[galaxy-dev] Trying to install GATK on up-to-date Galaxy install

[Dooley, Damion]

I seem to run into a bottleneck with the .’package_pixman_0_32_4’.  This seems 
to happen with both boris and devteam versions?  The same error is preventing 
cairo from installing.

libpng
  1.6.7   package Installed
pixman
  0.32.4  package Error   
/usr/local/galaxy/shared/tool_dependency/libpng/1.6.7/boris/package_libpng_1_6_7/7de5acbf6c85/lib:
 file not recognized: Is a directory
collect2: ld returned 1 exit status
make[2]: *** [clip-test] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2


I appreciate any pointers on this!

Regards,

Damion
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[galaxy-dev] R: Planemo 0.19.0 testing tools that produce dataset collections

[Nicola Soranzo]

Hi Greg,
in the inputs the param has name "input_gff", while in the test you are using 
name "input".

Cheers, 
Nicola 

 Von Kuster, Greg ha scritto 

>Hello Galaxy devs,
>
>I’m developing a tool that uses a multi-select list to accept any number of 
>input datasets.  The tool works fine when executing it within Galaxy, but when 
>running it through planemo testing, it never passes, so I’m wondering if there 
>are known issues with planemo testing tools that produce dataset collections.
>
>I’ve spent some time adding debugging log statements into the Galaxy framework 
>for planemo test runs, but haven’t uncovered anything obvious.  So if there 
>are no known issues with planemo testing dataset_collections, I’m wondering if 
>my tool config syntax is incorrect.
>
>Does anyone see anything obvious?  Any insight is much appreciated!
>
>Here is the command line.  Notice that I do not define any outputs since I am 
>using a dataset collection.  Is this causing a problem for planemo?
>
>
>python $__tool_directory__/genetrack.py
>--input_format $input_format_cond.input_format
>#if str($input_format_cond.input_format) == "genetracktool":
>#for $i in $input_format_cond.input_genetracktool:
> --input "${i}" "${i.hid}" "${i.name}"
>#end for
>#elif str($input_format_cond.input_format) == "gff":
>#for $i in $input_format_cond.input_gff:
> --input "${i}" "${i.hid}" "${i.name}"
>#end for
>#end if
>--sigma $sigma
>--exclusion $exclusion
>--up_width $up_width
>--down_width $down_width
>--filter $filter
>--chromosome $chromosome
>--chunk_size $chunk_size
>--output_format $output_format
>
>
>The input  dataset parameter looks like this:
>
>label="Predict peaks on" />
>
>The tool produces a list of outputs, so I’ve defined a collection like this:
>
>
>
> directory="output" ext="gff" visible="false" />
>
>
>
>I’m using planemo, version 0.19.0.
>
>Here is one of the tools’ functional test definitions.
>
>
> ftype="gff" />
>
>
>
>
>
>
>
>
>
>
> ftype="gff" />
>
>
>
>Here is the log from running the test with planemo.
>
>Genetrack ( genetrack ) > Test-3 ... requests.packages.urllib3.connectionpool 
>INFO 2015-11-04 15:22:03,292 Starting new HTTP connection (1): localhost
>galaxy.web.framework.webapp INFO 2015-11-04 15:22:03,295 Session authenticated 
>using Galaxy master api key
>requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,303 "GET 
>/api/users?key=test_key HTTP/1.1" 200 None
>requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,305 Starting 
>new HTTP connection (1): localhost
>galaxy.web.framework.webapp INFO 2015-11-04 15:22:03,308 Session authenticated 
>using Galaxy master api key
>requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,326 "POST 
>/api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None
>requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,328 Starting 
>new HTTP connection (1): localhost
>requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,418 "POST 
>/api/histories HTTP/1.1" 200 None
>requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,421 Starting 
>new HTTP connection (1): localhost
>requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,475 "POST 
>/api/tools HTTP/1.1" 400 None
>ERROR
>
>==
>ERROR: Genetrack ( genetrack ) > Test-1
>--
>Traceback (most recent call last):
>  File "/Users/gvk/work/git_workspace/galaxy/test/functional/test_toolbox.py", 
> line 289, in test_tool
>self.do_it( td )
>  File "/Users/gvk/work/git_workspace/galaxy/test/functional/test_toolbox.py", 
> line 58, in do_it
>raise e
>RunToolException: Error creating a job for these tool inputs - Unknown error 
>occurred while processing request.
> >> begin captured logging << 
>requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection 
>(1): localhost
>galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master 
>api key
>requests.packages.urllib3.connectionpool: DEBUG: "GET /api/users?key=test_key 
>HTTP/1.1" 200 None
>requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection 
>(1): localhost
>galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master 
>api key
>requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users HTTP/1.1" 
>200 None
>requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection 
>(1): localhost
>galaxy.web.framework.webapp: INFO: Sess

[galaxy-dev] Planemo 0.19.0 testing tools that produce dataset collections

[Von Kuster, Greg]

Hello Galaxy devs,

I’m developing a tool that uses a multi-select list to accept any number of 
input datasets.  The tool works fine when executing it within Galaxy, but when 
running it through planemo testing, it never passes, so I’m wondering if there 
are known issues with planemo testing tools that produce dataset collections.

I’ve spent some time adding debugging log statements into the Galaxy framework 
for planemo test runs, but haven’t uncovered anything obvious.  So if there are 
no known issues with planemo testing dataset_collections, I’m wondering if my 
tool config syntax is incorrect.

Does anyone see anything obvious?  Any insight is much appreciated!

Here is the command line.  Notice that I do not define any outputs since I am 
using a dataset collection.  Is this causing a problem for planemo?


python $__tool_directory__/genetrack.py
--input_format $input_format_cond.input_format
#if str($input_format_cond.input_format) == "genetracktool":
#for $i in $input_format_cond.input_genetracktool:
 --input "${i}" "${i.hid}" "${i.name}"
#end for
#elif str($input_format_cond.input_format) == "gff":
#for $i in $input_format_cond.input_gff:
 --input "${i}" "${i.hid}" "${i.name}"
#end for
#end if
--sigma $sigma
--exclusion $exclusion
--up_width $up_width
--down_width $down_width
--filter $filter
--chromosome $chromosome
--chunk_size $chunk_size
--output_format $output_format


The input  dataset parameter looks like this:



The tool produces a list of outputs, so I’ve defined a collection like this:







I’m using planemo, version 0.19.0.

Here is one of the tools’ functional test definitions.

















Here is the log from running the test with planemo.

Genetrack ( genetrack ) > Test-3 ... requests.packages.urllib3.connectionpool 
INFO 2015-11-04 15:22:03,292 Starting new HTTP connection (1): localhost
galaxy.web.framework.webapp INFO 2015-11-04 15:22:03,295 Session authenticated 
using Galaxy master api key
requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,303 "GET 
/api/users?key=test_key HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,305 Starting 
new HTTP connection (1): localhost
galaxy.web.framework.webapp INFO 2015-11-04 15:22:03,308 Session authenticated 
using Galaxy master api key
requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,326 "POST 
/api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,328 Starting 
new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,418 "POST 
/api/histories HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,421 Starting 
new HTTP connection (1): localhost
requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,475 "POST 
/api/tools HTTP/1.1" 400 None
ERROR

==
ERROR: Genetrack ( genetrack ) > Test-1
--
Traceback (most recent call last):
  File "/Users/gvk/work/git_workspace/galaxy/test/functional/test_toolbox.py", 
line 289, in test_tool
self.do_it( td )
  File "/Users/gvk/work/git_workspace/galaxy/test/functional/test_toolbox.py", 
line 58, in do_it
raise e
RunToolException: Error creating a job for these tool inputs - Unknown error 
occurred while processing request.
 >> begin captured logging << 
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection 
(1): localhost
galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master 
api key
requests.packages.urllib3.connectionpool: DEBUG: "GET /api/users?key=test_key 
HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection 
(1): localhost
galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master 
api key
requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users HTTP/1.1" 200 
None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection 
(1): localhost
galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master 
api key
requests.packages.urllib3.connectionpool: DEBUG: "POST 
/api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None
requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection 
(1): localhost
requests.packages.urllib3.connectionpool: DEBUG: "POST /api/histories HTTP/1.1" 
200 None
requests.packages.urllib3.connectionpool: INFO: S

Re: [galaxy-dev] installable revisions for repository suite definitions

[Aaron Petkau]

Okay, that makes sense.  I'll switch over to making sure each tool
dependency is in a separate repository with version names.  It was just one
repo which we were updating a lot that ended up with multiple versions so
it's an easy thing to do.

Thanks,

Aaron


On Wed, Nov 4, 2015 at 12:18 PM, Martin Čech  wrote:

> Hi Aaron,
>
> I think Galaxy will always install the latest revision of the selected
> installable revision. Our approach was that tool dependencies have
> versioned repositories (with versions in the names) so that it cannot
> happen that abyss 2.0 would be in the package_abyss_1_9_0 repo. With this
> in place you shouldn't care about the actual revision because it will
> always install correct version of the tool.
>
> Carefuly following this fragile approach you should be able to achieve
> what you want. :/
>
> Thank you.
>
> M.
>
>
>
> On Wed, Nov 4, 2015 at 1:09 PM Aaron Petkau 
> wrote:
>
>> Thanks Martin, that helps me out.  However, the issue I'm running into is
>> that it seems like specific revisions in my repository suite definition are
>> being ignored and it's only using the latest one.
>>
>> I think what may be happening is as follows.
>>
>> In my repository suite I have a dependency like:
>>
>> > toolshed="http://toolshed.g2.bx.psu.edu"; />
>>
>> Now, "package_x" defines dependencies for tools in a
>> "tool_dependencies.xml" file.  And it has been updated to a newer revision,
>> "1".
>>
>> Looking through the toolshed, it looks like revision "0" for "package_x"
>> isn't being set as an installable revision.  So, when installing my older
>> repository dependency suite, it's ignoring revision "0" and just installing
>> revision "1".
>>
>> Is there any way to force it to install revision "0" of package_x?
>> Should I never be updating the repositories for tool dependencies?
>>
>> This was all being tested out with toolshed tag "v15.05.1".
>>
>> Thanks,
>>
>> Aaron
>>
>>
>>
>> On Wed, Nov 4, 2015 at 10:28 AM, Martin Čech  wrote:
>>
>>> Hi Aaron,
>>>
>>> we touched this recently here:
>>> https://github.com/galaxyproject/tools-devteam/pull/267
>>>
>>> I believe that if you specify the repository_dependencies.xml of your
>>> suite in the following way:
>>>
>>> 
>>> >> name="fasta_clipping_histogram" owner="devteam" toolshed="
>>> http://toolshed.g2.bx.psu.edu"; />
>>>
>>> you will pin the exact revision of the tool (fasta_clipping_histogram
>>> here) to that suite. Then you can have suite_fastx_toolkit_0_0_13 and
>>> suite_fastx_toolkit_0_0_9 repositories which will install the requested
>>> versions of the tools.
>>>
>>> M.
>>>
>>> On Wed, Nov 4, 2015 at 10:47 AM Aaron Petkau 
>>> wrote:
>>>
 Okay, thanks Dave.  That makes sense.  Moving forward I'll just make a
 new suite with a version number in the name.

 Another question, does the same apply for tool dependency definitions?
 I've upgraded a suite of tools + dependency definitions, and now even if I
 make a new repository suite (to allow installing of my old set of tools,
 revision 0 in my example) it's installing the newer commit in one tool
 dependency definition repository.

 Thanks,

 Aaron

 On Mon, Nov 2, 2015 at 7:59 AM, Dave Bouvier  wrote:

> Aaron,
>
> Repository suite definitions are designed to only allow the latest
> revision to be installable. My recommendation in this case would be to
> define two separate suites tagged in some descriptive way, so the
> individual use cases would have their appropriate suites.
>
> -
> Dave Bouvier
> http://galaxyproject.org
> http://usegalaxy.org
>
>
> On 10/29/2015 02:23 PM, Aaron Petkau wrote:
>
>> Hello,
>>
>> I'm running into some issues with maintaining multiple installable
>> revisions for a repository suite and I'm not sure if there's something
>> I've missed.
>>
>> I have a local toolshed where I'm maintaining my tools, and I have a
>> repository suite definition, defining a number of dependencies.  So,
>> I have:
>>
>> suite_X (mercurial revision 0):
>> Dependency A
>> Dependency B
>>
>> I updated "suite_X" and changed the dependencies:
>>
>> suite_X (mercurial revision 1):
>>  Dependency A
>>  Dependency B
>>  Dependency C
>>
>> I would like to have both mercurial revision 0 and 1 installable in
>> Galaxy, but only revision 1 (the latest) is showing up as installable.
>> I found documentation at
>> https://wiki.galaxyproject.org/RepositoryRevisions but this seems to
>> only cover a repository containing a single tool, not a suite of
>> tools.
>>
>> Is there something I'm doing wrong or some setting I have to change
>> here?  My toolshed is running with Galaxy tag "v15.07".
>>
>> Thanks,
>>
>> Aaron
>>
>>
>> ___
>> Please keep all rep

[galaxy-dev] GCC2016 Training Topic Voting CLOSES THIS FRIDAY

[Dave Clements]

Hello all,

*Voting * on what training topics
 are offered at GCC2016
Training  *closes
this Friday*.  Please vote  in the next two days!

> As always, please let us know if you have any questions.

Thanks,

The GCC2016 Exec 

http://bit.ly/gcc2016vote

> There are nominated topics
>  spanning from
> basic usage to advanced deployment. No matter what you do with Galaxy,
> there are topics for you to choose from. Your vote
>  will determine the topics that are offered,
> which topics should be offered more than once, and which ones should not be
> scheduled at the same time. Your vote matters.



*Topic voting closes November 6.* The Training schedule, including
> instructors, will be published before early registration opens.



*About GCC2016 Training
> :*



The 2016 Galaxy Community Conference (GCC2016)
>  will be held June 25-29
> at Indiana University  in Bloomington, Indiana,
> United States. GCC2016 features two full days of training on June 26-27
> . Each day will
> have multiple tracks, with each track featuring several sessions throughout
> the day.



Workshops will be hands-on and participants will be strongly encouraged to
> bring a laptop and follow along.



If you work in data-intensive biomedical research, there is no better place
> than GCC2016 to present your work and to learn from others.


> --
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/
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Re: [galaxy-dev] installable revisions for repository suite definitions

[Martin Čech]

Hi Aaron,

I think Galaxy will always install the latest revision of the selected
installable revision. Our approach was that tool dependencies have
versioned repositories (with versions in the names) so that it cannot
happen that abyss 2.0 would be in the package_abyss_1_9_0 repo. With this
in place you shouldn't care about the actual revision because it will
always install correct version of the tool.

Carefuly following this fragile approach you should be able to achieve what
you want. :/

Thank you.

M.



On Wed, Nov 4, 2015 at 1:09 PM Aaron Petkau  wrote:

> Thanks Martin, that helps me out.  However, the issue I'm running into is
> that it seems like specific revisions in my repository suite definition are
> being ignored and it's only using the latest one.
>
> I think what may be happening is as follows.
>
> In my repository suite I have a dependency like:
>
>  toolshed="http://toolshed.g2.bx.psu.edu"; />
>
> Now, "package_x" defines dependencies for tools in a
> "tool_dependencies.xml" file.  And it has been updated to a newer revision,
> "1".
>
> Looking through the toolshed, it looks like revision "0" for "package_x"
> isn't being set as an installable revision.  So, when installing my older
> repository dependency suite, it's ignoring revision "0" and just installing
> revision "1".
>
> Is there any way to force it to install revision "0" of package_x?  Should
> I never be updating the repositories for tool dependencies?
>
> This was all being tested out with toolshed tag "v15.05.1".
>
> Thanks,
>
> Aaron
>
>
>
> On Wed, Nov 4, 2015 at 10:28 AM, Martin Čech  wrote:
>
>> Hi Aaron,
>>
>> we touched this recently here:
>> https://github.com/galaxyproject/tools-devteam/pull/267
>>
>> I believe that if you specify the repository_dependencies.xml of your
>> suite in the following way:
>>
>> 
>> > name="fasta_clipping_histogram" owner="devteam" toolshed="
>> http://toolshed.g2.bx.psu.edu"; />
>>
>> you will pin the exact revision of the tool (fasta_clipping_histogram
>> here) to that suite. Then you can have suite_fastx_toolkit_0_0_13 and
>> suite_fastx_toolkit_0_0_9 repositories which will install the requested
>> versions of the tools.
>>
>> M.
>>
>> On Wed, Nov 4, 2015 at 10:47 AM Aaron Petkau 
>> wrote:
>>
>>> Okay, thanks Dave.  That makes sense.  Moving forward I'll just make a
>>> new suite with a version number in the name.
>>>
>>> Another question, does the same apply for tool dependency definitions?
>>> I've upgraded a suite of tools + dependency definitions, and now even if I
>>> make a new repository suite (to allow installing of my old set of tools,
>>> revision 0 in my example) it's installing the newer commit in one tool
>>> dependency definition repository.
>>>
>>> Thanks,
>>>
>>> Aaron
>>>
>>> On Mon, Nov 2, 2015 at 7:59 AM, Dave Bouvier  wrote:
>>>
 Aaron,

 Repository suite definitions are designed to only allow the latest
 revision to be installable. My recommendation in this case would be to
 define two separate suites tagged in some descriptive way, so the
 individual use cases would have their appropriate suites.

 -
 Dave Bouvier
 http://galaxyproject.org
 http://usegalaxy.org


 On 10/29/2015 02:23 PM, Aaron Petkau wrote:

> Hello,
>
> I'm running into some issues with maintaining multiple installable
> revisions for a repository suite and I'm not sure if there's something
> I've missed.
>
> I have a local toolshed where I'm maintaining my tools, and I have a
> repository suite definition, defining a number of dependencies.  So, I
> have:
>
> suite_X (mercurial revision 0):
> Dependency A
> Dependency B
>
> I updated "suite_X" and changed the dependencies:
>
> suite_X (mercurial revision 1):
>  Dependency A
>  Dependency B
>  Dependency C
>
> I would like to have both mercurial revision 0 and 1 installable in
> Galaxy, but only revision 1 (the latest) is showing up as installable.
> I found documentation at
> https://wiki.galaxyproject.org/RepositoryRevisions but this seems to
> only cover a repository containing a single tool, not a suite of tools.
>
> Is there something I'm doing wrong or some setting I have to change
> here?  My toolshed is running with Galaxy tag "v15.07".
>
> Thanks,
>
> Aaron
>
>
> ___
> 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 

Re: [galaxy-dev] installable revisions for repository suite definitions

[Aaron Petkau]

Thanks Martin, that helps me out.  However, the issue I'm running into is
that it seems like specific revisions in my repository suite definition are
being ignored and it's only using the latest one.

I think what may be happening is as follows.

In my repository suite I have a dependency like:

http://toolshed.g2.bx.psu.edu"; />

Now, "package_x" defines dependencies for tools in a
"tool_dependencies.xml" file.  And it has been updated to a newer revision,
"1".

Looking through the toolshed, it looks like revision "0" for "package_x"
isn't being set as an installable revision.  So, when installing my older
repository dependency suite, it's ignoring revision "0" and just installing
revision "1".

Is there any way to force it to install revision "0" of package_x?  Should
I never be updating the repositories for tool dependencies?

This was all being tested out with toolshed tag "v15.05.1".

Thanks,

Aaron



On Wed, Nov 4, 2015 at 10:28 AM, Martin Čech  wrote:

> Hi Aaron,
>
> we touched this recently here:
> https://github.com/galaxyproject/tools-devteam/pull/267
>
> I believe that if you specify the repository_dependencies.xml of your
> suite in the following way:
>
> 
>  name="fasta_clipping_histogram" owner="devteam" toolshed="
> http://toolshed.g2.bx.psu.edu"; />
>
> you will pin the exact revision of the tool (fasta_clipping_histogram
> here) to that suite. Then you can have suite_fastx_toolkit_0_0_13 and
> suite_fastx_toolkit_0_0_9 repositories which will install the requested
> versions of the tools.
>
> M.
>
> On Wed, Nov 4, 2015 at 10:47 AM Aaron Petkau 
> wrote:
>
>> Okay, thanks Dave.  That makes sense.  Moving forward I'll just make a
>> new suite with a version number in the name.
>>
>> Another question, does the same apply for tool dependency definitions?
>> I've upgraded a suite of tools + dependency definitions, and now even if I
>> make a new repository suite (to allow installing of my old set of tools,
>> revision 0 in my example) it's installing the newer commit in one tool
>> dependency definition repository.
>>
>> Thanks,
>>
>> Aaron
>>
>> On Mon, Nov 2, 2015 at 7:59 AM, Dave Bouvier  wrote:
>>
>>> Aaron,
>>>
>>> Repository suite definitions are designed to only allow the latest
>>> revision to be installable. My recommendation in this case would be to
>>> define two separate suites tagged in some descriptive way, so the
>>> individual use cases would have their appropriate suites.
>>>
>>> -
>>> Dave Bouvier
>>> http://galaxyproject.org
>>> http://usegalaxy.org
>>>
>>>
>>> On 10/29/2015 02:23 PM, Aaron Petkau wrote:
>>>
 Hello,

 I'm running into some issues with maintaining multiple installable
 revisions for a repository suite and I'm not sure if there's something
 I've missed.

 I have a local toolshed where I'm maintaining my tools, and I have a
 repository suite definition, defining a number of dependencies.  So, I
 have:

 suite_X (mercurial revision 0):
 Dependency A
 Dependency B

 I updated "suite_X" and changed the dependencies:

 suite_X (mercurial revision 1):
  Dependency A
  Dependency B
  Dependency C

 I would like to have both mercurial revision 0 and 1 installable in
 Galaxy, but only revision 1 (the latest) is showing up as installable.
 I found documentation at
 https://wiki.galaxyproject.org/RepositoryRevisions but this seems to
 only cover a repository containing a single tool, not a suite of tools.

 Is there something I'm doing wrong or some setting I have to change
 here?  My toolshed is running with Galaxy tag "v15.07".

 Thanks,

 Aaron


 ___
 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:
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>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>
>
___
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Re: [galaxy-dev] support for newer versions of Torque

[Malcolm Tobias]

Any suggestions on how to handle this?

Without being to integrate Galaxy with our queuing system it's hard to use it 
as a production environment.

Cheers,
Malcolm

On Friday, October 30, 2015 08:16:17 AM Malcolm Tobias wrote:
> I'm having trouble "scrambling my eggs".
> 
> I'm trying to build PBS support into Galaxy on a cluster running Torque
> >5.0. The problem seems to be with pbs_python 4.4.0 which doesn't build
> against newer versions of Torque. I was able to download 4.6.0 and was able
> to build it from:
> 
> ftp://ftp.surfsara.nl/pub/outgoing/pbs_python.tar.gz
> 
> but I'm not sure how to integrate that build with Galaxy. It seems if 4.6.0
> was available from:
> 
> http://eggs.galaxyproject.org/pbs_python/
> 
> I'd have a chance.
> 
> Any thoughts?
> 
> Cheers,
> Malcolm
-- 
Malcolm Tobias
314.362.1594


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Re: [galaxy-dev] installable revisions for repository suite definitions

[Martin Čech]

Hi Aaron,

we touched this recently here:
https://github.com/galaxyproject/tools-devteam/pull/267

I believe that if you specify the repository_dependencies.xml of your suite
in the following way:


http://toolshed.g2.bx.psu.edu"; />

you will pin the exact revision of the tool (fasta_clipping_histogram here)
to that suite. Then you can have suite_fastx_toolkit_0_0_13 and
suite_fastx_toolkit_0_0_9 repositories which will install the requested
versions of the tools.

M.

On Wed, Nov 4, 2015 at 10:47 AM Aaron Petkau  wrote:

> Okay, thanks Dave.  That makes sense.  Moving forward I'll just make a new
> suite with a version number in the name.
>
> Another question, does the same apply for tool dependency definitions?
> I've upgraded a suite of tools + dependency definitions, and now even if I
> make a new repository suite (to allow installing of my old set of tools,
> revision 0 in my example) it's installing the newer commit in one tool
> dependency definition repository.
>
> Thanks,
>
> Aaron
>
> On Mon, Nov 2, 2015 at 7:59 AM, Dave Bouvier  wrote:
>
>> Aaron,
>>
>> Repository suite definitions are designed to only allow the latest
>> revision to be installable. My recommendation in this case would be to
>> define two separate suites tagged in some descriptive way, so the
>> individual use cases would have their appropriate suites.
>>
>> -
>> Dave Bouvier
>> http://galaxyproject.org
>> http://usegalaxy.org
>>
>>
>> On 10/29/2015 02:23 PM, Aaron Petkau wrote:
>>
>>> Hello,
>>>
>>> I'm running into some issues with maintaining multiple installable
>>> revisions for a repository suite and I'm not sure if there's something
>>> I've missed.
>>>
>>> I have a local toolshed where I'm maintaining my tools, and I have a
>>> repository suite definition, defining a number of dependencies.  So, I
>>> have:
>>>
>>> suite_X (mercurial revision 0):
>>> Dependency A
>>> Dependency B
>>>
>>> I updated "suite_X" and changed the dependencies:
>>>
>>> suite_X (mercurial revision 1):
>>>  Dependency A
>>>  Dependency B
>>>  Dependency C
>>>
>>> I would like to have both mercurial revision 0 and 1 installable in
>>> Galaxy, but only revision 1 (the latest) is showing up as installable.
>>> I found documentation at
>>> https://wiki.galaxyproject.org/RepositoryRevisions but this seems to
>>> only cover a repository containing a single tool, not a suite of tools.
>>>
>>> Is there something I'm doing wrong or some setting I have to change
>>> here?  My toolshed is running with Galaxy tag "v15.07".
>>>
>>> Thanks,
>>>
>>> Aaron
>>>
>>>
>>> ___
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>>>
>>>
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Re: [galaxy-dev] Galaxy Startup Failing

[Suderman Keith]

Hi Will,

I tried that and it didn’t work for me.  Are you using start-stop-daemon to 
launch python?  Or do you run “python scripts/paster.py serve” from 
/etc/init.d/galaxy?

If I use start-stop-daemon then python does not seem to be picking up the 
.venv.  I suspect it has something to do with .venv/bin/activate being sourced 
as root in one process and then python running as the galaxy user in another 
process.

If I run “python scripts/paster.py serve” in the /etc/init.d/galaxy script then 
Galaxy is running as the root user and this is (will be) a production server so 
that is not an option.

If I run python as the galaxy user from the /etc/init.d/galaxy script then I am 
back to the problem of python not being able to write to /var/run/galaxy.pid

Keith

> On Nov 3, 2015, at 7:39 PM, Will Holtz  wrote:
> 
> Hi Keith,
> 
> I've dealt with similar situations by adding the sourcing of 
> .venv/bin/activate to the etc/init.d/galaxy script. Then none of the 
> pre-existing pid code needs to be changed.
> 
> -Will
> 
> 
> On Tue, Nov 3, 2015 at 8:55 AM, Suderman Keith  > wrote:
> The solution was rather simple, once I figured it out.
> 
> The /etc/init.d/galaxy script was invoking scripts/paster.py script directly 
> so .venv/bin/activate was not being sourced.  The solution was to modify 
> /etc/init.d/galaxy to call a startup script that sourced .venv/bin/activate 
> before starting Galaxy.  I can write my solution up in more detail, but now I 
> am having some problems setting the pid file correctly.
> 
> If I use the --make-pidfile and --pidfile options for start-stop-daemon in 
> /etc/init.d/galaxy then /var/run/galaxy.pid contains the pid of the startup 
> script and not the pid of the Galaxy instance.
> 
> If I try to set the pid in the startup script Galaxy won't start as the 
> script (now running as the Galaxy user) can't create/write the 
> /var/run/galaxy.pid file.
> 
> My hack-around has been to touch the pid file (in case it doesn't exist) and 
> then chown it to the galaxy user in /etc/init.d/galaxy, but this doesn't 
> strike me as the correct way to do this.  Do any sysadmin gurus have any 
> better suggestions?
> 
> Cheers,
> Keith
> 
> > On Nov 1, 2015, at 9:31 PM, Keith Suderman  > > wrote:
> >
> > Greetings,
> >
> > I am trying to upgrade our Galaxy instance to the latest stable code from 
> > master and now our instance won't start using my /etc/init.d/galaxy script. 
> >  That is:
> >
> >> sudo service galaxy start
> >
> > no longer works. It says it does (i.e. prints "[OK]"), but Galaxy isn't 
> > running and nothing is written to the log. I am using the init.d script 
> > from simison [1], which is basically the same as the one posted to the 
> > Galaxy wiki [2], both of which are quite old.
> >
> > Galaxy does start with:
> >
> >> sudo su galaxy
> >> ./run.sh --daemon
> >
> > so I have left Galaxy running in a screen session for now, but that is less 
> > than ideal.
> >
> > I suspect something to do with the .venv as `./run.sh --skip-venv` also 
> > fails and I don't recall Galaxy being that finicky about a venv being 
> > active. Does anyone know how I can get the /etc/init.d/galaxy script (i.e. 
> > start-stop-daemon) to activate the venv for paster.py?
> >
> > Cheers,
> > Keith
> >
> > 1. http://simison.com/brian/GalaxyAdmin_notes.html 
> > 
> > 2. 
> > https://wiki.galaxyproject.org/Events/GCC2012/TrainingDay/WS5?highlight=%28init.d%29
> >  
> > 
> >
> > --
> > Research Associate
> > Department of Computer Science
> > Vassar College
> > Poughkeepsie, NY
> >
> >
> > ___
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> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >  https://lists.galaxyproject.org/ 
> >
> > To search Galaxy mailing lists use the unified search at:
> >  http://galaxyproject.org/search/mailinglists/ 
> > 
> 
> ___
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> 
> 
> 
> -- 
> The information contained in this e-mail message or any attachment(s) may be 
> confidential and/or privileged and is intended for use only by the 
> individual(s) to whom this message is addressed.  If you are not the intended 
> recipie

Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused

[Suderman Keith]

I am not very good with Apache rewrite rules, but I think there is a problem 
with (at least) the first rule.  I see in the Apache documentation [1] that the 
following “doesn’t make sense, not supported":

^/somepath(.*) http://thishost/otherpath$1 [P]

The [P] flag is for forwarding to a proxy, but you are forwarding to localhost 
(i.e. http://thishost) not a proxy. So try changing the first rule to

RewriteRule ^/galaxy_test(.*) http://localhost:8081$1 

That is, remove the [P] from the end, and see if that makes a difference.  The 
other rules look ok, although so did the above at first glance, so you might 
want to add one rules at a time to help you isolate rules that are causing 
problems.

Hope that helps,
Keith

1. http://httpd.apache.org/docs/current/mod/mod_rewrite.html

> On Nov 4, 2015, at 6:08 AM, Makis Ladoukakis  wrote:
> 
> So yeah you might be on to something here. When I commented the Rewrite rules 
> I could access my galaxy instance from myservername:8081 with or without the 
> index.html file placed in /var/www/html. When I did place it in the directory 
> though and I tried with the rewrite rules my server gave me the following 
> error:
> 
>  script not found or unable to stat: /var/www/cgi-bin/common
> 
> and once again the galaxy page was blank.
> 
> Any ideas why? What is apache's problem with the rewrite rules being there?
> 
> thank you,
> Makis
> 
> Subject: Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused
> From: suder...@cs.vassar.edu
> Date: Tue, 3 Nov 2015 13:06:03 -0500
> CC: federico.zambe...@gmail.com; galaxy-dev@lists.galaxyproject.org
> To: makis4e...@hotmail.com
> 
> Very odd that you were getting "Address is use" errors then..  What have you 
> set the port to in your galaxy.ini file?
> 
> The missing index.html/index.php won't make a difference to Galaxy, but it 
> might prevent Apache from starting up.  I would put a simple index.html file, 
> say:
> 
> You should not see this.
> 
> in /var/www/html just so Apache is happy and if you see that at least you 
> will know Apache is up and running and listening on the correct ports. I 
> would also forego the Apache rewrite rules until you know Galaxy is working.
> 
> Keith
> 
> On Nov 3, 2015, at 12:15 PM, Makis Ladoukakis  > wrote:
> 
> Νο, no other service is running on 8081. This is the output of netstat -tulpn:
> 
> tcp0  0 0.0.0.0:33060.0.0.0:*   LISTEN
>   -
> tcp0  0 0.0.0.0:22  0.0.0.0:*   LISTEN
>   -
> tcp0  0 127.0.0.1:250.0.0.0:*   LISTEN
>   -
> tcp6   0  0 :::80   :::*LISTEN
>   -
> tcp6   0  0 :::22   :::*LISTEN
>   -
> tcp6   0  0 ::1:25  :::*LISTEN
>   -
> udp0  0 0.0.0.0:123 0.0.0.0:* 
>   -
> udp0  0 127.0.0.1:323   0.0.0.0:* 
>   -
> udp0  0 0.0.0.0:53530.0.0.0:* 
>   -
> udp0  0 0.0.0.0:33715   0.0.0.0:* 
>   -
> udp6   0  0 :::123  :::*  
>   -
> udp6   0  0 ::1:323 :::* 
> 
> And no I only have an info.php in that directory. Does that affect Galaxy in 
> any way?
> 
> Thank you,
> Makis
> 
> Subject: Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused
> From: suder...@cs.vassar.edu 
> Date: Tue, 3 Nov 2015 12:07:12 -0500
> CC: federico.zambe...@gmail.com ; 
> galaxy-dev@lists.galaxyproject.org 
> To: makis4e...@hotmail.com 
> 
> Do you have another service running on 8081?  I see the server is complaining 
> about that address already being in use.  Also, do you have an index.html or 
> welcome.html in /var/www/html?
> 
> Cheers,
> Keith
> 
> On Nov 3, 2015, at 11:39 AM, Makis Ladoukakis  > wrote:
> 
> Hello,
> 
> Unfortunately I cannot change web servers at the moment. There are a lot of 
> applications that I would need to make changes for the nginx configuration 
> plus i am not very experienced with nginx (apparently not with apache as well 
> outside debian systems).
> 
> Thank you,
> Makis
> 
> > To: galaxy-dev@lists.galaxyproject.org 
> > 
> > From: federico.zambe...@gmail.com 
> > Date: Tue, 3 Nov 2015 17:19:59 +0100
> > Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection  
> > refused
> > 
> > Il 03/11/15 11:53, Makis Ladoukakis ha scritto:
> > 
> > >
> > > Nothing seems to work on my server. Is Galaxy even compatible with
> > > CentOS? Is

Re: [galaxy-dev] installable revisions for repository suite definitions

[Aaron Petkau]

Okay, thanks Dave.  That makes sense.  Moving forward I'll just make a new
suite with a version number in the name.

Another question, does the same apply for tool dependency definitions?
I've upgraded a suite of tools + dependency definitions, and now even if I
make a new repository suite (to allow installing of my old set of tools,
revision 0 in my example) it's installing the newer commit in one tool
dependency definition repository.

Thanks,

Aaron

On Mon, Nov 2, 2015 at 7:59 AM, Dave Bouvier  wrote:

> Aaron,
>
> Repository suite definitions are designed to only allow the latest
> revision to be installable. My recommendation in this case would be to
> define two separate suites tagged in some descriptive way, so the
> individual use cases would have their appropriate suites.
>
> -
> Dave Bouvier
> http://galaxyproject.org
> http://usegalaxy.org
>
>
> On 10/29/2015 02:23 PM, Aaron Petkau wrote:
>
>> Hello,
>>
>> I'm running into some issues with maintaining multiple installable
>> revisions for a repository suite and I'm not sure if there's something
>> I've missed.
>>
>> I have a local toolshed where I'm maintaining my tools, and I have a
>> repository suite definition, defining a number of dependencies.  So, I
>> have:
>>
>> suite_X (mercurial revision 0):
>> Dependency A
>> Dependency B
>>
>> I updated "suite_X" and changed the dependencies:
>>
>> suite_X (mercurial revision 1):
>>  Dependency A
>>  Dependency B
>>  Dependency C
>>
>> I would like to have both mercurial revision 0 and 1 installable in
>> Galaxy, but only revision 1 (the latest) is showing up as installable.
>> I found documentation at
>> https://wiki.galaxyproject.org/RepositoryRevisions but this seems to
>> only cover a repository containing a single tool, not a suite of tools.
>>
>> Is there something I'm doing wrong or some setting I have to change
>> here?  My toolshed is running with Galaxy tag "v15.07".
>>
>> Thanks,
>>
>> Aaron
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>http://galaxyproject.org/search/mailinglists/
>>
>>
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Re: [galaxy-dev] login problem (redirection to the login page)

[Floreline TOUCHARD]

Update :
When I clic several time on the galaxy name, I got this on the log :

Exception happened during processing of request from ('127.0.0.1', 45055)
Traceback (most recent call last):
  File
path/to/galaxy-master/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
self.finish_request(request, client_address)
  File "/usr/lib64/python2.6/SocketServer.py", line 332, in finish_request
self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib64/python2.6/SocketServer.py", line 628, in __init__
self.finish()
  File "/usr/lib64/python2.6/SocketServer.py", line 671, in finish
self.wfile.flush()
  File "/usr/lib64/python2.6/socket.py", line 303, in flush
self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe


2015-11-04 15:09 GMT+01:00 Floreline TOUCHARD 
:

> Here is some details :
> when I enable the access to Galaxy without authentication I'm redirected
> to the welcome page, but still I'm not connected (I can login/register)
>
> 2015-11-04 14:42 GMT+01:00 Floreline TOUCHARD <
> floreline.touch...@gmail.com>:
>
>> Thanks for the "bidouille" ;)
>>
>> It didn't work for me.
>> I have my Galaxy instance configured to run jobs on a cluster. I don't
>> know where the problem come from.
>>
>> 2015-11-04 14:19 GMT+01:00 Yvan Le Bras :
>>
>>> Hi Floreline,
>>>
>>> Did you use several workers and/or handler ? I have had the same issue
>>> on Galaxy instances from our cloud, and a "not beautiful manner" I found to
>>> succeed authenticate was to clic several times on the galaxy name (top left
>>> of your instance) to force reload the page before login. ;)
>>>
>>> If this "bidouille" can help before you obtain a real solution to fix
>>> this..
>>>
>>> Cheers,
>>>
>>> Yvan
>>>
>>> --
>>>
>>> *De: *"Floreline TOUCHARD" 
>>> *À: *galaxy-dev@lists.galaxyproject.org
>>> *Envoyé: *Mercredi 4 Novembre 2015 14:00:24
>>> *Objet: *[galaxy-dev] login problem (redirection to the login page)
>>>
>>>
>>> Hi,
>>>
>>> this is not the first time I encounter this problem : I change the
>>> authentication mode (external to internal). And since then I cannot login
>>> with any account. Each time I'm redirected to the login page. Yet I haven't
>>> any log error. I have the galaxy-master 15.07 version.
>>> I cleared the firefox cache and cookies, from the browser and command
>>> line. But the problem's still there.
>>> The last time I uninstalled my postgresql database.
>>> I saw this post :
>>> http://dev.list.galaxyproject.org/Login-problem-tt4139426.html
>>> Is there a way to find the modifications (without unistall my galaxy
>>> instance) ?
>>>
>>> Thanks !
>>> F.T
>>>
>>> ___
>>> 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/
>>>
>>>
>>>
>>>
>>> --
>>>
>>> -
>>> Yvan Le Bras, PhD
>>>
>>> @Yvan2935
>>>
>>> <°><
>>>   e-Biogenouest project
>>>  http://www.e-biogenouest.org
>>>CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu,
>>> 35042 Rennes Cedex
>>>  tél.:  +33 (0) 2 99 84 71 79 /
>>>  +33 (0) 6.10.43.96.51
>>>
>>> yvan.le_b...@irisa.fr
>>>
>>>
>>
>
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Re: [galaxy-dev] login problem (redirection to the login page)

[Floreline TOUCHARD]

Here is some details :
when I enable the access to Galaxy without authentication I'm redirected to
the welcome page, but still I'm not connected (I can login/register)

2015-11-04 14:42 GMT+01:00 Floreline TOUCHARD 
:

> Thanks for the "bidouille" ;)
>
> It didn't work for me.
> I have my Galaxy instance configured to run jobs on a cluster. I don't
> know where the problem come from.
>
> 2015-11-04 14:19 GMT+01:00 Yvan Le Bras :
>
>> Hi Floreline,
>>
>> Did you use several workers and/or handler ? I have had the same issue on
>> Galaxy instances from our cloud, and a "not beautiful manner" I found to
>> succeed authenticate was to clic several times on the galaxy name (top left
>> of your instance) to force reload the page before login. ;)
>>
>> If this "bidouille" can help before you obtain a real solution to fix
>> this..
>>
>> Cheers,
>>
>> Yvan
>>
>> --
>>
>> *De: *"Floreline TOUCHARD" 
>> *À: *galaxy-dev@lists.galaxyproject.org
>> *Envoyé: *Mercredi 4 Novembre 2015 14:00:24
>> *Objet: *[galaxy-dev] login problem (redirection to the login page)
>>
>>
>> Hi,
>>
>> this is not the first time I encounter this problem : I change the
>> authentication mode (external to internal). And since then I cannot login
>> with any account. Each time I'm redirected to the login page. Yet I haven't
>> any log error. I have the galaxy-master 15.07 version.
>> I cleared the firefox cache and cookies, from the browser and command
>> line. But the problem's still there.
>> The last time I uninstalled my postgresql database.
>> I saw this post :
>> http://dev.list.galaxyproject.org/Login-problem-tt4139426.html
>> Is there a way to find the modifications (without unistall my galaxy
>> instance) ?
>>
>> Thanks !
>> F.T
>>
>> ___
>> 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/
>>
>>
>>
>>
>> --
>>
>> -
>> Yvan Le Bras, PhD
>>
>> @Yvan2935
>>
>>   <°><
>>   e-Biogenouest project
>>  http://www.e-biogenouest.org
>>CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu,
>> 35042 Rennes Cedex
>>  tél.:  +33 (0) 2 99 84 71 79 /  +33
>> (0) 6.10.43.96.51
>>
>> yvan.le_b...@irisa.fr
>>
>>
>
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[galaxy-dev] FASTQ Groomer tool

[Fernandez Edgar]

Hello gents,

I just installed "FASTQ Groomer tool" for the teachers to try it out and I've 
been getting the following error than I do not understand:

galaxy.jobs DEBUG 2015-11-04 08:16:19,957 (756) Working directory for job is: 
/home/galaxy/galaxy-prod/database/job_working_directory/000/756
galaxy.jobs.handler WARNING 2015-11-04 08:16:19,958 (756) Tool 
'toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4' 
removed from tool config, unable to run job
galaxy.jobs.handler ERROR 2015-11-04 08:16:20,159 failure running job 756
Traceback (most recent call last):
  File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 273, in 
__monitor_step
job_state = self.__check_job_state( job )
  File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 342, in 
__check_job_state
state, job_destination = self.__verify_job_ready( job, job_wrapper )
  File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 362, in 
__verify_job_ready
job_wrapper.fail( e )
  File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/__init__.py", line 984, in fail
self.sa_session.flush()
  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/scoping.py", line 150, in do
return getattr(self.registry(), name)(*args, **kwargs)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2004, in 
flush
self._flush(objects)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2122, in 
_flush
transaction.rollback(_capture_exception=True)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/util/langhelpers.py", line 60, 
in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2086, in 
_flush
flush_context.execute()
  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 373, 
in execute
rec.execute(self)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 532, 
in execute
uow
 File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 170, 
in save_obj
mapper, table, update)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 673, 
in _emit_update_statements
execute(statement, multiparams)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 914, in 
execute
return meth(self, multiparams, params)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/elements.py", line 323, in 
_execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1010, in 
_execute_clauseelement
compiled_sql, distilled_params
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1146, in 
_execute_context
context)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1332, in 
_handle_dbapi_exception
exc_info
  File "build/bdist.linux-x86_64/egg/sqlalchemy/util/compat.py", line 199, in 
raise_from_cause
reraise(type(exception), exception, tb=exc_tb)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1139, in 
_execute_context
context)
  File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 442, 
in do_execute
cursor.execute(statement, parameters)
  File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py", line 173, in 
execute
self.errorhandler(self, exc, value)
  File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py", line 36, in 
defaulterrorhandler
raise errorclass, errorvalue
ProgrammingError: (_mysql_exceptions.ProgrammingError) (1064, "You have an 
error in your SQL syntax; check the manual that corresponds to your MySQL 
server version for the right syntax to use near '), blurb='tool error' WHERE 
history_dataset_association.id = 1498' at line 1") [SQL: u'UPDATE 
history_dataset_association SET update_time=%s, info=%s, blurb=%s WHERE 
history_dataset_association.id = %s'] [parameters: (datetime.datetime(2015, 11, 
4, 13, 16, 20, 153739), ('This tool was disabled before the job completed.  
Please contact your Galaxy administrator.',), 'tool error', 1498L)]


According to the tool shed repo, fastq_groomer is installed properly.
Mysql is at its latest for oracle linux 6:
[0]# mysql --version
mysql  Ver 14.14 Distrib 5.1.73, for redhat-linux-gnu (x86_64) using readline 
5.1

[0]# rpm -qa | grep -i mysql
mysql-5.1.73-5.el6_6.x86_64


The only thing I have not done is update galaxy for the last 6 months because 
they're students using it and I do not want to change anything while it's in 
production.
I'm a little bit lost: Would you please indicate what I should check next?

Cordialement / Regards,

Edgar Fernandez
System Administrator (Linux)
Direction Générale des Technologies de l'Information et de la Communication
*  Bur. : 1-514-343-6111 poste 16568

Université de Montréal
PAVILLON ROGER-GAUDRY, bureau X-218

___
Please keep all repli

Re: [galaxy-dev] login problem (redirection to the login page)

[Floreline TOUCHARD]

Thanks for the "bidouille" ;)

It didn't work for me.
I have my Galaxy instance configured to run jobs on a cluster. I don't know
where the problem come from.

2015-11-04 14:19 GMT+01:00 Yvan Le Bras :

> Hi Floreline,
>
> Did you use several workers and/or handler ? I have had the same issue on
> Galaxy instances from our cloud, and a "not beautiful manner" I found to
> succeed authenticate was to clic several times on the galaxy name (top left
> of your instance) to force reload the page before login. ;)
>
> If this "bidouille" can help before you obtain a real solution to fix
> this..
>
> Cheers,
>
> Yvan
>
> --
>
> *De: *"Floreline TOUCHARD" 
> *À: *galaxy-dev@lists.galaxyproject.org
> *Envoyé: *Mercredi 4 Novembre 2015 14:00:24
> *Objet: *[galaxy-dev] login problem (redirection to the login page)
>
>
> Hi,
>
> this is not the first time I encounter this problem : I change the
> authentication mode (external to internal). And since then I cannot login
> with any account. Each time I'm redirected to the login page. Yet I haven't
> any log error. I have the galaxy-master 15.07 version.
> I cleared the firefox cache and cookies, from the browser and command
> line. But the problem's still there.
> The last time I uninstalled my postgresql database.
> I saw this post :
> http://dev.list.galaxyproject.org/Login-problem-tt4139426.html
> Is there a way to find the modifications (without unistall my galaxy
> instance) ?
>
> Thanks !
> F.T
>
> ___
> 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/
>
>
>
>
> --
>
> -
> Yvan Le Bras, PhD
>
> @Yvan2935
>
>   <°><
>   e-Biogenouest project
>http://www.e-biogenouest.org
>CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu,
> 35042 Rennes Cedex
>  tél.:  +33 (0) 2 99 84 71 79 /  +33
> (0) 6.10.43.96.51
>
> yvan.le_b...@irisa.fr
>
>
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Re: [galaxy-dev] login problem (redirection to the login page)

[Yvan Le Bras]

Hi Floreline, 

Did you use several workers and/or handler ? I have had the same issue on 
Galaxy instances from our cloud, and a "not beautiful manner" I found to 
succeed authenticate was to clic several times on the galaxy name (top left of 
your instance) to force reload the page before login. ;) 

If this "bidouille" can help before you obtain a real solution to fix this.. 

Cheers, 

Yvan 

- Mail original -

> De: "Floreline TOUCHARD" 
> À: galaxy-dev@lists.galaxyproject.org
> Envoyé: Mercredi 4 Novembre 2015 14:00:24
> Objet: [galaxy-dev] login problem (redirection to the login page)

> Hi,

> this is not the first time I encounter this problem : I change the
> authentication mode (external to internal). And since then I cannot login
> with any account. Each time I'm redirected to the login page. Yet I haven't
> any log error. I have the galaxy-master 15.07 version.
> I cleared the firefox cache and cookies, from the browser and command line.
> But the problem's still there.
> The last time I uninstalled my postgresql database.
> I saw this post :
> http://dev.list.galaxyproject.org/Login-problem-tt4139426.html
> Is there a way to find the modifications (without unistall my galaxy
> instance) ?

> Thanks !
> F.T

> ___
> 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/
-- 
-
 
Yvan Le Bras, PhD @Yvan2935 <°>< 
e-Biogenouest project http://www.e-biogenouest.org 
CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, 35042 Rennes Cedex 
tél.: +33 (0) 2 99 84 71 79 / +33 (0) 6.10.43.96.51 
yvan.le_b...@irisa.fr 
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  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] login problem (redirection to the login page)

[Floreline TOUCHARD]

Hi,

this is not the first time I encounter this problem : I change the
authentication mode (external to internal). And since then I cannot login
with any account. Each time I'm redirected to the login page. Yet I haven't
any log error. I have the galaxy-master 15.07 version.
I cleared the firefox cache and cookies, from the browser and command line.
But the problem's still there.
The last time I uninstalled my postgresql database.
I saw this post :
http://dev.list.galaxyproject.org/Login-problem-tt4139426.html
Is there a way to find the modifications (without unistall my galaxy
instance) ?

Thanks !
F.T
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  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused

[Makis Ladoukakis]

So yeah you might be on to something here. When I commented the Rewrite rules I 
could access my galaxy instance from myservername:8081 with or without the 
index.html file placed in /var/www/html. When I did place it in the directory 
though and I tried with the rewrite rules my server gave me the following error:

 script not found or unable to stat: /var/www/cgi-bin/common

and once again the galaxy page was blank.

Any ideas why? What is apache's problem with the rewrite rules being there?

thank you,
Makis

Subject: Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused
From: suder...@cs.vassar.edu
Date: Tue, 3 Nov 2015 13:06:03 -0500
CC: federico.zambe...@gmail.com; galaxy-dev@lists.galaxyproject.org
To: makis4e...@hotmail.com

Very odd that you were getting "Address is use" errors then..  What have you 
set the port to in your galaxy.ini file?
The missing index.html/index.php won't make a difference to Galaxy, but it 
might prevent Apache from starting up.  I would put a simple index.html file, 
say:
You should not see this.
in /var/www/html just so Apache is happy and if you see that at least you will 
know Apache is up and running and listening on the correct ports. I would also 
forego the Apache rewrite rules until you know Galaxy is working.
Keith
On Nov 3, 2015, at 12:15 PM, Makis Ladoukakis  
wrote:Νο, no other service is running on 8081. This is the output of netstat 
-tulpn:

tcp0  0 0.0.0.0:33060.0.0.0:*   LISTEN  
-
tcp0  0 0.0.0.0:22  0.0.0.0:*   LISTEN  
-
tcp0  0 127.0.0.1:250.0.0.0:*   LISTEN  
-
tcp6   0  0 :::80   :::*LISTEN  
-
tcp6   0  0 :::22   :::*LISTEN  
-
tcp6   0  0 ::1:25  :::*LISTEN  
-
udp0  0 0.0.0.0:123 0.0.0.0:*   
-
udp0  0 127.0.0.1:323   0.0.0.0:*   
-
udp0  0 0.0.0.0:53530.0.0.0:*   
-
udp0  0 0.0.0.0:33715   0.0.0.0:*   
-
udp6   0  0 :::123  :::*
-
udp6   0  0 ::1:323 :::* 

And no I only have an info.php in that directory. Does that affect Galaxy in 
any way?

Thank you,
Makis

Subject: Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused
From: suder...@cs.vassar.edu
Date: Tue, 3 Nov 2015 12:07:12 -0500
CC: federico.zambe...@gmail.com; galaxy-dev@lists.galaxyproject.org
To: makis4e...@hotmail.com

Do you have another service running on 8081?  I see the server is complaining 
about that address already being in use.  Also, do you have an index.html or 
welcome.html in /var/www/html?
Cheers,Keith
On Nov 3, 2015, at 11:39 AM, Makis Ladoukakis  
wrote:Hello,

Unfortunately I cannot change web servers at the moment. There are a lot of 
applications that I would need to make changes for the nginx configuration plus 
i am not very experienced with nginx (apparently not with apache as well 
outside debian systems).

Thank you,
Makis

> To: galaxy-dev@lists.galaxyproject.org
> From: federico.zambe...@gmail.com
> Date: Tue, 3 Nov 2015 17:19:59 +0100
> Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection
> refused
> 
> Il 03/11/15 11:53, Makis Ladoukakis ha scritto:
> 
> >
> > Nothing seems to work on my server. Is Galaxy even compatible with
> > CentOS? Is there something else that I am missing?
> >
> 
> Hello, I'm running a production Galaxy Server on CentOS and I can assure 
> you it is perfectly feasible. But I'm using NGINX as a web server so I'm 
> not able to help you with Apache configuration, sorry. Did you try to 
> use NGINX instead of Apache in order to see if the problem is Apache 
> related or system related?
> 
> Best,
> Federico Z.
> 
> 
> >
> >
> > 
> > From: david.trudg...@utsouthwestern.edu
> > To: makis4e...@hotmail.com; jcsanch...@gmail.com
> > CC: galaxy-...@lists.bx.psu.edu
> > Date: Fri, 23 Oct 2015 17:30:51 +
> > Subject: RE: [galaxy-dev] FW: Galaxy on Centos via Apache - connection
> > refused
> >
> > SELinux policies are very strict on CentOS by default. Apache isn't
> > allowed to access files outside of its standard directories, nor access
> > network resources. Your local Galaxy apps server is a network resource -
> > even though it's local.
> >
> > If you want to keep SELinux on then use audit2allow to see what policies
> > will enable access:
> >
> > cat /var/log/audit/audit.log | audit2allow -v
> >
> > Then you can use setsebool (temporary) and setsebool -P (permanent) to
> > enable.
> >
> > --
> > David Trudgian Ph.D.
> > Computational Scientist, BioHPC
> > UT Southwestern Medical Center
> > D

Re: [galaxy-dev] atlas 3.10 IUC error

[Olivier CLAUDE]

Thanks Peter, Nicola,

Ok, I'll try to switch on an 64bits computer then, maybe there's some other 
errors due to this.
Thanks a lot.

Olivier

-Message d'origine-
De : Peter Cock [mailto:p.j.a.c...@googlemail.com] 
Envoyé : mardi 3 novembre 2015 19:24
À : o.cla...@outlook.fr
Cc : Nicola Soranzo ; galaxy-dev@lists.galaxyproject.org
Objet : Re: [galaxy-dev] atlas 3.10 IUC error

On Tue, Nov 3, 2015 at 6:16 PM,   wrote:
> Hi Nicola
>
> It is an i686. Is it a problem ?
>
> Cheers,
> Olivier

Currently only for 64bit Linux are pre-compiled binaries used:

https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_atlas_3_10/tool_dependencies.xml

There's a special case for Mac, but otherwise the current Atlas recipe would 
attempt to compile from source for 32bit Linux. And that is failing for some 
reason...

The easiest fix would be if pre-compiled binaries for 32bit Linux were 
available, we would need  and/or 
 actions, e.g.

https://github.com/peterjc/galaxy_blast/blob/master/packages/package_blast_plus_2_2_30/tool_dependencies.xml

However, the compile from source recipe will need looking at...

Peter
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