Re: [galaxy-dev] parse history file/uploaded file with dynamic_options script

[Von Kuster, Greg]

Hi Linda,

I think your parameter definition will need to send the file_name of the 
HistoryDatasetAssociation, something like this...


> 
> 
> 
> 
> In my dynamic_options.py script, I want to parse the headers from 
> 'amplitudes' file and show them in the checkboxes section.
> 
> My problem seems to be the following.
> 
> In python, amplitudes is a galaxy object:
> 
> 
> How do I parse/access this file to get the headers?
> 
> It seems to be partly the same problem as asked last week in this 
> conversation:
> http://dev.list.galaxyproject.org/Question-about-using-dynamic-options-and-refresh-on-change-for-rendering-2-associated-select-lists-td4667943.html
>  
> 
> Thanks!
> Linda
> 
> -- 
> Linda Bakker
> Bioinformatics Research Assistant
> Plant Research International, Wageningen UR
> Building 107 (Radix), room W1.Fa.054
> Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
> tel: +31-317-480756
> email: linda.bak...@wur.nl
> 
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[galaxy-dev] 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] Planemo 0.19.0 testing tools that produce dataset collections

[Von Kuster, Greg]

Nicola, thanks a bunch!  Your eyes are phenomenal!

Greg

> On Nov 4, 2015, at 8:09 PM, Nicola Soranzo  wrote:
> 
> 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
>> --
>&

Re: [galaxy-dev] [ICS ACI Info] Galaxy Server Administration Inquiry

[Von Kuster, Greg]

Hello Jimmy,

The Institute for CyberScience at Penn State does not directly provide support 
for System Administration training for Galaxy.  However, the Galaxy community 
does have a lot of resources that help fulfill this need.

- There is a Galaxy Admin User Group that hosts regular formal meetings and has 
other informal communications.  For information, see 
https://wiki.galaxyproject.org/Community/GalaxyAdmins
- The Galaxy Admin wiki is a great place to get information - see 
https://wiki.galaxyproject.org/Admin
- The Galaxy Training Network schedules training sessions - see 
https://wiki.galaxyproject.org/Teach/Resources

- The Galaxy mailing lists are also a good place for information - see 
https://wiki.galaxyproject.org/MailingLists.
- The Galaxy Biostar forum is another great source of information - see 
https://wiki.galaxyproject.org/Support/Biostar
- The Galaxy Support wiki is good as well - see 
https://wiki.galaxyproject.org/Support

I’m associated with the Galaxy Community, so if these options do not meet your 
needs or if you have additional question, please let us know and we’ll try to 
get you hooked up with those that are best suited to meet your needs.

Thanks very much,

Greg Von Kuster


Good morning,

I noticed on the Galaxy server website that Penn State is an contributor to the 
Galaxy project. I wanted to know if you all provide comprehensive training for 
system administrators administering Galaxy server(s)?

Thanks

Jimmy Griffin
Principal Consultant
National Institute of Allergy and Infectious Diseases, NIH
Contractor - Net eSolutions

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Re: [galaxy-dev] removing tool from toolshed

[Von Kuster, Greg]

Hi Jose,

You can currently only deprecate the repository.  To allow for reproducibility, 
it cannot be completely deleted in case it has been installed into a Galaxy 
instance.  Deprecating the repository will eliminate it from most Tool Shed 
features and hide it from most views.  Use the Repository Actions pop-up to 
find this feature.

Greg Von Kustert


> On Mar 18, 2016, at 12:11 PM, Xianrong Wong  wrote:
> 
> Hi, 
>I've recently packaged some of my scripts and deposited them into the test 
> toolshed.  Are there ways to remove some of them ie remove the repository 
> completely?
> 
> Jose
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Re: [galaxy-dev] Issue with GATK in workflow

[Von Kuster, Greg]

Hi Scott,

I’m not positive, but this behavior may be related to this issue:

https://github.com/galaxyproject/galaxy/issues/1881

Greg Von Kuster

On Apr 15, 2016, at 10:52 AM, Scott Szakonyi 
mailto:scott.b.szakony...@nd.edu>> wrote:

Hello all,

We have indexed a genome using the appropriate data manager, for GATK, and our 
reference is showing up and working for individual walkers in GATK 2.8.  When 
designing a workflow, however, the reference genome is not appearing as an 
option for many walkers, including indel realigner and realigner target 
creator.  It is appearing for haplotype caller.  Again outside of the workflow 
environment the indexed references show up for all walkers.

Any thoughts on this issue?

Thanks!

--
Scott B. Szakonyi
Research Programmer

Center for Research Computing
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
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Re: [galaxy-dev] Issue with GATK in workflow

[Von Kuster, Greg]

Hi Scott,

It is likely that the bahavior you are experiencing is due to a bug in the 
Workflow framework, so I’d advise submitting an issue describing the problem 
here 
https://github.com/galaxyproject/galaxy/issues<http://github.com/galaxyproject/galaxy/issues>
 if the behavior is different than that described in this existing issue: 
https://github.com/galaxyproject/galaxy/issues/1881.

This will be the best path toward getting a fix.  Sorry I cannot be of more 
help, but I am not an expert with the core Workflow framework.

Greg Von Kuster

On Apr 18, 2016, at 11:56 AM, Scott Szakonyi 
mailto:scott.b.szakony...@nd.edu>> wrote:

Hi Greg,

That does look quite similar, but the workarounds presented are not solving the 
issue for us. If you can offer any additional strategies, I would truly 
appreciate it.

Best,

Scott

On Fri, Apr 15, 2016 at 10:56 AM, Von Kuster, Greg 
mailto:g...@psu.edu>> wrote:
Hi Scott,

I’m not positive, but this behavior may be related to this issue:

https://github.com/galaxyproject/galaxy/issues/1881

Greg Von Kuster

On Apr 15, 2016, at 10:52 AM, Scott Szakonyi 
mailto:scott.b.szakony...@nd.edu><mailto:scott.b.szakony...@nd.edu<mailto:scott.b.szakony...@nd.edu>>>
 wrote:

Hello all,

We have indexed a genome using the appropriate data manager, for GATK, and our 
reference is showing up and working for individual walkers in GATK 2.8.  When 
designing a workflow, however, the reference genome is not appearing as an 
option for many walkers, including indel realigner and realigner target 
creator.  It is appearing for haplotype caller.  Again outside of the workflow 
environment the indexed references show up for all walkers.

Any thoughts on this issue?

Thanks!

--
Scott B. Szakonyi
Research Programmer

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

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

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Re: [galaxy-dev] Using operations on multiple datasets

[Von Kuster, Greg]

In addition to Bjoern’s response, tools written to take a single input like 
this:





will automatically accept a dataset collection, both in workflows and in the 
tool form UI.


> On Jul 5, 2016, at 5:25 PM, Björn Grüning  wrote:
> 
> Hi,
> 
> Am 05.07.2016 um 23:18 schrieb D K:
>> Sorry for the crosspost to Biostars, but I didn't get a response, so I
>> thought I'd post here:
>> 
>> I just noticed that Galaxy allows creation of lists of datasets by clicking
>> on the "Operations on multiple datasets" in the history panel. How does one
>> use this with a custom tool (e.g. what does one put between the 
>>  tags). Is the list treated as a text file with a list of each
>> file? I couldn't find any examples or documentation online. I'd appreciate
>> it if someone could point me in the right direction.
> 
> You can not use this feature in a tool, it's pure UI. But you can use
> multiple="True"
> 
> https://github.com/galaxyproject/tools-iuc/blob/180a403421967d36f995941b1a4561349d75cfc5/tools/mothur/merge.files.xml#L32
> 
> maybe this helps?
> Cheers,
> Bjoern
> 
>> Thanks!
>> 
>> 
>> 
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Re: [galaxy-dev] Metadata access using tool config

[Von Kuster, Greg]

Hi Katherine,

For the job related stuff, I’m doing this in my tools that provide statistics 
for the Galaxy ChIP-exo instance I’m setting up for a lab here at Penn State.  
You can see variations of tool examples here: 
https://github.com/gregvonkuster/cegr-galaxy/tree/master/tools/cegr_statistics. 
 These tools are all included in workflows where the tool is generating 
metadata about the tool that executed immediatly prior to one of these 
metadata-generating tools.  I use the while loop in the command to keep the 
this tool from executing in the workflow before its immediate predecessor is 
completed.  I assume you are doing something similar, where your tool will 
generate metadata for some different tool that has already been executed.

Here is an example of a basic command line in one of these tool configs that 
will provide the job stuff to the underlying script.





Cheers!

Greg Von Kuster

On Jul 7, 2016, at 11:40 AM, Katherine Beaulieu 
mailto:katherine.beaulieu...@gmail.com>> wrote:

Hi everyone,
I am working on a tool which attempts to create a file which stores all the 
metadata associated with a job execution. The things I know how to access right 
now are the file extension, name history id, dataset id. I'd like to know how 
to access other things like the job id, uuid, file size, job command-line, job 
end time, job start time, core allocated, job runtime and any other important 
information associated with tool execution. I would prefer to get this 
information from the tool config file or my tool script and not have the user 
create an api key which they have to submit as a parameter to my tool. Let me 
know if you guys have any ideas!
Katherine
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Re: [galaxy-dev] Metadata access using tool config

[Von Kuster, Greg]

Hi Katherine,

Probably about the only way to get the job start time is job.create_time (a 
close estimate to the actual start time) and the end time is job.update_time 
(again, a close estimate), so you can calculate the job’s estimated execution 
time using something like this:

import datetime
execute_time = job.update_time - job.create_time
execute_time = datetime.timedelta(seconds=execute_time.seconds)


On Jul 8, 2016, at 9:03 AM, Katherine Beaulieu 
mailto:katherine.beaulieu...@gmail.com>> wrote:

Actually just figured out the history content api id, just needing the extra 
stuff about the job like runtime and start and end times.

On Fri, Jul 8, 2016 at 8:55 AM, Katherine Beaulieu 
mailto:katherine.beaulieu...@gmail.com>> wrote:
Hi Greg,
Thanks for the link to your github repo, some of the information there was very 
useful. Do you have any idea on how to access some of the stuff you don't 
yourself pass to your python script such as the history content api id, or the 
job runtime? For example for the job runtime I feel like it should be:

#set job = $input.creating_job
#set tool_id = $job.runtime

But that just gives an error.

On Thu, Jul 7, 2016 at 12:56 PM, Von Kuster, Greg 
mailto:g...@psu.edu>> wrote:
Hi Katherine,

For the job related stuff, I’m doing this in my tools that provide statistics 
for the Galaxy ChIP-exo instance I’m setting up for a lab here at Penn State.  
You can see variations of tool examples here: 
https://github.com/gregvonkuster/cegr-galaxy/tree/master/tools/cegr_statistics. 
 These tools are all included in workflows where the tool is generating 
metadata about the tool that executed immediatly prior to one of these 
metadata-generating tools.  I use the while loop in the command to keep the 
this tool from executing in the workflow before its immediate predecessor is 
completed.  I assume you are doing something similar, where your tool will 
generate metadata for some different tool that has already been executed.

Here is an example of a basic command line in one of these tool configs that 
will provide the job stuff to the underlying script.





Cheers!

Greg Von Kuster

On Jul 7, 2016, at 11:40 AM, Katherine Beaulieu 
mailto:katherine.beaulieu...@gmail.com>> wrote:

Hi everyone,
I am working on a tool which attempts to create a file which stores all the 
metadata associated with a job execution. The things I know how to access right 
now are the file extension, name history id, dataset id. I'd like to know how 
to access other things like the job id, uuid, file size, job command-line, job 
end time, job start time, core allocated, job runtime and any other important 
information associated with tool execution. I would prefer to get this 
information from the tool config file or my tool script and not have the user 
create an api key which they have to submit as a parameter to my tool. Let me 
know if you guys have any ideas!
Katherine
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Re: [galaxy-dev] Toolshed partial installation ? deeptools error

[Von Kuster, Greg]

This looks like the issue I’ve recently seen as well - I just discussed this 
with @bgruening on gitter - https://gitter.im/galaxy-iuc/iuc.  I’m using a 
work-around of creating the __deeptools conda env manually.  In my case, I’m 
not installing the whole suite, just the bamCoverage tool from the TS - 
https://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_bam_coverage/5d11599b8a7d.
  My work-around is to create the conda env manually:

$conda create -n __deeptools@2.5.1 deep tools=2.5.1

This env is created in the conda environment outside of Galaxy, so I just copy 
it to the conda environment I’ve configured for Galaxy.  This works, but it 
seems there is some issue with the installation from the TS, so perhaps a more 
ling term fix is needed.


On Oct 2, 2017, at 8:59 AM, julie dubois 
mailto:dubju...@gmail.com>> wrote:

Hi dev team,

I have a very big problem since I updated to galaxy 17.05 with
deeptools from toolshed.

Due to a bug in galaxy 17.05 with toolshed installed tools (reported
in this issue https://github.com/galaxyproject/galaxy/issues/4591), I
re-installed deeptools to try to resolve it.
Not resolved really but it's another problem. I temporarly bypassed it.

Here is my problem : I've installed deeptools from toolshed and when
we try to use "compute matrix" for example, we have this error message
:

Fatal error: Exit code 1 ()
Traceback (most recent call last):
 File "/usr/local/bin/computeMatrix", line 4, in 
   from deeptools.computeMatrix import main
ImportError: No module named deeptools.computeMatrix

It seems that wrapper are installed but not the tool "deeptools".

For more information, here it's the way for the installation :
search and install via toolshed
Install "suite_deeptools" (version 2.5.1.1.0 : 3d68b716965a)
Info in Manage tool dependencies : version=2.5.1, resolver=Conda,
green check symbol in the line with a list of all deeptools.

Galaxy 17.05, commit cfabe37 (21 sept 2017)

I've tried to uninstall/reinstall dependencies with conda but without success.

Have you any idea to install the deeptools please ?

Thanks.
Julie
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[galaxy-dev] Problems with the test tool shed?

[Von Kuster, Greg]

Hi all,

I’m wondering if the TTS can be restarted.  I’ve been seeing this of-and-on all 
afternoon.

Thanks!

Galaxy

The Test Tool Shed could not be reached

You are seeing this message because a request to The Test Tool Shed timed out 
or was refused. This may be a temporary issue which could be resolved by 
retrying the operation you were performing. If you receive this message 
repeatedly or for an extended amount of time, please contact an administrator.


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