Re: [galaxy-dev] Picard installation dependency issues

[Marius van den Beek]

Hi Scott, Martin,

there was still a small problem in cairo.
I made a PR to fix this (
https://github.com/galaxyproject/tools-devteam/pull/300)
I should have paid a bit more attention ...

Cheers,
Marius

On 1 December 2015 at 22:46, Scott Szakonyi 
wrote:

> Hi Martin,
>
> I've been able to resolve all of the issues with Picard dependencies
> except for Cairo. It's still failing with this error:
>
> Tool shed repository:package_cairo_1_12_14
> Tool shed repository changeset revision:f5ab0fdf3716
> Tool dependency status:Error
> Tool dependency installation error:/bin/sh: -c: line 14: syntax error:
> unexpected end of file
>
> If you have any suggestions about this error, I'd be pleased to attempt to
> resolve it.
>
> Best,
>
> Scott
>
> On Tue, Dec 1, 2015 at 10:01 AM, Scott Szakonyi  > wrote:
>
>> Hi Martin,
>>
>> Thanks very much for your reply, and also to Marius.
>>
>> After some investigation, it appears that there is a firewall issue on my
>> Galaxy server which is preventing the download of the file via FTP. I'm
>> looking into options for that now.
>>
>> Best,
>>
>> Scott
>>
>> On Tue, Dec 1, 2015 at 9:56 AM, Martin Čech  wrote:
>>
>>> Hello Scott,
>>>
>>> thanks to Marius van den Beek the first two issues should be fixed with
>>> this PR: https://github.com/galaxyproject/tools-devteam/pull/299
>>>
>>> These changes were already propagated to the Main Tool Shed.
>>> Note for tool developers: for future endeavours please use packages from
>>> the IUC repository (
>>> https://github.com/galaxyproject/tools-iuc/tree/master/packages)
>>>
>>> As of the timeout for the readline package it seems the problem was on
>>> the ftp.gnu side and it is now resolved.
>>> In the future Galaxy plans to use a smart caching proxy to handle
>>> all source codes required by the Tool Shed installations. This effort is
>>> lead by Eric Rasche and you can see it here
>>> https://github.com/galaxyproject/cargo-port
>>>
>>> Thank you for the report (and for using Galaxy :)).
>>>
>>> Martin
>>>
>>> On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi <
>>> scott.b.szakony...@nd.edu> wrote:
>>>
 Hi all,

 I'm installing the latest revision of Picard tools (efc56ee1ade4).
 Picard installs successfully, and the tools are appearing in the
 appropriate menu, but several packages that install with Picard are
 reporting dependency issues, and I'm concerned that not all the tools will
 work appropriately. The tools reporting issues are:

- package_cairo_1_12_14 (last lines of long warning/error sequence)
-
   
 /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib:
  file not recognized: Is a directory
   collect2: ld returned 1 exit status
   make[3]: *** [libcairo.la] Error 1
   make[2]: *** [all] Error 2
   make[1]: *** [all-recursive] Error 1
   make: *** [all] Error 2
   - package_pixman_0_32_4
-
   /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In 
 function `_start':
   (.text+0x20): undefined reference to `main'
   collect2: ld returned 1 exit status
   make[2]: *** [clip-test] Error 1
   make[1]: *** [all-recursive] Error 1
   make: *** [all] Error 2
- package_readline_6_2
- Error downloading from URL
   ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz:
   

 Is anyone else having issues with these packages? Any suggestions for
 resolving these problems?

 Thanks!

 --
 Scott B. Szakonyi
 Research Programmer

 *Center for Research Computing*
 107 Information Technology Center
 Notre Dame, IN 46556
 http://crc.nd.edu
 ___
 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/
>>>
>>>
>>
>>
>> --
>> Scott B. Szakonyi
>> Research Programmer
>>
>> *Center for Research Computing*
>> 107 Information Technology Center
>> Notre Dame, IN 46556
>> http://crc.nd.edu
>>
>
>
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
>
> ___
> 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:
>   

[galaxy-dev] bx-python issue with intersect and subtract tools

[Poole, Richard]

Hi all,

I just used the subtract tool (installed under Operate on Genomic Intervals) on 
my own Galaxy server for the first time in a very long time and got this error 
message from the tool:


Traceback (most recent call last):
  File 
"/Users/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/subtract/c19a2a29c561/subtract/gops_subtract.py",
 line 16, in 
from bx.intervals.io import GenomicInterval, NiceReaderWrapper
ImportError: No module named bx.intervals.io

So I uninstalled the intersect and subtract tools, plus the bx-python 0.7.1 
package plus the galaxy-ops package and reinstalled both tools from the 
toolshed using the latest revisions of each from devteam. I now get this error 
message:


/Users/galaxy/galaxy-dist/lib/galaxy/__init__.py:63: UserWarning: Module bx was 
already imported from 
/Users/galaxy/galaxy-dist/tool-dependencies/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.7/site-packages/bx/__init__.pyc,
 but 
/Users/galaxy/galaxy-dist/eggs/bx_python-0.7.2-py2.7-macosx-10.6-intel-ucs2.egg 
is being added to sys.path
  self.check_version_conflict()
Traceback (most recent call last):
  File 
"/Users/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/subtract/c19a2a29c561/subtract/gops_subtract.py",
 line 21, in 
from utils.gff_util import GFFFeature, GFFReaderWrapper, 
convert_bed_coords_to_gff
ImportError: No module named utils.gff_util

Does this suggest an incompatibility somehow with the the egg which is 
installed at startup and is versions 0.7.2 - I tried manually editing the egg 
file but could not switch that to 0.7.1

I also then tried updating Galaxy to latest release 15.07 and even 15.10 which 
appeared in the git tag list as I writing this email, but no fix there - my 
Galaxy is running on a Mac OS X 10.10.5 Yosemite.

Any thoughts on how to resolve this problem?

Cheers,
Rich




Richard J Poole PhD
Wellcome Trust Fellow
Department of Cell and Developmental Biology
University College London
518 Rockefeller
21 University Street, London WC1E 6DE
Office (518 Rockefeller): +44 20 7679 6577 (int. 46577)
Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133)

___
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/

Re: [galaxy-dev] Publish tool with Python dependencies to the toolshed

[Björn Grüning]

Hi,

> Thanks Martin and Bjoern for your advice.
> 
> Bjoern, does this modification to the galaxy.ini need to be made on all 
> Galaxy instances that want to install and run this tool once its 
> available in the shed? I assume it has nothing to do with the ability to 
> publish it in the first place.

It's only needed by Galaxy instance which runs these tools.

The reason is that Galaxy's Python env and the Python env from the Tool
needs to be completely separated. In theory it is now possible that you
run tools against Python 3.5 in a Python 2.6 Galaxy installation.

Cheers,
Bjoern

> Thanks
> Ulf
> 
> On 01/12/15 16:41, Björn Grüning wrote:
>> Hi Ulf,
>>
>> just adding to Martins great explanation that you should set
>>
>>   enable_beta_tool_command_isolation = True
>>
>> in your galaxy.ini file if you are using a strict Python dependency with
>> package_python_2_7_10.
>>
>> Cheers,
>> Bjoern
>>
>> Am 01.12.2015 um 17:07 schrieb Martin Čech:
>>> Hi Ulf,
>>>
>>> you most probably want your tool to depend on package_python_2_7_10 from
>>> the iuc (it will ensure your tool has access to 2.7.10 no matter what
>>> python the Galaxy executing your tool is using)
>>>
>>> The package is being developed here
>>> https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_python_2_7_10
>>> and
>>> is available at the MTS here
>>> https://toolshed.g2.bx.psu.edu/view/iuc/package_python_2_7_10/73631e818d3d
>>>
>>> You will need to add to your wrapper's xml something like:
>>>
>>> 
>>> python
>>> 
>>>
>>> And you have to include tool_dependencies.xml file which will look
>>> something like:
>>>
>>> 
>>> 
>>> 
>>> >> prior_installation_required="True" />
>>> 
>>> 
>>>
>>> Please let me know if you have more questions.
>>>
>>> M.
>>>
>>> On Tue, Dec 1, 2015 at 10:54 AM Ulf Schaefer 
>>> wrote:
>>>
 Dear all

 I have a Python script that I would like to publish to the tool shed. It
 has a couple dependencies, all Python modules (argparse, PyVCF, PyYAML).
 It also needs a Python version 2.7<=X<3, which is not available per
 default everywhere.

 Firstly, how do I specify these dependencies in the tool 
 tag?

 And secondly, once I have a correct set of tool definition files with
 tests and test data, how do I best get it onto the tool shed?

 I had a look through the wiki and the planemo documentation.
 Unfortunately how to handle these dependencies did not become
 immediately obvious (to me).

 Thanks for any pointers and sorry if this has been answered some place I
 did not look.

 Cheers
 Ulf

 --
 Ulf Schaefer, PhD
 Bioinformatics Scientist
 Bioinformatics Unit - Infectious Disease Informatics
 National Infection Service
 Public Health England
 61 Colindale Ave, London NW9 5EQ
 ulf.schae...@phe.gov.uk
 http://www.gov.uk/phe
 Protecting and improving the nation’s health

 **
 The information contained in the EMail and any attachments is confidential
 and intended solely and for the attention and use of the named
 addressee(s). It may not be disclosed to any other person without the
 express authority of Public Health England, or the intended recipient, or
 both. If you are not the intended recipient, you must not disclose, copy,
 distribute or retain this message or any part of it. This footnote also
 confirms that this EMail has been swept for computer viruses by
 Symantec.Cloud, but please re-sweep any attachments before opening or
 saving. http://www.gov.uk/PHE
 **
 ___
 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/
>>>
> 
> **
> The information contained in the EMail and any attachments is confidential 
> and intended solely and for the attention and use of the named addressee(s). 
> It may not be disclosed to any other person without the express authority of 
> Public Health England, or the intended recipient, or both. If you 

Re: [galaxy-dev] Picard installation dependency issues

[Martin Čech]

This is now updated in MTS. Thanks guys.

M.

On Tue, Dec 1, 2015 at 4:55 PM Marius van den Beek 
wrote:

> Hi Scott, Martin,
>
> there was still a small problem in cairo.
> I made a PR to fix this (
> https://github.com/galaxyproject/tools-devteam/pull/300)
> I should have paid a bit more attention ...
>
> Cheers,
> Marius
>
> On 1 December 2015 at 22:46, Scott Szakonyi 
> wrote:
>
>> Hi Martin,
>>
>> I've been able to resolve all of the issues with Picard dependencies
>> except for Cairo. It's still failing with this error:
>>
>> Tool shed repository:package_cairo_1_12_14
>> Tool shed repository changeset revision:f5ab0fdf3716
>> Tool dependency status:Error
>> Tool dependency installation error:/bin/sh: -c: line 14: syntax error:
>> unexpected end of file
>>
>> If you have any suggestions about this error, I'd be pleased to attempt
>> to resolve it.
>>
>> Best,
>>
>> Scott
>>
>> On Tue, Dec 1, 2015 at 10:01 AM, Scott Szakonyi <
>> scott.b.szakony...@nd.edu> wrote:
>>
>>> Hi Martin,
>>>
>>> Thanks very much for your reply, and also to Marius.
>>>
>>> After some investigation, it appears that there is a firewall issue on
>>> my Galaxy server which is preventing the download of the file via FTP. I'm
>>> looking into options for that now.
>>>
>>> Best,
>>>
>>> Scott
>>>
>>> On Tue, Dec 1, 2015 at 9:56 AM, Martin Čech  wrote:
>>>
 Hello Scott,

 thanks to Marius van den Beek the first two issues should be fixed with
 this PR: https://github.com/galaxyproject/tools-devteam/pull/299

 These changes were already propagated to the Main Tool Shed.
 Note for tool developers: for future endeavours please use packages
 from the IUC repository (
 https://github.com/galaxyproject/tools-iuc/tree/master/packages)

 As of the timeout for the readline package it seems the problem was on
 the ftp.gnu side and it is now resolved.
 In the future Galaxy plans to use a smart caching proxy to
 handle all source codes required by the Tool Shed installations.
 This effort is lead by Eric Rasche and you can see it here
 https://github.com/galaxyproject/cargo-port

 Thank you for the report (and for using Galaxy :)).

 Martin

 On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi <
 scott.b.szakony...@nd.edu> wrote:

> Hi all,
>
> I'm installing the latest revision of Picard tools (efc56ee1ade4).
> Picard installs successfully, and the tools are appearing in the
> appropriate menu, but several packages that install with Picard are
> reporting dependency issues, and I'm concerned that not all the tools will
> work appropriately. The tools reporting issues are:
>
>- package_cairo_1_12_14 (last lines of long warning/error sequence)
>-
>   
> /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib:
>  file not recognized: Is a directory
>   collect2: ld returned 1 exit status
>   make[3]: *** [libcairo.la] Error 1
>   make[2]: *** [all] Error 2
>   make[1]: *** [all-recursive] Error 1
>   make: *** [all] Error 2
>   - package_pixman_0_32_4
>-
>   /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In 
> function `_start':
>   (.text+0x20): undefined reference to `main'
>   collect2: ld returned 1 exit status
>   make[2]: *** [clip-test] Error 1
>   make[1]: *** [all-recursive] Error 1
>   make: *** [all] Error 2
>- package_readline_6_2
>- Error downloading from URL
>   ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz:
>   
>
> Is anyone else having issues with these packages? Any suggestions for
> resolving these problems?
>
> Thanks!
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
> ___
> 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/


>>>
>>>
>>> --
>>> Scott B. Szakonyi
>>> Research Programmer
>>>
>>> *Center for Research Computing*
>>> 107 Information Technology Center
>>> Notre Dame, IN 46556
>>> http://crc.nd.edu
>>>
>>
>>
>>
>> --
>> Scott B. Szakonyi
>> Research Programmer
>>
>> *Center for Research Computing*
>> 107 Information Technology Center
>> Notre Dame, IN 46556
>> http://crc.nd.edu
>>
>> ___
>> Please 

Re: [galaxy-dev] Picard installation dependency issues

[Scott Szakonyi]

Hi Martin,

I've been able to resolve all of the issues with Picard dependencies except
for Cairo. It's still failing with this error:

Tool shed repository:package_cairo_1_12_14
Tool shed repository changeset revision:f5ab0fdf3716
Tool dependency status:Error
Tool dependency installation error:/bin/sh: -c: line 14: syntax error:
unexpected end of file

If you have any suggestions about this error, I'd be pleased to attempt to
resolve it.

Best,

Scott

On Tue, Dec 1, 2015 at 10:01 AM, Scott Szakonyi 
wrote:

> Hi Martin,
>
> Thanks very much for your reply, and also to Marius.
>
> After some investigation, it appears that there is a firewall issue on my
> Galaxy server which is preventing the download of the file via FTP. I'm
> looking into options for that now.
>
> Best,
>
> Scott
>
> On Tue, Dec 1, 2015 at 9:56 AM, Martin Čech  wrote:
>
>> Hello Scott,
>>
>> thanks to Marius van den Beek the first two issues should be fixed with
>> this PR: https://github.com/galaxyproject/tools-devteam/pull/299
>>
>> These changes were already propagated to the Main Tool Shed.
>> Note for tool developers: for future endeavours please use packages from
>> the IUC repository (
>> https://github.com/galaxyproject/tools-iuc/tree/master/packages)
>>
>> As of the timeout for the readline package it seems the problem was on
>> the ftp.gnu side and it is now resolved.
>> In the future Galaxy plans to use a smart caching proxy to handle
>> all source codes required by the Tool Shed installations. This effort is
>> lead by Eric Rasche and you can see it here
>> https://github.com/galaxyproject/cargo-port
>>
>> Thank you for the report (and for using Galaxy :)).
>>
>> Martin
>>
>> On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi <
>> scott.b.szakony...@nd.edu> wrote:
>>
>>> Hi all,
>>>
>>> I'm installing the latest revision of Picard tools (efc56ee1ade4).
>>> Picard installs successfully, and the tools are appearing in the
>>> appropriate menu, but several packages that install with Picard are
>>> reporting dependency issues, and I'm concerned that not all the tools will
>>> work appropriately. The tools reporting issues are:
>>>
>>>- package_cairo_1_12_14 (last lines of long warning/error sequence)
>>>-
>>>   
>>> /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib:
>>>  file not recognized: Is a directory
>>>   collect2: ld returned 1 exit status
>>>   make[3]: *** [libcairo.la] Error 1
>>>   make[2]: *** [all] Error 2
>>>   make[1]: *** [all-recursive] Error 1
>>>   make: *** [all] Error 2
>>>   - package_pixman_0_32_4
>>>-
>>>   /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In 
>>> function `_start':
>>>   (.text+0x20): undefined reference to `main'
>>>   collect2: ld returned 1 exit status
>>>   make[2]: *** [clip-test] Error 1
>>>   make[1]: *** [all-recursive] Error 1
>>>   make: *** [all] Error 2
>>>- package_readline_6_2
>>>- Error downloading from URL
>>>   ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz:
>>>   
>>>
>>> Is anyone else having issues with these packages? Any suggestions for
>>> resolving these problems?
>>>
>>> Thanks!
>>>
>>> --
>>> Scott B. Szakonyi
>>> Research Programmer
>>>
>>> *Center for Research Computing*
>>> 107 Information Technology Center
>>> Notre Dame, IN 46556
>>> http://crc.nd.edu
>>> ___
>>> 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/
>>
>>
>
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
>



-- 
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
___
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/

Re: [galaxy-dev] Picard installation dependency issues

[Scott Szakonyi]

Excellent! Install completed! Thanks very much.

On Tue, Dec 1, 2015 at 3:57 PM, Martin Čech  wrote:

> This is now updated in MTS. Thanks guys.
>
> M.
>
> On Tue, Dec 1, 2015 at 4:55 PM Marius van den Beek 
> wrote:
>
>> Hi Scott, Martin,
>>
>> there was still a small problem in cairo.
>> I made a PR to fix this (
>> https://github.com/galaxyproject/tools-devteam/pull/300)
>> I should have paid a bit more attention ...
>>
>> Cheers,
>> Marius
>>
>> On 1 December 2015 at 22:46, Scott Szakonyi 
>> wrote:
>>
>>> Hi Martin,
>>>
>>> I've been able to resolve all of the issues with Picard dependencies
>>> except for Cairo. It's still failing with this error:
>>>
>>> Tool shed repository:package_cairo_1_12_14
>>> Tool shed repository changeset revision:f5ab0fdf3716
>>> Tool dependency status:Error
>>> Tool dependency installation error:/bin/sh: -c: line 14: syntax error:
>>> unexpected end of file
>>>
>>> If you have any suggestions about this error, I'd be pleased to attempt
>>> to resolve it.
>>>
>>> Best,
>>>
>>> Scott
>>>
>>> On Tue, Dec 1, 2015 at 10:01 AM, Scott Szakonyi <
>>> scott.b.szakony...@nd.edu> wrote:
>>>
 Hi Martin,

 Thanks very much for your reply, and also to Marius.

 After some investigation, it appears that there is a firewall issue on
 my Galaxy server which is preventing the download of the file via FTP. I'm
 looking into options for that now.

 Best,

 Scott

 On Tue, Dec 1, 2015 at 9:56 AM, Martin Čech  wrote:

> Hello Scott,
>
> thanks to Marius van den Beek the first two issues should be fixed
> with this PR: https://github.com/galaxyproject/tools-devteam/pull/299
>
> These changes were already propagated to the Main Tool Shed.
> Note for tool developers: for future endeavours please use packages
> from the IUC repository (
> https://github.com/galaxyproject/tools-iuc/tree/master/packages)
>
> As of the timeout for the readline package it seems the problem was on
> the ftp.gnu side and it is now resolved.
> In the future Galaxy plans to use a smart caching proxy to
> handle all source codes required by the Tool Shed installations.
> This effort is lead by Eric Rasche and you can see it here
> https://github.com/galaxyproject/cargo-port
>
> Thank you for the report (and for using Galaxy :)).
>
> Martin
>
> On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi <
> scott.b.szakony...@nd.edu> wrote:
>
>> Hi all,
>>
>> I'm installing the latest revision of Picard tools (efc56ee1ade4).
>> Picard installs successfully, and the tools are appearing in the
>> appropriate menu, but several packages that install with Picard are
>> reporting dependency issues, and I'm concerned that not all the tools 
>> will
>> work appropriately. The tools reporting issues are:
>>
>>- package_cairo_1_12_14 (last lines of long warning/error
>>sequence)
>>-
>>   
>> /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib:
>>  file not recognized: Is a directory
>>   collect2: ld returned 1 exit status
>>   make[3]: *** [libcairo.la] Error 1
>>   make[2]: *** [all] Error 2
>>   make[1]: *** [all-recursive] Error 1
>>   make: *** [all] Error 2
>>   - package_pixman_0_32_4
>>-
>>   /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: 
>> In function `_start':
>>   (.text+0x20): undefined reference to `main'
>>   collect2: ld returned 1 exit status
>>   make[2]: *** [clip-test] Error 1
>>   make[1]: *** [all-recursive] Error 1
>>   make: *** [all] Error 2
>>- package_readline_6_2
>>- Error downloading from URL
>>   ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz:
>>   
>>
>> Is anyone else having issues with these packages? Any suggestions for
>> resolving these problems?
>>
>> Thanks!
>>
>> --
>> Scott B. Szakonyi
>> Research Programmer
>>
>> *Center for Research Computing*
>> 107 Information Technology Center
>> Notre Dame, IN 46556
>> http://crc.nd.edu
>> ___
>> 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/
>
>


 --
 Scott B. Szakonyi
 Research Programmer

 *Center for Research Computing*
 107 Information Technology Center
 Notre Dame, IN 

[galaxy-dev] Aberrant data allocation and SNP mapping problem

[Felix Mayr]

Dear Galaxy dev,

I have two problems, which might be related to each other. 

1) For a long time already, I continuously have ‘left over’ data allocation 
after deleting and purging histories. Someone from your team has repeatedly 
resolved that problem, but it root of the problem still persists. I know have 
91% allocation, when only having two histories of 67.48 and 59.45 GB.  The fix 
for automatic recalculation doesn’t seem to work…? 

2) I recently performed SNP mapping using a CloudMap based pipeline. The 
problem: the SNP mapping plots shows the exact same mapping/plots of the SNPs. 
They can not be the same. What is not the problem: the input files, as they are 
different in size, first and last lines of the files, and they produce very 
different SNP mapping mutation tables. Therefore, I think there might be a 
problem that the workflow somehow uses the same intermediate file for 
generating the SNP mapping plots. I already re-uploaded and rerun the workflows 
in new histories multiple times, but the same result each time. I would upload 
and run another data set for which I already have SNP mapping plots to see 
whether I again get the same plots or not, but that is now not possible as I am 
close to the data quota. 

I hope you can help solve these problems. 

All best,

Felix



˜
Felix Mayr, MSc.
Max Planck Institute for Biology of Ageing
Research Group of Dr. Martin Denzel
Metabolic and Genetic Regulation of Ageing
Joseph-Stelzmann-Str. 9b
D-50931 Cologne
Germany
+49.221.3797.0465
www.age.mpg.de/science/research-labs/denzel/

___
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/

Re: [galaxy-dev] Publish tool with Python dependencies to the toolshed

[Ulf Schaefer]

Thanks Martin and Bjoern for your advice.

Bjoern, does this modification to the galaxy.ini need to be made on all 
Galaxy instances that want to install and run this tool once its 
available in the shed? I assume it has nothing to do with the ability to 
publish it in the first place.

Thanks
Ulf

On 01/12/15 16:41, Björn Grüning wrote:
> Hi Ulf,
>
> just adding to Martins great explanation that you should set
>
>   enable_beta_tool_command_isolation = True
>
> in your galaxy.ini file if you are using a strict Python dependency with
> package_python_2_7_10.
>
> Cheers,
> Bjoern
>
> Am 01.12.2015 um 17:07 schrieb Martin Čech:
>> Hi Ulf,
>>
>> you most probably want your tool to depend on package_python_2_7_10 from
>> the iuc (it will ensure your tool has access to 2.7.10 no matter what
>> python the Galaxy executing your tool is using)
>>
>> The package is being developed here
>> https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_python_2_7_10
>> and
>> is available at the MTS here
>> https://toolshed.g2.bx.psu.edu/view/iuc/package_python_2_7_10/73631e818d3d
>>
>> You will need to add to your wrapper's xml something like:
>>
>> 
>> python
>> 
>>
>> And you have to include tool_dependencies.xml file which will look
>> something like:
>>
>> 
>> 
>> 
>> > prior_installation_required="True" />
>> 
>> 
>>
>> Please let me know if you have more questions.
>>
>> M.
>>
>> On Tue, Dec 1, 2015 at 10:54 AM Ulf Schaefer 
>> wrote:
>>
>>> Dear all
>>>
>>> I have a Python script that I would like to publish to the tool shed. It
>>> has a couple dependencies, all Python modules (argparse, PyVCF, PyYAML).
>>> It also needs a Python version 2.7<=X<3, which is not available per
>>> default everywhere.
>>>
>>> Firstly, how do I specify these dependencies in the tool 
>>> tag?
>>>
>>> And secondly, once I have a correct set of tool definition files with
>>> tests and test data, how do I best get it onto the tool shed?
>>>
>>> I had a look through the wiki and the planemo documentation.
>>> Unfortunately how to handle these dependencies did not become
>>> immediately obvious (to me).
>>>
>>> Thanks for any pointers and sorry if this has been answered some place I
>>> did not look.
>>>
>>> Cheers
>>> Ulf
>>>
>>> --
>>> Ulf Schaefer, PhD
>>> Bioinformatics Scientist
>>> Bioinformatics Unit - Infectious Disease Informatics
>>> National Infection Service
>>> Public Health England
>>> 61 Colindale Ave, London NW9 5EQ
>>> ulf.schae...@phe.gov.uk
>>> http://www.gov.uk/phe
>>> Protecting and improving the nation’s health
>>>
>>> **
>>> The information contained in the EMail and any attachments is confidential
>>> and intended solely and for the attention and use of the named
>>> addressee(s). It may not be disclosed to any other person without the
>>> express authority of Public Health England, or the intended recipient, or
>>> both. If you are not the intended recipient, you must not disclose, copy,
>>> distribute or retain this message or any part of it. This footnote also
>>> confirms that this EMail has been swept for computer viruses by
>>> Symantec.Cloud, but please re-sweep any attachments before opening or
>>> saving. http://www.gov.uk/PHE
>>> **
>>> ___
>>> 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/
>>

**
The information contained in the EMail and any attachments is confidential and 
intended solely and for the attention and use of the named addressee(s). It may 
not be disclosed to any other person without the express authority of Public 
Health England, or the intended recipient, or both. If you are not the intended 
recipient, you must not disclose, copy, distribute or retain this message or 
any part of it. This footnote also confirms that this EMail has been swept for 
computer viruses by Symantec.Cloud, but please re-sweep any attachments before 
opening or saving. http://www.gov.uk/PHE
**
___

Re: [galaxy-dev] Aberrant data allocation and SNP mapping problem

[Dannon Baker]

You're currently seeing 91% usage?  I just checked again and your disk
calculation should have been up to date (the recalc procedure did not
change anything), and I'm seeing 50% usage on your account.

On Tue, Dec 1, 2015 at 3:45 AM, Felix Mayr  wrote:
> The login emailaddress I use is felix.m...@gmail.com.
>
>
> ˜
> Felix Mayr, MSc.
> Max Planck Institute for Biology of Ageing
> Research Group of Dr. Martin Denzel
> Metabolic and Genetic Regulation of Ageing
> Joseph-Stelzmann-Str. 9b
> D-50931 Cologne
> Germany
> +49.221.3797.0465
> www.age.mpg.de/science/research-labs/denzel/
>
> On 01 Jan 2015, at 09:44, Felix Mayr  wrote:
>
> Dear Galaxy dev,
>
> I have two problems, which might be related to each other.
>
> 1) For a long time already, I continuously have ‘left over’ data allocation
> after deleting and purging histories. Someone from your team has repeatedly
> resolved that problem, but it root of the problem still persists. I know
> have 91% allocation, when only having two histories of 67.48 and 59.45 GB.
> The fix for automatic recalculation doesn’t seem to work…?
>
> 2) I recently performed SNP mapping using a CloudMap based pipeline. The
> problem: the SNP mapping plots shows the exact same mapping/plots of the
> SNPs. They can not be the same. What is not the problem: the input files, as
> they are different in size, first and last lines of the files, and they
> produce very different SNP mapping mutation tables. Therefore, I think there
> might be a problem that the workflow somehow uses the same intermediate file
> for generating the SNP mapping plots. I already re-uploaded and rerun the
> workflows in new histories multiple times, but the same result each time. I
> would upload and run another data set for which I already have SNP mapping
> plots to see whether I again get the same plots or not, but that is now not
> possible as I am close to the data quota.
>
> I hope you can help solve these problems.
>
> All best,
>
> Felix
>
>
>
> ˜
> Felix Mayr, MSc.
> Max Planck Institute for Biology of Ageing
> Research Group of Dr. Martin Denzel
> Metabolic and Genetic Regulation of Ageing
> Joseph-Stelzmann-Str. 9b
> D-50931 Cologne
> Germany
> +49.221.3797.0465
> www.age.mpg.de/science/research-labs/denzel/
>
>
>
> ___
> 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/

Re: [galaxy-dev] Aberrant data allocation and SNP mapping problem

[Jennifer Hillman-Jackson]

Hi Felix,

I have recalculated disk for you again. Our team is aware of this problem
and is working on a more permanent solution.

We will take a look at your workflow/histories to rule out a tool or
workflow function problem. If this does turn out to be a method issue
instead, then contacting the authors of the Cloudman pipeline would be
recommended as the next step. https://usegalaxy.org/u/gm2123/p/cloudmap

Thanks for using Galaxy and we will get back to you in a bit about the
workflow,

Jen

--
Jennifer Hillman-Jackson
Galaxy Application Support
http://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org


On Tue, Dec 1, 2015 at 12:45 AM, Felix Mayr  wrote:

> The login emailaddress I use is felix.m...@gmail.com.
>
>
> ˜
> Felix Mayr, MSc.
> Max Planck Institute for Biology of Ageing
> Research Group of Dr. Martin Denzel
> Metabolic and Genetic Regulation of Ageing
> Joseph-Stelzmann-Str. 9b
> D-50931 Cologne
> Germany
> +49.221.3797.0465
> www.age.mpg.de/science/research-labs/denzel/
>
> On 01 Jan 2015, at 09:44, Felix Mayr  wrote:
>
> Dear Galaxy dev,
>
> I have two problems, which might be related to each other.
>
> 1) For a long time already, I continuously have ‘left over’ data
> allocation after deleting and purging histories. Someone from your team has
> repeatedly resolved that problem, but it root of the problem still
> persists. I know have 91% allocation, when only having two histories of
> 67.48 and 59.45 GB.  The fix for automatic recalculation doesn’t seem to
> work…?
>
> 2) I recently performed SNP mapping using a CloudMap based pipeline. The
> problem: the SNP mapping plots shows the exact same mapping/plots of the
> SNPs. They can not be the same. What is not the problem: the input files,
> as they are different in size, first and last lines of the files, and they
> produce very different SNP mapping mutation tables. Therefore, I think
> there might be a problem that the workflow somehow uses the same
> intermediate file for generating the SNP mapping plots. I already
> re-uploaded and rerun the workflows in new histories multiple times, but
> the same result each time. I would upload and run another data set for
> which I already have SNP mapping plots to see whether I again get the same
> plots or not, but that is now not possible as I am close to the data quota.
>
> I hope you can help solve these problems.
>
> All best,
>
> Felix
>
>
>
> ˜
> Felix Mayr, MSc.
> Max Planck Institute for Biology of Ageing
> Research Group of Dr. Martin Denzel
> Metabolic and Genetic Regulation of Ageing
> Joseph-Stelzmann-Str. 9b
> D-50931 Cologne
> Germany
> +49.221.3797.0465
> www.age.mpg.de/science/research-labs/denzel/
>
>
>
> ___
> 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/

Re: [galaxy-dev] Aberrant data allocation and SNP mapping problem

[Felix Mayr]

The login emailaddress I use is felix.m...@gmail.com 
.


˜
Felix Mayr, MSc.
Max Planck Institute for Biology of Ageing
Research Group of Dr. Martin Denzel
Metabolic and Genetic Regulation of Ageing
Joseph-Stelzmann-Str. 9b
D-50931 Cologne
Germany
+49.221.3797.0465
www.age.mpg.de/science/research-labs/denzel/

> On 01 Jan 2015, at 09:44, Felix Mayr  wrote:
> 
> Dear Galaxy dev,
> 
> I have two problems, which might be related to each other. 
> 
> 1) For a long time already, I continuously have ‘left over’ data allocation 
> after deleting and purging histories. Someone from your team has repeatedly 
> resolved that problem, but it root of the problem still persists. I know have 
> 91% allocation, when only having two histories of 67.48 and 59.45 GB.  The 
> fix for automatic recalculation doesn’t seem to work…? 
> 
> 2) I recently performed SNP mapping using a CloudMap based pipeline. The 
> problem: the SNP mapping plots shows the exact same mapping/plots of the 
> SNPs. They can not be the same. What is not the problem: the input files, as 
> they are different in size, first and last lines of the files, and they 
> produce very different SNP mapping mutation tables. Therefore, I think there 
> might be a problem that the workflow somehow uses the same intermediate file 
> for generating the SNP mapping plots. I already re-uploaded and rerun the 
> workflows in new histories multiple times, but the same result each time. I 
> would upload and run another data set for which I already have SNP mapping 
> plots to see whether I again get the same plots or not, but that is now not 
> possible as I am close to the data quota. 
> 
> I hope you can help solve these problems. 
> 
> All best,
> 
> Felix
> 
> 
> 
> ˜
> Felix Mayr, MSc.
> Max Planck Institute for Biology of Ageing
> Research Group of Dr. Martin Denzel
> Metabolic and Genetic Regulation of Ageing
> Joseph-Stelzmann-Str. 9b
> D-50931 Cologne
> Germany
> +49.221.3797.0465
> www.age.mpg.de/science/research-labs/denzel/ 
> 

___
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/

[galaxy-dev] December 2015 Galactic News

[Dave Clements]

Hello all,

The *December Galactic News
* is hot off the
presses.

   -

   81 new publications, including 4 highlighted pubs
   
   -

   Event News 
   -

  Spanish Galaxy Community Meetup: 18 December, Barcelona
  

  -

  Galaxy Day 2015 Presentations are online
  

  -

  All upcoming events
  
  -

   Who's Hiring
   
   -

   Two new public Galaxy servers
   

   -

   New Releases
   
   -

  Planemo 0.19.0 - 0.21.1
  

  -

   ToolShed Contributions in October and November
   
   -

   and lots of other news too
   .

Get your copy now!

The Galaxy Team  wishes you and
yours a happy holiday season


-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/
___
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/

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

[Martin Čech]

Hans Rudolph,

thanks to Marius van den Beek this issue should be fixed with this PR:
https://github.com/galaxyproject/tools-devteam/pull/299

These changes were already propagated to the Main Tool Shed.

Note for tool developers: for future endeavours please use packages from
the IUC repository (
https://github.com/galaxyproject/tools-iuc/tree/master/packages)

Thank you for the report (and for using Galaxy :)).

Martin


On Tue, Dec 1, 2015 at 6:25 AM Hans Rudolph  wrote:

> Hello Galaxy-devs,
>
> I am setting up galaxy on current os x 10.11 and encounter this trouble
> using galaxy to install pixman-0.32.4:
> the package gets downloaded successfully from
> http://cairographics.org/releases/pixman-0.32.4.tar.gz
> … while following the installation process in terminal I see this output
> during the process …presumably indicating an gcc problem
> ...
> install_environment.STDOUT DEBUG 2015-12-01 10:44:18,096 checking build
> system type... x86_64-apple-darwin15.0.0
> install_environment.STDOUT DEBUG 2015-12-01 10:44:18,099 checking for
> gcc... gcc
> checking build system type... x86_64-apple-darwin15.0.0
> checking host system type... x86_64-apple-darwin15.0.0
> checking for gcc... gcc
> checking whether the C compiler works... no
> configure: error: in
> `/Users/hans/galaxy/database/tmp/tmp-toolshed-mtdKC9F_F/pixman-0.32.4':
> configure: error: C compiler cannot create executables
> See `config.log' for more details
>
> Curiously, if I download the pixman package (same URL) outside of galaxy
> and run ./configure … gcc seems to work :
> ...
> checking build system type... x86_64-apple-darwin15.0.0
> checking host system type... x86_64-apple-darwin15.0.0
> checking for gcc... gcc
> checking whether the C compiler works… yes
> ...
> and ./configure finishes OK.
>
> to actually compile/make pixman properly, I have to use the ./configure
> —disable-mmx option to avoid another known error
> (*pixman-mmx.c:100:20: **error: **constraint 'K' expects an integer
> constant expression*
> : "y" (__A), "K" (__N))
>
> Perhaps someone is using galaxy on Mac OS X how this difference in gcc
> handling arises?
> Thanks very much,
>
> Hans Rudolph
> ___
> 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/

[galaxy-dev] Publish tool with Python dependencies to the toolshed

[Ulf Schaefer]

Dear all

I have a Python script that I would like to publish to the tool shed. It 
has a couple dependencies, all Python modules (argparse, PyVCF, PyYAML). 
It also needs a Python version 2.7<=X<3, which is not available per 
default everywhere.

Firstly, how do I specify these dependencies in the tool  tag?

And secondly, once I have a correct set of tool definition files with 
tests and test data, how do I best get it onto the tool shed?

I had a look through the wiki and the planemo documentation. 
Unfortunately how to handle these dependencies did not become 
immediately obvious (to me).

Thanks for any pointers and sorry if this has been answered some place I 
did not look.

Cheers
Ulf

-- 
Ulf Schaefer, PhD
Bioinformatics Scientist
Bioinformatics Unit - Infectious Disease Informatics
National Infection Service
Public Health England
61 Colindale Ave, London NW9 5EQ
ulf.schae...@phe.gov.uk
http://www.gov.uk/phe
Protecting and improving the nation’s health

**
The information contained in the EMail and any attachments is confidential and 
intended solely and for the attention and use of the named addressee(s). It may 
not be disclosed to any other person without the express authority of Public 
Health England, or the intended recipient, or both. If you are not the intended 
recipient, you must not disclose, copy, distribute or retain this message or 
any part of it. This footnote also confirms that this EMail has been swept for 
computer viruses by Symantec.Cloud, but please re-sweep any attachments before 
opening or saving. http://www.gov.uk/PHE
**
___
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/

Re: [galaxy-dev] Picard installation dependency issues

[Martin Čech]

Hello Scott,

thanks to Marius van den Beek the first two issues should be fixed with
this PR: https://github.com/galaxyproject/tools-devteam/pull/299

These changes were already propagated to the Main Tool Shed.
Note for tool developers: for future endeavours please use packages from
the IUC repository (
https://github.com/galaxyproject/tools-iuc/tree/master/packages)

As of the timeout for the readline package it seems the problem was on the
ftp.gnu side and it is now resolved.
In the future Galaxy plans to use a smart caching proxy to handle
all source codes required by the Tool Shed installations. This effort is
lead by Eric Rasche and you can see it here
https://github.com/galaxyproject/cargo-port

Thank you for the report (and for using Galaxy :)).

Martin

On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi 
wrote:

> Hi all,
>
> I'm installing the latest revision of Picard tools (efc56ee1ade4). Picard
> installs successfully, and the tools are appearing in the appropriate menu,
> but several packages that install with Picard are reporting dependency
> issues, and I'm concerned that not all the tools will work appropriately.
> The tools reporting issues are:
>
>- package_cairo_1_12_14 (last lines of long warning/error sequence)
>-
>   
> /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib:
>  file not recognized: Is a directory
>   collect2: ld returned 1 exit status
>   make[3]: *** [libcairo.la] Error 1
>   make[2]: *** [all] Error 2
>   make[1]: *** [all-recursive] Error 1
>   make: *** [all] Error 2
>   - package_pixman_0_32_4
>-
>   /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In 
> function `_start':
>   (.text+0x20): undefined reference to `main'
>   collect2: ld returned 1 exit status
>   make[2]: *** [clip-test] Error 1
>   make[1]: *** [all-recursive] Error 1
>   make: *** [all] Error 2
>- package_readline_6_2
>- Error downloading from URL
>   ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz:
>   
>
> Is anyone else having issues with these packages? Any suggestions for
> resolving these problems?
>
> Thanks!
>
> --
> Scott B. Szakonyi
> Research Programmer
>
> *Center for Research Computing*
> 107 Information Technology Center
> Notre Dame, IN 46556
> http://crc.nd.edu
> ___
> 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/

[galaxy-dev] Multiple web servers and handlers Galaxy failed

[Makis Ladoukakis]

Hello everyone,

I am trying to setup a Galaxy instance for a multi-user production environment 
and I tried to follow the instructions here:

https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy

but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh 
--daemon) I got the following error in my browser:Bad Gateway
The proxy server received an invalid
response from an upstream server.


I don't get any errors from the paster.log files so I am guessing the error is 
somewhere in my apache configuration although I can't see where it could be.


Has anyone encountered this problem before?

Kind regards,
Makis


P.S. My apache configuration is as follows:

I added that to my apache httpd.conf file:

#for galaxy
#RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P]
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) 
/home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*) 
/home/galaxy/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L]

LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so


Sethandler uwsgi-handler
uWSGISocket 127.0.0.1:4001
uWSGImaxVars 512


I am also attaching my job_conf.xml and galaxy.ini file.

  

galaxy.ini
Description: Binary data


job_conf.xml
Description: XML document
___
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/

Re: [galaxy-dev] Picard installation dependency issues

[Scott Szakonyi]

Hi Martin,

Thanks very much for your reply, and also to Marius.

After some investigation, it appears that there is a firewall issue on my
Galaxy server which is preventing the download of the file via FTP. I'm
looking into options for that now.

Best,

Scott

On Tue, Dec 1, 2015 at 9:56 AM, Martin Čech  wrote:

> Hello Scott,
>
> thanks to Marius van den Beek the first two issues should be fixed with
> this PR: https://github.com/galaxyproject/tools-devteam/pull/299
>
> These changes were already propagated to the Main Tool Shed.
> Note for tool developers: for future endeavours please use packages from
> the IUC repository (
> https://github.com/galaxyproject/tools-iuc/tree/master/packages)
>
> As of the timeout for the readline package it seems the problem was on the
> ftp.gnu side and it is now resolved.
> In the future Galaxy plans to use a smart caching proxy to handle
> all source codes required by the Tool Shed installations. This effort is
> lead by Eric Rasche and you can see it here
> https://github.com/galaxyproject/cargo-port
>
> Thank you for the report (and for using Galaxy :)).
>
> Martin
>
> On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi 
> wrote:
>
>> Hi all,
>>
>> I'm installing the latest revision of Picard tools (efc56ee1ade4).
>> Picard installs successfully, and the tools are appearing in the
>> appropriate menu, but several packages that install with Picard are
>> reporting dependency issues, and I'm concerned that not all the tools will
>> work appropriately. The tools reporting issues are:
>>
>>- package_cairo_1_12_14 (last lines of long warning/error sequence)
>>-
>>   
>> /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib:
>>  file not recognized: Is a directory
>>   collect2: ld returned 1 exit status
>>   make[3]: *** [libcairo.la] Error 1
>>   make[2]: *** [all] Error 2
>>   make[1]: *** [all-recursive] Error 1
>>   make: *** [all] Error 2
>>   - package_pixman_0_32_4
>>-
>>   /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In 
>> function `_start':
>>   (.text+0x20): undefined reference to `main'
>>   collect2: ld returned 1 exit status
>>   make[2]: *** [clip-test] Error 1
>>   make[1]: *** [all-recursive] Error 1
>>   make: *** [all] Error 2
>>- package_readline_6_2
>>- Error downloading from URL
>>   ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz:
>>   
>>
>> Is anyone else having issues with these packages? Any suggestions for
>> resolving these problems?
>>
>> Thanks!
>>
>> --
>> Scott B. Szakonyi
>> Research Programmer
>>
>> *Center for Research Computing*
>> 107 Information Technology Center
>> Notre Dame, IN 46556
>> http://crc.nd.edu
>> ___
>> 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/
>
>


-- 
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
___
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/

Re: [galaxy-dev] Publish tool with Python dependencies to the toolshed

[Martin Čech]

Hi Ulf,

you most probably want your tool to depend on package_python_2_7_10 from
the iuc (it will ensure your tool has access to 2.7.10 no matter what
python the Galaxy executing your tool is using)

The package is being developed here
https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_python_2_7_10
and
is available at the MTS here
https://toolshed.g2.bx.psu.edu/view/iuc/package_python_2_7_10/73631e818d3d

You will need to add to your wrapper's xml something like:


python


And you have to include tool_dependencies.xml file which will look
something like:








Please let me know if you have more questions.

M.

On Tue, Dec 1, 2015 at 10:54 AM Ulf Schaefer 
wrote:

> Dear all
>
> I have a Python script that I would like to publish to the tool shed. It
> has a couple dependencies, all Python modules (argparse, PyVCF, PyYAML).
> It also needs a Python version 2.7<=X<3, which is not available per
> default everywhere.
>
> Firstly, how do I specify these dependencies in the tool 
> tag?
>
> And secondly, once I have a correct set of tool definition files with
> tests and test data, how do I best get it onto the tool shed?
>
> I had a look through the wiki and the planemo documentation.
> Unfortunately how to handle these dependencies did not become
> immediately obvious (to me).
>
> Thanks for any pointers and sorry if this has been answered some place I
> did not look.
>
> Cheers
> Ulf
>
> --
> Ulf Schaefer, PhD
> Bioinformatics Scientist
> Bioinformatics Unit - Infectious Disease Informatics
> National Infection Service
> Public Health England
> 61 Colindale Ave, London NW9 5EQ
> ulf.schae...@phe.gov.uk
> http://www.gov.uk/phe
> Protecting and improving the nation’s health
>
> **
> The information contained in the EMail and any attachments is confidential
> and intended solely and for the attention and use of the named
> addressee(s). It may not be disclosed to any other person without the
> express authority of Public Health England, or the intended recipient, or
> both. If you are not the intended recipient, you must not disclose, copy,
> distribute or retain this message or any part of it. This footnote also
> confirms that this EMail has been swept for computer viruses by
> Symantec.Cloud, but please re-sweep any attachments before opening or
> saving. http://www.gov.uk/PHE
> **
> ___
> 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/