[galaxy-dev] GalaxyAdmins Meetup This Thursday

[Dave Clements]

Hello all,

The June online meetup of GalaxyAdmins will be this Thursday
.
This month features two talks:


*1. Galaxy in Production at the University of Minnesota*

[image: Minnesota Supercomputing Institute] 



[image: Galaxy Radio Telescope]


Galaxy has been deployed in several contexts by the Minnesota
Supercomputing Institute (MSI)  at the University
of Minnesota - Twin Citites . This month Evan Bollig
 and JJ Johnson
 of MSI will discuss several aspects of
this work relevant to the GalaxyAdmins
 group:

   -

   customizations made to Galaxy that enable MSI to leverage it as a Tier I
   service  for our users (e.g.,
   scheduling, quotas, billing, and sharing).
   -

   Pulsar  for Galaxy-P
    tools on Windows.
   -

   the CLIA-certified
   

pipelines
   and how Galaxy is integrated into clinical workflows

*2. Galaxy Radio Telescope*

The GRT  aims to collect
job run information from Galaxy servers that opt into the process. Galaxy
Admins can sign in to the GRT, register their Galaxy servers, and get back
API keys per-Galaxy instance. Then they set up a cron job (preferably
weekly, but we may explore options here later), and submit job data to the
GRT.

See https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_06_16
for full details and links.  The conference room link will be posted an
hour before the meetup.

GalaxyAdmins is a discussion group for Galaxy community members that
administer Galaxy installations.

Hope to see you (online) on Thursday,

Dave Clements and Hans-Rudolf Hotz
-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/
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[galaxy-dev] Infinite recursion on conda dependency manager

[Peter van Heusden]

Hi there

I've got a package in our lab conda channel (its still in testing phase)
called goget. This is specified as a requirement for the build_ctb_gene
tool like this:


   goget


When the tool runs, I see infinite recursion on the conda side:

https://gist.github.com/pvanheus/c16a07a2c954741a311881cc7606df8d

Any ideas?

Thanks,
Peter
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[galaxy-dev] History is not up-to-date

[Rathert , Philipp , Dr .]

Dear All,





I have a problem with my histories. 

We are running the Docker galaxy stable version 16.04 and when I start a tool 
the history does not show that it is running. it is not specific for any tool 
but for all.














however, something is running in the back



129.69.102.30 - - [14/Jun/2016:12:57:21 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A16.601Z
 HTTP/1.1" 200 - "http://129.69.102.42/  " "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) 
Version/9.0.3 Safari/601.4.4"

[pid: 271|app: 0|req: 74/163] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:21 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A16.601Z
 => generated 2511 bytes in 33 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 2)

129.69.102.30 - - [14/Jun/2016:12:57:25 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A20.635Z
 HTTP/1.1" 200 - "http://129.69.102.42/  " "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) 
Version/9.0.3 Safari/601.4.4"

[pid: 271|app: 0|req: 75/164] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:25 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A20.635Z
 => generated 2511 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 1)

129.69.102.30 - - [14/Jun/2016:12:57:29 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A24.673Z
 HTTP/1.1" 200 - "http://129.69.102.42/  " "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) 
Version/9.0.3 Safari/601.4.4"

[pid: 271|app: 0|req: 76/165] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:29 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A24.673Z
 => generated 2112 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 0)

129.69.102.30 - - [14/Jun/2016:12:57:33 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A28.711Z
 HTTP/1.1" 200 - "http://129.69.102.42/  " "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) 
Version/9.0.3 Safari/601.4.4"

[pid: 272|app: 0|req: 90/166] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:33 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A28.711Z
 => generated 2112 bytes in 32 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 0)

129.69.102.30 - - [14/Jun/2016:12:57:37 +] "GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A32.749Z
 HTTP/1.1" 200 - "http://129.69.102.42/  " "Mozilla/5.0 
(Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) 
Version/9.0.3 Safari/601.4.4"

[pid: 271|app: 0|req: 77/167] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 
14 12:57:37 2016] GET 
/api/histories/5114a2a207b7caff/contents?v=dev=update_time-ge=2016-06-14T12%3A49%3A32.749Z
 => generated 2112 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 
switches on core 3)

 





I am not sure how to fix this and I am happy for any suggestion.



Cheers,



Philipp

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Re: [galaxy-dev] cleanup datasets error

[Rathert , Philipp , Dr .]

Hi Bjoern,



I edited the galaxy.ini directly and started the script. Unfortunately I get a 
different error:





Traceback (most recent call last):

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 544, in 

    main()

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 104, in main

    app = CleanupDatasetsApplication( config )

  File "scripts/cleanup_datasets/cleanup_datasets.py", line 529, in __init__

    self.model = galaxy.model.mapping.init( config.file_path, 
config.database_connection, engine_options={}, create_tables=False, 
object_store=self.object_store )

  File "/galaxy-central/lib/galaxy/model/mapping.py", line 2541, in init

    engine = build_engine( url, engine_options, database_query_profiling_proxy, 
trace_logger )

  File "/galaxy-central/lib/galaxy/model/orm/engine_factory.py", line 20, in 
build_engine

    engine = create_engine( url, proxy=proxy, **engine_options )

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/__init__.py",
 line 386, in create_engine

    return strategy.create(*args, **kwargs)

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/strategies.py",
 line 75, in create

    dbapi = dialect_cls.dbapi(**dbapi_args)

  File 
"/galaxy-central/.venv/local/lib/python2.7/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py",
 line 579, in dbapi

    import psycopg2

ImportError: No module named psycopg2



Can I install the python-psycopq2 module via apt-get in the container and would 
this help to fix thee issue?



Cheers,



Philipp



-Original message-
From: Rathert, Philipp, Dr. 
Sent: Tuesday 14th June 2016 9:56
To: Bjoern Gruening 
Cc: galaxy-dev 
Subject: Re: [galaxy-dev] cleanup datasets error

Hi Bjoern,

This is wired. It worked before...
I will add this to the galaxy.ini in the config folder and try again.

Cheers,
Philipp

---Philipp on the road---

Am 14.06.2016 um 09:50 schrieb Bjoern Gruening  >:

 Hi,
 
 I don't think this will work with the script. This script reads the config 
file you specify config/galaxy.ini. And hence it needs to be added in this 
file, not via -e variables.
 This is probably something we should improve.
 
 Ciao,
 Bjoern
 
 
 > cleanup datasets error
 > 
 > HI Björn,
 > 
 > 
 > 
 > I have added these to the galaxy.ini via the docker specific e-
 > variables during startup of the container.
 > 
 > 
 > 
 > How can I check if they are broken?
 > 
 > 
 > 
 > Cheers,
 > 
 > 
 > 
 > Philipp
 > 
 > 
 > 
 > *From:*Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] *Sent:*
 > Tuesday, June 14, 2016 9:30 AM *To:* Rathert, Philipp, Dr.
 > ; galaxy-dev
 >  *Subject:* Re: [galaxy-dev]
 > cleanup datasets error
 > 
 > 
 > 
 > Hi Philipp,
 > 
 > have you followed this from the readme?
 > 
 > 
 > Note that if you would like to run any of the cleanup scripts
 >,
 > you will need to add the following to
 > |/export/galaxy-central/config/galaxy.ini|:
 > 
 > |database_connection =
 > postgresql://galaxy:galaxy@localhost:5432/galaxy| |file_path =
 > /export/galaxy-central/database/files|
 > 
 > Or is this broken? Cheers, Bjoern
 > 
 > On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:
 > 
 > Dear all,
 > 
 > 
 > 
 > when I want to start the cleanup datasets script I get the following
 > error.
 > 
 > 
 > 
 > (.venv)root@galaxy:/galaxy-central# python
 > /galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py
 > config/galaxy.ini -d -10 -1
 > 
 > Traceback (most recent call last):
 > 
 > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
 > line 544, in 
 > 
 > main()
 > 
 > File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py",
 > line 99, in main
 > 
 > for key, value in config_parser.items( "app:main" ):
 > 
 > File "/usr/lib/python2.7/ConfigParser.py", line 642, in items
 > 
 > raise NoSectionError(section)
 > 
 > ConfigParser.NoSectionError: No section: 'app:main'
 > 
 > 
 > 
 > 
 > 
 > We are using the docker galaxy stable 16.04 version. Before this
 > script always worked without producing any error.
 > 
 > 
 > 
 > It would be great if anybody has an idea how to fix this...
 > 
 > 
 > 
 > Thank you very much in advance.
 > 
 > 
 > 
 > Cheers,
 > 
 > 
 > 
 > Philipp
 > 
 > 
 > 
 > 
 > 
 > -Original message- *From:* Marius van den Beek
 >   *Sent:*
 > Tuesday 7th June 2016 14:06 *To:* Marco Tangaro
 >   *Cc:* galaxy-dev
 > 
 >  *Subject:* Re:
 > [galaxy-dev] Python tool wrapper with multiple 

Re: [galaxy-dev] cleanup datasets error

[Philipp Rathert]

HI Björn,

 

I have added these to the galaxy.ini via the docker specific e- variables 
during startup of the container.

 

How can I check if they are broken?

 

Cheers,

 

Philipp

 

From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com] 
Sent: Tuesday, June 14, 2016 9:30 AM
To: Rathert, Philipp, Dr. ; galaxy-dev 

Subject: Re: [galaxy-dev] cleanup datasets error

 

Hi Philipp,

have you followed this from the readme?




Note that if you would like to run any of the  

 cleanup scripts, you will need to add the following to 
/export/galaxy-central/config/galaxy.ini:

database_connection = postgresql://galaxy:galaxy@localhost:5432/galaxy
file_path = /export/galaxy-central/database/files

Or is this broken?
Cheers,
Bjoern



On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:

Dear all,







when I want to start the cleanup datasets script I get the following error.





(.venv)root@galaxy:/galaxy-central# python 
/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini 
-d -10 -1

Traceback (most recent call last):

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 
544, in 

main()

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 99, 
in main

for key, value in config_parser.items( "app:main" ):

  File "/usr/lib/python2.7/ConfigParser.py", line 642, in items

raise NoSectionError(section)

ConfigParser.NoSectionError: No section: 'app:main'









We are using the docker galaxy stable 16.04 version. Before this script always 
worked without producing any error. 







It would be great if anybody has an idea how to fix this...





Thank you very much in advance.





Cheers,





Philipp 









-Original message-
From: Marius van den Beek   

Sent: Tuesday 7th June 2016 14:06
To: Marco Tangaro   
Cc: galaxy-dev   

Subject: Re: [galaxy-dev] Python tool wrapper with multiple input and output 
files




Hi Marco, 

 

you've got an interesting use-case there.

You may want to use either a dataset list (if you only supply rna_n.bam),

or a paired dataset list (rna_n.bam and dna_n.bam). 

I would probably implement a conditional, where the user selects either a 
dataset list or a paired dataset list.

The output would then be another collection of output files.

Have a look at the test tool folder, and see if any of the tools named 
collection_*.xml fits what you would like to do

https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools

These two may be a good basis for what you want to achieve:

https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml

[this one creates an output collection]

https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml

[this one has a conditional to either select a list or a paired list as input]

 

Let us know if you need more help!

 

Cheers,

Marius

 

On 7 June 2016 at 09:50, Marco Tangaro  > wrote:

Dear experts,
my name is Marco and I'm working to port our python tool to the Galaxy 
framework.
The main script needs a rna.bam file as input, a reference fasta file, both 
mandatory. Finally, you can add a dna.bam file, but this is optional.
Therefore an example command is:

script.py -i rna.bam -f reference.fa -j dna.bam

The outout is a tabular.
Again the -j dna.bam option is completely optional.
So quite soon it turned out that I had to use a python wrapper to parse our 
script. Now the wrapper works fine.


The next step is to run the tool over multiple input file and we would like to 
avoid to use a workflow.

The idea is that to each input file corresponds an output file. The reference 
is still the same.
For instance, we have:

rna_1.bam + dna_1.bam -> output_1.txt
rna_2.bam + dna_2.bam -> output_2.txt
rna_3.bam + dna_3.bam -> output_3.txt
...
and so on.


But I don't know the best strategy to give to my wrapper multiple input files.
Moreover I have to be sure, when the dna_xyz.bam files are uploaded, that they 
correspond to the right rna_xyz.bam file.

I would like to have as output a page which is showing as results the link to 
the single output files as suggested here.
https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
planning to integrate a javascript interface.

I've browsed a lot, but on multiple input file the posts are old.
I'm using the last galaxy release (16_04).

I'm quite new to the galaxy world...
Thanks a lot for your suggestions,
Marco


___
Please keep all replies on 

Re: [galaxy-dev] cleanup datasets error

[Bjoern Gruening]

Hi Philipp,

have you followed this from the readme?

Note that if you would like to run any of thecleanup scripts 
, 
you will need to add the following 
to|/export/galaxy-central/config/galaxy.ini|:


|database_connection = postgresql://galaxy:galaxy@localhost:5432/galaxy
file_path = /export/galaxy-central/database/files|

Or is this broken?
Cheers,
Bjoern


On 14.06.2016 09:21, Rathert, Philipp, Dr. wrote:

cleanup datasets error

Dear all,


when I want to start the cleanup datasets script I get the following 
error.



(.venv)root@galaxy:/galaxy-central# python 
/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py 
config/galaxy.ini -d -10 -1


Traceback (most recent call last):

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", 
line 544, in 


main()

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", 
line 99, in main


for key, value in config_parser.items( "app:main" ):

  File "/usr/lib/python2.7/ConfigParser.py", line 642, in items

raise NoSectionError(section)

ConfigParser.NoSectionError: No section: 'app:main'



We are using the docker galaxy stable 16.04 version. Before this 
script always worked without producing any error.



It would be great if anybody has an idea how to fix this...


Thank you very much in advance.


Cheers,


Philipp



-Original message-
*From:* Marius van den Beek 
*Sent:* Tuesday 7th June 2016 14:06
*To:* Marco Tangaro 
*Cc:* galaxy-dev 
*Subject:* Re: [galaxy-dev] Python tool wrapper with multiple input 
and output files


Hi Marco,

you've got an interesting use-case there.
You may want to use either a dataset list (if you only supply rna_n.bam),
or a paired dataset list (rna_n.bam and dna_n.bam).
I would probably implement a conditional, where the user selects 
either a dataset list or a paired dataset list.

The output would then be another collection of output files.
Have a look at the test tool folder, and see if any of the tools named 
collection_*.xml fits what you would like to do

https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools
These two may be a good basis for what you want to achieve:
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml
[this one creates an output collection]
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml
[this one has a conditional to either select a list or a paired list 
as input]


Let us know if you need more help!

Cheers,
Marius

On 7 June 2016 at 09:50, Marco Tangaro > wrote:

Dear experts,
my name is Marco and I'm working to port our python tool to the Galaxy 
framework.
The main script needs a rna.bam file as input, a reference fasta file, 
both mandatory. Finally, you can add a dna.bam file, but this is optional.

Therefore an example command is:

script.py -i rna.bam -f reference.fa -j dna.bam

The outout is a tabular.
Again the -j dna.bam option is completely optional.
So quite soon it turned out that I had to use a python wrapper to 
parse our script. Now the wrapper works fine.



The next step is to run the tool over multiple input file and we would 
like to avoid to use a workflow.


The idea is that to each input file corresponds an output file. The 
reference is still the same.

For instance, we have:

rna_1.bam + dna_1.bam -> output_1.txt
rna_2.bam + dna_2.bam -> output_2.txt
rna_3.bam + dna_3.bam -> output_3.txt
...
and so on.


But I don't know the best strategy to give to my wrapper multiple 
input files.
Moreover I have to be sure, when the dna_xyz.bam files are uploaded, 
that they correspond to the right rna_xyz.bam file.


I would like to have as output a page which is showing as results the 
link to the single output files as suggested here.

https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
planning to integrate a javascript interface.

I've browsed a lot, but on multiple input file the posts are old.
I'm using the last galaxy release (16_04).

I'm quite new to the galaxy world...
Thanks a lot for your suggestions,
Marco

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To search Galaxy mailing lists 

[galaxy-dev] cleanup datasets error

[Rathert , Philipp , Dr .]

Dear all,



when I want to start the cleanup datasets script I get the following error.



(.venv)root@galaxy:/galaxy-central# python 
/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini 
-d -10 -1

Traceback (most recent call last):

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 
544, in 

    main()

  File "/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py", line 99, 
in main

    for key, value in config_parser.items( "app:main" ):

  File "/usr/lib/python2.7/ConfigParser.py", line 642, in items

    raise NoSectionError(section)

ConfigParser.NoSectionError: No section: 'app:main'






We are using the docker galaxy stable 16.04 version. Before this script always 
worked without producing any error. 



It would be great if anybody has an idea how to fix this...



Thank you very much in advance.



Cheers,



Philipp 





-Original message-
From: Marius van den Beek 
Sent: Tuesday 7th June 2016 14:06
To: Marco Tangaro 
Cc: galaxy-dev 
Subject: Re: [galaxy-dev] Python tool wrapper with multiple input and 
outputfiles


Hi Marco,

you've got an interesting use-case there.
You may want to use either a dataset list (if you only supply rna_n.bam),
or a paired dataset list (rna_n.bam and dna_n.bam). 
I would probably implement a conditional, where the user selects either a 
dataset list or a paired dataset list.
The output would then be another collection of output files.
Have a look at the test tool folder, and see if any of the tools named 
collection_*.xml fits what you would like to do
https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools
These two may be a good basis for what you want to achieve:
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml
[this one creates an output collection]
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_two_paired.xml
[this one has a conditional to either select a list or a paired list as input]

Let us know if you need more help!

Cheers,
Marius

On 7 June 2016 at 09:50, Marco Tangaro  > wrote:
Dear experts,
my name is Marco and I'm working to port our python tool to the Galaxy 
framework.
The main script needs a rna.bam file as input, a reference fasta file, both 
mandatory. Finally, you can add a dna.bam file, but this is optional.
Therefore an example command is:

script.py -i rna.bam -f reference.fa -j dna.bam

The outout is a tabular.
Again the -j dna.bam option is completely optional.
So quite soon it turned out that I had to use a python wrapper to parse our 
script. Now the wrapper works fine.


The next step is to run the tool over multiple input file and we would like to 
avoid to use a workflow.

The idea is that to each input file corresponds an output file. The reference 
is still the same.
For instance, we have:

rna_1.bam + dna_1.bam -> output_1.txt
rna_2.bam + dna_2.bam -> output_2.txt
rna_3.bam + dna_3.bam -> output_3.txt
...
and so on.


But I don't know the best strategy to give to my wrapper multiple input files.
Moreover I have to be sure, when the dna_xyz.bam files are uploaded, that they 
correspond to the right rna_xyz.bam file.

I would like to have as output a page which is showing as results the link to 
the single output files as suggested here.
https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
planning to integrate a javascript interface.

I've browsed a lot, but on multiple input file the posts are old.
I'm using the last galaxy release (16_04).

I'm quite new to the galaxy world...
Thanks a lot for your suggestions,
Marco

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