Wed, Mar 2, 2016 at 12:00 PM, Nate Coraor  wrote:

> On Tue, Mar 1, 2016 at 1:19 PM, Ryan G 
> wrote:
>
>> Hi all - We recently merged in Galaxy 15.10 changes into our staging
>> instance and have noticed jobs are no longer dispatched.  There is no
>> obvious problem in the log file.
>>
>> I see in github, commits have recently been made to revert something, but
>> I'm not clear what.
>>
>> Is there something going on with the job runner?  Better yet, how can I
>> track down what my issue is?
>>
>
> Hi Ryan,
>
> There aren't any current issues with job running that I'm aware of.
> Typically the first thing to check is your job_conf.xml and make sure that
> handlers defined are the same as handlers (with matching server names) that
> you are starting). The log for your handlers should show them loading the
> job_conf.xml and setting up job plugins if they are identified as handlers
> in the config.
>
> --nate
>
>
>>
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>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
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Re: [galaxy-dev] Tool Visibility feature

[SAPET, Frederic]

Hi John

Yes, I have do that :

>ls lib/galaxy/tools/toolbox/filters/examples.py*
lib/galaxy/tools/toolbox/filters/examples.py  
lib/galaxy/tools/toolbox/filters/examples.py.sample

I'm currently trying to set up another galaxy server, I will try Galaxy 16.01 
with this functionality.

Thank you for the wiki.

Fred


-Message d'origine-
De : John Chilton [mailto:jmchil...@gmail.com] 
Envoyé : mercredi 2 mars 2016 21:20
À : SAPET, Frederic 
Cc : galaxy-dev@lists.galaxyproject.org
Objet : Re: [galaxy-dev] Tool Visibility feature

I have fixed the path to the filter directory on the wiki, have you copied 
lib/galaxy/tools/toolbox/filters/examples.py.sample to 
lib/galaxy/tools/toolbox/filters/examples.py?

-John

On Fri, Feb 19, 2016 at 4:22 PM, SAPET, Frederic  
wrote:
> Hello
>
> I'm trying to set up this feature :
> https://wiki.galaxyproject.org/Admin/Config/Access%20Control
>
> it seems that some files have been moved from : 
> lib/galaxy/tools/filters/ to lib/galaxy/tools/toolbox/filters/
>
> by the way, when I uncomment " user_tool_filters = 
> examples:restrict_upload_to_admins, examples:restrict_encode" in my 
> galaxy.ini file, it does not work.
>
> When I click on "Manage your ToolBox filters" 
> (/user/toolbox_filters?cntrller=user) in my User preferences panel, I'm 
> facing this error :
>
> Internal Server Error
> Galaxy was unable to successfully complete your request
>
> URL: http://galaxy.biogemma.fr/user/toolbox_filters?cntrller=user
> sys.path: [
> '/softs/bioinfo/galaxy-prod/eggs/Parsley-1.1-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/Fabric-1.7.0-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/ssh-1.7.14-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/paramiko-1.11.1-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/SVGFig-1.1.6-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/drmaa-0.7.6-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/Whoosh-2.4.1-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/Beaker-1.4-py2.6.egg',
> 
> '/softs/bioinfo/galaxy-prod/eggs/MySQL_python-1.2.3c1_5.1.41_static-py2.6-linux-x86_64-ucs4.egg',
> '/softs/bioinfo/galaxy-prod/eggs/sqlalchemy_migrate-0.9.6-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/Tempita-0.5.1-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/decorator-3.1.2-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/sqlparse-0.1.14-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/six-1.9.0-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/Babel-1.3-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/pytz-2013.9-py2.6.egg',
> 
> '/softs/bioinfo/galaxy-prod/eggs/mercurial-3.2.4-py2.6-linux-x86_64-ucs4.egg',
> '/softs/bioinfo/galaxy-prod/eggs/Mako-0.4.1-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/kombu-3.0.24-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/ordereddict-1.1-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/importlib-1.0.3-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/anyjson-0.3.3-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/PyYAML-3.10-py2.6-linux-x86_64-ucs4.egg',
> '/softs/bioinfo/galaxy-prod/eggs/WebHelpers-1.3-py2.6.egg',
> 
> '/softs/bioinfo/galaxy-prod/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg',
> 
> '/softs/bioinfo/galaxy-prod/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg',
> 
> '/softs/bioinfo/galaxy-prod/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg',
> 
> '/softs/bioinfo/galaxy-prod/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg',
> '/softs/bioinfo/galaxy-prod/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg',
> 
> '/softs/bioinfo/galaxy-prod/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg',
> 
> '/softs/bioinfo/galaxy-prod/eggs/bx_python-0.7.2-py2.6-linux-x86_64-ucs4.egg',
> 
> '/softs/bioinfo/galaxy-prod/eggs/SQLAlchemy-1.0.8-py2.6-linux-x86_64-ucs4.egg',
> '/softs/bioinfo/galaxy-prod/eggs/WebOb-0.8.5-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/Routes-2.1-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/repoze.lru-0.6-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/amqp-1.4.6-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/wchartype-0.1-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/docutils-0.7-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/PasteDeploy-1.5.0-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg',
> '/softs/bioinfo/galaxy-prod/lib',
> '/usr/lib/python2.6/site-packages/pip-7.1.2-py2.6.egg',
> '/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg',
> '/usr/lib/python2.6/site-packages/bz2file-0.98-py2.6.egg',
> '/usr/lib64/python26.zip',
> '/usr/lib64/python2.6',
> '/usr/lib64/python2.6/plat-linux2',
> '/usr/lib64/python2.6/lib-tk',
> '/usr/lib64/python2.6/lib-old',
> '/usr/lib64/python2.6/lib-dynload',
> '/usr/lib64/python2.6/site-packages/gtk-2.0',
> '/usr/lib64/python2.6/site-packages',
> 

[galaxy-dev] switch to git

[Briand, Sheldon (NRC/CNRC)]

Hi,

I've done the recently announced security update for my running release which 
is 15.01.  I figured I had better switch to git now while I was at it.  However 
I'm having trouble matching revisions in git.

I have looked at the instructions in the Develop/SourceCode page of the Wiki.  
I've used git log show-notes=hg2git after fetching them.  It seems those notes 
stop at changeset 16698 while I am now showing changeset 17151 with the hg log 
-b $(hg branch) command and 17161 with hg tip.

What should my next step be?

Thanks,
-Sheldon



Sheldon Briand
Computer Systems and Applications Analyst
National Research Council/Government of Canada
sheldon.bri...@canada.ca/ Tel: (902) 426-1677

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Re: [galaxy-dev] Python script can't can't import BioPython modules in Galaxy 16.01

[Linda Bakker]

I guess this relates directly to my question as well...



On 03/03/2016 01:06 PM, Makis Ladoukakis wrote:

Hello everyone,

I've recently upgraded to Galaxy 16.01 and i have some issues with a 
python wrapper from a tool. When I run it via Galaxy I get the 
following error:


Traceback (most recent call last):
   File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", line 12, 
in 
 from Bio import SeqIO
ImportError: No module named Bio

However when I click on the "view details" icon to copy the command 
from the tool and run it on my command line the tool works perfectly. 
In addition this issue occurs while I already have installed BioPython.


When I type Python and write  "from Bio import SeqIO" I get no error.

Can this be an issue related to the virtual environment that is 
initialized each time Galaxy starts?


Thank you in advance,
Makis Ladoukakis





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--
Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: +31-317-480756
email: linda.bak...@wur.nl

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Re: [galaxy-dev] Python script can't can't import BioPython modules in Galaxy 16.01

[Peter Cock]

On Thu, Mar 3, 2016 at 12:06 PM, Makis Ladoukakis
 wrote:
> Hello everyone,
>
> I've recently upgraded to Galaxy 16.01 and i have some issues with a python
> wrapper from a tool. When I run it via Galaxy I get the following error:
>
> Traceback (most recent call last):
>   File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py",
> line 12, in 
> from Bio import SeqIO
> ImportError: No module named Bio
>
>
> However when I click on the "view details" icon to copy the command from the
> tool and run it on my command line the tool works perfectly. In addition
> this issue occurs while I already have installed BioPython.
>
> When I type Python and write  "from Bio import SeqIO" I get no error.
>
> Can this be an issue related to the virtual environment that is initialized
> each time Galaxy starts?
>
> Thank you in advance,
> Makis Ladoukakis

Almost certainly, yes, this is due to the new venv setup in Galaxy.

If you had manually installed Biopython, I would suggest you install it
again but inside the venv.

If you installed Biopython via the Tool Shed package, that is more troubling.
Try doing a re-install via the Tool Shed.

Peter
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[galaxy-dev] Python script can't can't import BioPython modules in Galaxy 16.01

[Makis Ladoukakis]

Hello everyone,

I've recently upgraded to Galaxy 16.01 and i have some issues with a python 
wrapper from a tool. When I run it via Galaxy I get the following error:

Traceback (most recent call last):
  File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", 
line 12, in 
from Bio import SeqIO
ImportError: No module named Bio
However when I click on the "view details" icon to copy the command from the 
tool and run it on my command line the tool works perfectly. In addition this 
issue occurs while I already have installed BioPython.

When I type Python and write  "from Bio import SeqIO" I get no error.

Can this be an issue related to the virtual environment that is initialized 
each time Galaxy starts?

Thank you in advance,
Makis Ladoukakis




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Re: [galaxy-dev] trouble with python packages after galaxy update

[Peter Cock]

On Thu, Mar 3, 2016 at 9:14 AM, Peter Cock  wrote:
> On Thu, Mar 3, 2016 at 8:24 AM, Linda Bakker  wrote:
>> Hi Guys,
>> So i updated my galaxy instance to release_16.01
>> I usually started galaxy in a venv and used pip to install any packages my
>> tool needed. (in this case, numpy and scipy)
>>
>> ...
>>
>> (.venv)@server:/galaxy-dist$ ./run.sh
>> Activating virtualenv at .venv
>> Ignoring indexes: https://pypi.python.org/simple
>> Collecting pip==8.0.2+gx2
>>   Downloading
>> https://wheels.galaxyproject.org/packages/pip-8.0.2+gx2-py2.py3-none-any.whl
>> (1.2MB)
>> 100% || 1.2MB 339kB/s
>> Installing collected packages: pip
>>   Found existing installation: pip 8.0.3
>> Uninstalling pip-8.0.3:
>>   Successfully uninstalled pip-8.0.3
>> Successfully installed pip-8.0.2+gx2
>>
>> And later on i get the message that i should upgrade my pip...
>> I am confused...
>
> From what I understand from following some of the relevant issues
> on GitHub, this is a side effect of Galaxy using its own modified version
> of pip as of Galaxy v16.01, although this isn't clear from the release notes:
>
> https://docs.galaxyproject.org/en/master/releases/16.01_announce.html
>
> Nate (CC'd) can explain further I think.

I filed this specific issue on GitHub,
https://github.com/galaxyproject/galaxy/issues/1845

An example of the pip upgrade warning:

$ ./run.sh
...
You are using pip version 8.0.2+gx2, however version 8.0.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
...


Peter
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Re: [galaxy-dev] trouble with python packages after galaxy update

[Peter Cock]

On Thu, Mar 3, 2016 at 8:24 AM, Linda Bakker  wrote:
> Hi Guys,
> So i updated my galaxy instance to release_16.01
> I usually started galaxy in a venv and used pip to install any packages my
> tool needed. (in this case, numpy and scipy)
>
> ...
>
> (.venv)@server:/galaxy-dist$ ./run.sh
> Activating virtualenv at .venv
> Ignoring indexes: https://pypi.python.org/simple
> Collecting pip==8.0.2+gx2
>   Downloading
> https://wheels.galaxyproject.org/packages/pip-8.0.2+gx2-py2.py3-none-any.whl
> (1.2MB)
> 100% || 1.2MB 339kB/s
> Installing collected packages: pip
>   Found existing installation: pip 8.0.3
> Uninstalling pip-8.0.3:
>   Successfully uninstalled pip-8.0.3
> Successfully installed pip-8.0.2+gx2
>
> And later on i get the message that i should upgrade my pip...
> I am confused...

From what I understand from following some of the relevant issues
on GitHub, this is a side effect of Galaxy using its own modified version
of pip as of Galaxy v16.01, although this isn't clear from the release notes:

https://docs.galaxyproject.org/en/master/releases/16.01_announce.html

Nate (CC'd) can explain further I think.

Regards,

Peter
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Re: [galaxy-dev] Problems with planemo functional tests

[Gildas Le Corguillé]

Hi,

Do you still have the config/galaxy.ini.sample file unchanged ?

We observed this message when some .sample are missing or were modified.

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr 

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org 

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



> Le 3 mars 2016 à 07:31, Léo Biscassi  a écrit :
> 
> Hi, the command that you suggested not working, the same output is presented. 
> I tested with the following commands:
> 
> sudo planemo test 
> /home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml 
> --galaxy_root=/home/leobiscassi/programs/galaxy
> 
> sudo planemo test 
> /home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml
> 
> What is the influence of xUnit file in the process? I did the question 
> because the warning message showing "Cannot locate xUnit report option for 
> tests - update Galaxy for more detailed breakdown".
> 
> P.S.: My Galaxy instance is the latest stable version.
> 
> Best regards,
> 
> On Thu, Mar 3, 2016 at 2:53 AM Björn Grüning  > wrote:
> Hi,
> 
> maybe I'm mistaken something, its way to early here ... but you need to
> specify a path to the tool you want to test.
> 
> For example:
> 
> planemo test /foo/bar/foo.xml
> 
> or to a directory full of tools.
> 
> planemo test /foo/bar
> 
> Hope this helps,
> Bjoern
> 
> Am 03.03.2016 um 04:48 schrieb Léo Biscassi:
> > Hi Folks,
> > I tried follow this tutorial [1], but I have problems in execute the
> > command "planemo t --galaxy_root=/home/leobiscassi/programs/galaxy" for
> > perform functional tests, any suggestion?
> > Bellow some images about this problem:
> >
> > imagem1.jpg
> > *Figure 1: *Command
> >
> > imagem2.jpg
> > *Figure 2:* Error
> >
> > imagem3.jpg
> > *Figure 3: *Galaxy Path
> >
> > Planemo's version is 0.23.0.
> >
> > [1] https://planemo.readthedocs.org/en/latest/writing_standalone.html 
> > 
> >
> > P.S: The command is utilized for same tool presented in tutorial.
> >
> > Att.
> > --
> > *Léo Biscassi*
> > Facebook - https://pt-br.facebook.com/lbiscassi 
> > 
> > Linkedin - https://br.linkedin.com/in/leobiscassi 
> > 
> > Skype - biscassi.leo
> > Twitter - https://twitter.com/leobiscassi 
> >
> >
> > ___
> > 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/ 
> > 
> >
> -- 
> Léo Biscassi
> Facebook - https://pt-br.facebook.com/lbiscassi 
> 
> Linkedin - https://br.linkedin.com/in/leobiscassi 
> 
> Skype - biscassi.leo
> Twitter - https://twitter.com/leobiscassi 
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Re: [galaxy-dev] nginx data upload request never reaches /api/tools

[Preussner, Jens]

Hi John,

thanks for your answer. The nginx config can be found at 
https://gist.github.com/jenzopr/623c3541419ce33f662c
What I did was the following:
1) Stopping both servers, nginx and galaxy
2) Removing all log files and the tmp files in upload_store
3) Restarting the servers
4) Starting a fresh browser session, deleting all cookies.
5) Navigating to my galaxy via the browser (172.16.12.122/galaxy, not 
172.16.12.122:8080)
6) Login and upload a file test.txt

The file appears in the upload_store, but this time I got a 403 although I was 
logged in properly.
Best,
Jens

-Original Message-
From: John Chilton [mailto:jmchil...@gmail.com] 
Sent: Mittwoch, 2. März 2016 21:30
To: Preussner, Jens
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] nginx data upload request never reaches /api/tools

Can you share your nginx config? Perhaps with a gist or something.

-John

On Mon, Feb 29, 2016 at 12:35 PM, Preussner, Jens 
 wrote:
> Hi all,
>
>
>
> I set up the data upload using nginx as described in the wiki 
> (https://wiki.galaxyproject.org/Admin/Config/nginxProxy, using the 
> subdirectory /galaxy).
>
> The uploaded file also appears inside the uploade_store folder on the 
> galaxy server, but galaxy does not add the file.
>
> Investigating the log files, I found the corresponding lines in the
> nginx.error.log:
>
>
>
> # Post request is received
>
> 2016/02/29 12:55:37 [notice] 13156#0: *4 "^(GET|HEAD|POST)$" matches 
> "POST",
> client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
> "172.16.12.122", referrer: http://172.16.12.122/galaxy/
>
> # Upload starts
>
> 2016/02/29 12:55:37 [info] 13156#0: *4 started uploading file 
> "boxes.txt" to "/mnt/idrive1/database/tmp/upload_store/0020132707" 
> (field "files_0|file_data", content type "text/plain"), client: 
> 172.16.17.17,
> server: , request: "POST /_upload HTTP/1.1", host: "172.16.12.122",
> referrer: http://172.16.12.122/galaxy/
>
> # Upload done, the file is present in the given path
>
> 2016/02/29 12:55:37 [info] 13156#0: *4 finished uploading file "boxes.txt"
> to "/mnt/idrive1/database/tmp/upload_store/0020132707", client:
> 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
> "172.16.12.122", referrer: "http://172.16.12.122/galaxy/;
>
> # Redirection starts?
>
> 2016/02/29 12:55:37 [notice] 13156#0: *4 "^(GET|HEAD|POST)$" matches 
> "POST",
> client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
> "172.16.12.122", referrer: "http://172.16.12.122/galaxy/;
>
> 2016/02/29 12:55:37 [notice] 13156#0: *4 "nginx_redir=([^&]+)" does 
> not match "", client: 172.16.17.17, server: , request: "POST /_upload 
> HTTP/1.1",
> host: "172.16.12.122", referrer: "http://172.16.12.122/galaxy/;
>
> 2016/02/29 12:55:37 [notice] 13156#0: *4 "" matches "/_upload_done", client:
> 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
> "172.16.12.122", referrer: "http://172.16.12.122/galaxy/;
>
> # Redirection should be done here
>
> 2016/02/29 12:55:37 [notice] 13156#0: *4 rewritten data:
> "/galaxy/api/tools", args: "", client: 172.16.17.17, server: , request:
> "POST /_upload HTTP/1.1", host: "172.16.12.122", referrer:
> "http://172.16.12.122/galaxy/;
>
> # ModSecurity seems to block the redirect?
>
> 2016/02/29 12:55:37 [info] 13156#0: *4 ModSecurity: invalid "Content-Length"
> header, client: 172.16.17.17, server: , request: "POST /_upload 
> HTTP/1.1",
> host: "172.16.12.122", referrer: "http://172.16.12.122/galaxy/;
>
> 2016/02/29 12:55:37 [notice] 13156#0: *4 "^(GET|HEAD|POST)$" matches 
> "GET",
> client: 172.16.17.17, server: , request: "POST /_upload HTTP/1.1", host:
> "172.16.12.122", referrer: "http://172.16.12.122/galaxy/;
>
>
>
> A ModSecurityEnabled off; within the /_upload and /_upload_done of the 
> nginx config did not help.
>
> Any idea why the Content-Length header causes problems and is blocked 
> by modSec? Any workaround for ModSec to accept everything that goes 
> from internal to internal?
>
>
>
> Thanks for your help!
>
>
>
> Best,
>
> Jens
>
>
>
>
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[galaxy-dev] trouble with python packages after galaxy update

[Linda Bakker]

Hi Guys,
So i updated my galaxy instance to release_16.01
I usually started galaxy in a venv and used pip to install any packages 
my tool needed. (in this case, numpy and scipy)


source my_galaxy_dir/.venv/bin/activate
pip install scipy (dependency numpy also installed)
./run.sh

But since the last update, i am having problems with this.
Did something change? because it looks like it searches for an existing 
venv and then activates a new venv in my already active one??


Depending on what i try, when i execute my tool in galaxy, my messages 
range from


ImportError: No module named scipy
or ValueError: numpy.dtype has the wrong size, try recompiling 




I tried running galaxy without a venv, re-creating my venv. renaming my venv
installing numpy, then scipy, not using pip at all.
removing numpy and reinstalling without cache.
I also played around with pip, doing nothing after creating my venv, or 
first upgrading my pip, but then after i start galaxy i get this message:


(.venv)@server:/galaxy-dist$ ./run.sh
Activating virtualenv at .venv
Ignoring indexes: https://pypi.python.org/simple
Collecting pip==8.0.2+gx2
  Downloading 
https://wheels.galaxyproject.org/packages/pip-8.0.2+gx2-py2.py3-none-any.whl 
(1.2MB)

100% || 1.2MB 339kB/s
Installing collected packages: pip
  Found existing installation: pip 8.0.3
Uninstalling pip-8.0.3:
  Successfully uninstalled pip-8.0.3
Successfully installed pip-8.0.2+gx2

And later on i get the message that i should upgrade my pip...
I am confused...can someone tell me the correct way to start galalxy 
within or without my venv and how to correctly install my packages?

Thanks!


with regards,
Linda Bakker

--
Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: +31-317-480756
email: linda.bak...@wur.nl

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