Re: [galaxy-dev] Unable to update to latest version of galaxy

[Kandalaft, Iyad]

Eleanor,

Can you please clarify if starting galaxy worked when you did:

. ./galaxy_env/bin/activate
cd galaxy_dist
sh run.sh


If it didn't, activate the python environment and run:

pip-2.6 install pycrypto
- or -
pip install pycrypto

If I recall correctly, the init script shipped with Galaxy does not activate 
the python environment.
I modified the init script to issue a login sudo in order to source the 
environment.  In .bashrc, I have it source the python environment.  This 
ensures that the python environment is always activated before galaxy is 
started regardless of how I start it.

Iyad Kandalaft
Bioinformatics Programmer
Microbial Biodiversity Bioinformatics
Science & Technology Branch
Agriculture & Agri-Food Canada
iyad.kandal...@agr.gc.ca | (613) 759-1228

From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
on behalf of Eleanor Morgan [e.mor...@curtin.edu.au]
Sent: July 16, 2014 10:35 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Unable to update to latest version of galaxy

Hi all,

I am new to galaxy.  We have a local install that we intend to turn into a 
production server at some stage.  We initially installed galaxy using the April 
2014 version.  We set up a Virtual Python Environment following the 
instructions set out on this page:

https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_a_clean_environment

When I updated to the June version of galaxy and tried to start up the server 
using the recommended shell script placed in /etc/init.d I got the following 
error message:


Starting galaxy...

Some eggs are out of date, attempting to fetch...

Traceback (most recent call last):

  File "./scripts/fetch_eggs.py", line 37, in 

c.resolve() # Only fetch eggs required by the config

  File "/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve

egg.resolve()

  File "/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve

return self.version_conflict( e.args[0], e.args[1] )

  File "/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in 
version_conflict

r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, 
egg.fetch )

  File "/usr/lib/python2.6/site-packages/pkg_resources.py", line 550, in resolve

raise VersionConflict(dist,req) # XXX put more info here

pkg_resources.VersionConflict: (pycrypto 2.0.1 
(/usr/lib64/python2.6/site-packages), Requirement.parse('pycrypto>=2.1,!=2.4'))

Fetch failed.

…done.


This error message implies that I need to update pycrypto on our system, but my 
understanding is that the virtual python environment takes care of these sorts 
of dependencies. Can someone please advise?  Here are two series of commands 
that I tried to start the system:


First attempt:
sudo bash
/etc/init.d/galaxy stop
su - galaxy
cd /galaxy/galaxy-dist
hg pull
hg update latest_2014.06.02
exit
/etc/init.d/galaxy start

After galaxy start failed I tried:
su – galaxy
cd /galaxy
. ./galaxy_env/bin/activate
cd galaxy_dist
sh run.sh

I also tried reinstalling the virtual environment to no avail.

Regards,
Eleanor



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[galaxy-dev] Unable to update to latest version of galaxy

[Eleanor Morgan]

Hi all,

I am new to galaxy.  We have a local install that we intend to turn into a 
production server at some stage.  We initially installed galaxy using the April 
2014 version.  We set up a Virtual Python Environment following the 
instructions set out on this page:

https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_a_clean_environment

When I updated to the June version of galaxy and tried to start up the server 
using the recommended shell script placed in /etc/init.d I got the following 
error message:


Starting galaxy...

Some eggs are out of date, attempting to fetch...

Traceback (most recent call last):

  File "./scripts/fetch_eggs.py", line 37, in 

c.resolve() # Only fetch eggs required by the config

  File "/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve

egg.resolve()

  File "/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve

return self.version_conflict( e.args[0], e.args[1] )

  File "/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in 
version_conflict

r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, 
egg.fetch )

  File "/usr/lib/python2.6/site-packages/pkg_resources.py", line 550, in resolve

raise VersionConflict(dist,req) # XXX put more info here

pkg_resources.VersionConflict: (pycrypto 2.0.1 
(/usr/lib64/python2.6/site-packages), Requirement.parse('pycrypto>=2.1,!=2.4'))

Fetch failed.

...done.


This error message implies that I need to update pycrypto on our system, but my 
understanding is that the virtual python environment takes care of these sorts 
of dependencies. Can someone please advise?  Here are two series of commands 
that I tried to start the system:


First attempt:
sudo bash
/etc/init.d/galaxy stop
su - galaxy
cd /galaxy/galaxy-dist
hg pull
hg update latest_2014.06.02
exit
/etc/init.d/galaxy start

After galaxy start failed I tried:
su - galaxy
cd /galaxy
. ./galaxy_env/bin/activate
cd galaxy_dist
sh run.sh

I also tried reinstalling the virtual environment to no avail.

Regards,
Eleanor


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Re: [galaxy-dev] Download URL needs user to be logged in first

[Kandalaft, Iyad]

You need to add the api key to the URL. E.g:
http://barium-rbh/capaibl/api/histories/1cd8e2f6b131e891/contents/f68b550c4724eeae/display?to_ext=html&key=APIKEYHERE
 

Otherwise, Galaxy doesn't know who's trying to access the data and if they have 
authorization.

Regards,

Iyad Kandalaft
Bioinformatics Programmer
Microbial Biodiversity Bioinformatics
Science & Technology Branch
Agriculture & Agri-Food Canada
iyad.kandal...@agr.gc.ca | (613) 759-1228


From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
on behalf of John Chilton [jmchil...@gmail.com]
Sent: July 16, 2014 8:46 AM
To: neil.burd...@csiro.au
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Download URL needs user to be logged in first

I am not really sure what link you are referring to - can you tell me
how you found this link? "History -> Export to file" or is it via the
API?

Regardless, if you trust your users and want to disable security
mechanisms I believe (and I could be wrong) you should be able to by
finding the relevant controllers in Galaxy and changing either the
decorator to allow anonymous access or changing the checks on the
histories/datasets to disable checking if the supplied user is
authorized. Though this will make everyones data available to everyone
else (or the world if this is a publicly accessible Galaxy instance).

-John

On Wed, Jul 16, 2014 at 5:43 AM,   wrote:
> Hi,
>galaxy provides a download_url to download zipped up files. However, the
> user must first log into Galaxy to commence the download. Is there a way to
> turn this feature off, so that users can click on the link and download the
> data without first login
>
> Thanks
> Neil
>
> ___
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Re: [galaxy-dev] How to configure galaxy with a cluster

[王渭巍]

Hi, Bjoern
Would you share your  procedure to make some tools to run on a cluster. 
I have tried 
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster using Torque, 
but got errors. 
I think maybe it's job_conf.xml. Would you share yours?  Thanks a lot

Ben 


From: Björn Grüning
Date: 2014-07-16 16:34
To: 王渭巍; Thomas Bellembois; galaxy-dev
Subject: Re: [galaxy-dev] How to configure galaxy with a cluster
Hi Ben,
 
that is not possible at the moment. The idea is to keep the 
user-inferface as easy as possible for the user. You, as admin, can 
decide which resource a specific tool with a specific input will use. 
You will never see any options like that in a tool, but you can write a 
tool by yourself if you like, or "enhance" the megablast tool.
 
Cheers,
Bjoern
 
 
Am 16.07.2014 09:43, schrieb 王渭巍:
> Thanks a lot, Thomas! It really helps, I added tools section followed your 
> suggestion...
>
> here is my job_conf.xml ( I am using Torque,  I have 3 servers. One for 
> galaxy server, two for cluster computing.  )
>
> 
> 
> 
> 
> 
> 
> 
> 
> 
> walltime=72:00:00,nodes=1:ppn=8
> 128
> 
> 
> 
> 
> 
> 
>
> and still no cluster options in "megablast" item.  How can I see cluster 
> options in the page, for example, the page will let me choose to use local 
> server or a cluster.
>
> Ben
>
>
>
> From: Thomas Bellembois
> Date: 2014-07-15 17:41
> To: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] How to configure galaxy with a cluster
> Hello Ben,
>
> you can configure your Galaxy instance to use your cluster in the
> job_conf.xml file:
>
> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
>
> You can set up your instance to use your cluster by default for all jobs
> or only for specific jobs.
>
> Here is a part of my job_conf.xml for example:
>
>  
> 
>   load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
>
>  
>   load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
>  
>
>  
>  
>  
>  
>
>  
>  
>  
>-r yes -b n -cwd -S /bin/bash
> -V -pe galaxy 1
>  
>  
>-r yes -b n -cwd -S /bin/bash
> -V -pe galaxy 12
>  
>
>  
>
>  
>  
>   id="toolshed.g2.bx.psu.edu/repos/bhaas/trinityrnaseq/trinityrnaseq/0.0.1" 
> destination="sge_big"/>
>  
>  
>   id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.1.00"
> destination="sge_big"/>
>   id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.1.00"
> destination="sge_big"/>
>   id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.00"
> destination="sge_big"/>
>   id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00"
> destination="sge_big"/>
>   id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.1.00"
> destination="sge_big"/>
>   id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.1.00"
> destination="sge_big"/>
>   id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.1.00"
> destination="sge_big"/>
> 
>
> Moreover you Galaxy user and Galaxy server must be allowed to submit
> jobs to your scheduler.
>
> Hope it  helps,
>
> Thomas
>
>
>
>
> ___
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Re: [galaxy-dev] Download URL needs user to be logged in first

[Neil.Burdett]

Hi John,
   What I've implemented on our local system is the user uploads their 
data, then automatically a workflow is run on that data (so the user doesn't 
need to select a tool to execute). I email the user once the job is complete 
with a link to that the user can download the results. I auto get the download 
results using the api i.e:

~/scripts/api/display.py api_key 
http://barium-rbh/capaibl/api/histories/1cd8e2f6b131e891/contents/f68b550c4724eeae

This returns something like:

Member Information
--
accessible: True
file_name: /export/barium-data3/galaxy-suvr/database/files/000/dataset_421.dat
visible: True
file_size: 521
file_ext: html
id: f68b550c4724eeae
misc_info: 
uuid: None
download_url: 
/capaibl/api/histories/1cd8e2f6b131e891/contents/f68b550c4724eeae/display
state: ok
display_types: []
display_apps: []
misc_blurb: 521 bytes
peek: HTML file
data_type: html
deleted: False
history_id: 4181f0f3af1244e2
genome_build: ?
hid: 120
visualizations: []
metadata_data_lines: 17
metadata_dbkey: ?
name: Processing input data (0171-T0-AV45)
model_class: HistoryDatasetAssociation
purged: False
api_type: file

>From this I get the "download_url" and add the server name to it and an 
>extension to get:

http://barium-rbh/capaibl/api/histories/1cd8e2f6b131e891/contents/f68b550c4724eeae/display?to_ext=html

Which i add to the email. When the user clicks on it they are able to download 
the zipped up files. However, they can only do this after first login into 
Galaxy otherwise they get a "API Authentication Required for this request" 
error on the webpage.

Neil

From: John Chilton [jmchil...@gmail.com]
Sent: Wednesday, July 16, 2014 10:46 PM
To: Burdett, Neil (DP&S, Herston - RBWH)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Download URL needs user to be logged in first

I am not really sure what link you are referring to - can you tell me
how you found this link? "History -> Export to file" or is it via the
API?

Regardless, if you trust your users and want to disable security
mechanisms I believe (and I could be wrong) you should be able to by
finding the relevant controllers in Galaxy and changing either the
decorator to allow anonymous access or changing the checks on the
histories/datasets to disable checking if the supplied user is
authorized. Though this will make everyones data available to everyone
else (or the world if this is a publicly accessible Galaxy instance).

-John

On Wed, Jul 16, 2014 at 5:43 AM,   wrote:
> Hi,
>galaxy provides a download_url to download zipped up files. However, the
> user must first log into Galaxy to commence the download. Is there a way to
> turn this feature off, so that users can click on the link and download the
> data without first login
>
> Thanks
> Neil
>
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
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>   http://galaxyproject.org/search/mailinglists/

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[galaxy-dev] cleanup_datasets.py not deleting files...

[Neil.Burdett]

Hi,
I'm trying to use the cleanup_datasets.py file to remove all files on my 
system older than 20 days. My crontab looks like this:

# m h  dom mon dow   command
34 10 * * * cd /export/barium-data3/galaxy-suvr && python 
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -1 > 
/home/galaxy/crontab_purge_milxcloud.log 2>&1 && python 
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -2 -r >> 
/home/galaxy/crontab_purge_milxcloud.log 2>&1 && python 
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -3 -r >> 
/home/galaxy/crontab_purge_milxcloud.log 2>&1 && python 
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -5 -r >> 
/home/galaxy/crontab_purge_milxcloud.log 2>&1 && python 
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -4 -r >> 
/home/galaxy/crontab_purge_milxcloud.log 2>&1 && python 
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 20 -6 -r >> 
/home/galaxy/crontab_purge_milxcloud.log 2>&1

The crontab executes and the contents of 
/home/galaxy/crontab_purge_milxcloud.log is:

cat /home/galaxy/crontab_purge_milxcloud.log
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:02 - Handling stuff older than 20 days
Datasets will NOT be removed from disk.

Deleted 0 histories
Elapsed time:  0.170083045959
##
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:02 - Handling stuff older than 20 days
Datasets will be removed from disk.

Purged 0 histories.
Elapsed time:  0.174137830734
##
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:03 - Handling stuff older than 20 days
Datasets will be removed from disk.

Purged 0 datasets
Freed disk space:  0
Elapsed time:  0.168104887009
##
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:04 - Handling stuff older than 20 days
Datasets will be removed from disk.

# Purged 0 folders.
Elapsed time:  0.168635129929
##
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:05 - Handling stuff older than 20 days
Datasets will be removed from disk.

# Purged 0 libraries .
Elapsed time:  0.166506052017
##
psycopg2 egg successfully loaded for postgres dialect
##

# 2014-07-17 10:34:06 - Handling stuff older than 20 days
Datasets will be removed from disk.

Examined 0 datasets, marked 0 datasets and 0 dataset instances (HDA) as deleted
Total elapsed time:  0.00744795799255
##

However, today is the 17th July and when I look into  the database directory 
i.e. ~/database/files/000 I still have files from the 18th June so older than 
20 days i.e.:

drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_213_files
-rw-r--r-- 1 galaxy nogroup 1061 Jun 18 09:19 dataset_213.dat
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_215_files
-rw-r--r-- 1 galaxy nogroup  270 Jun 18 09:19 dataset_215.dat
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_221_files
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_219_files
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_220_files
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_222_files
drwxr-xr-x 2 galaxy nogroup 4096 Jun 18 09:19 dataset_218_files
-rw-r--r-- 1 galaxy nogroup  994 Jun 18 09:19 dataset_216.dat
-rw-r--r-- 1 galaxy nogroup  161 Jun 18 09:19 dataset_214.dat

Am I doing something wrong? Using wrong arguments/file etc ?

Thanks
Neil
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Re: [galaxy-dev] writing datatypes

[Greg Von Kuster]

Assuming this comment:

>> Finally, we will talk to the devteam to
rewrite EMBOSS to depend on our separate data type repositories.

refers to the emboss_5 repository owned by devteam, then what is being proposed 
should work (although I may not be fully understanding what is being proposed). 
 

If the emboss datatypes are split up and the emboss_5 repository's 
repository_dependencies.xml file is altered, then  a new installable revision 
of the emboss_5 repository will be created.  This implies that any previous 
installation cannot be updated to include the split up emboss datatypes.  
Instead, a new installation of the emboss_5 repository will be required.  This 
new installation may depend on emboss datatypes that conflict with those in the 
older emboss_5 installation, and the 2nd version of the conflicting datatypes 
will not be loaded into the Galaxy datatypes registry.  However, if the 
datatypes are the same, this shouldn't be a problem since the 1st version will 
have been loaded.


On Jul 16, 2014, at 4:52 PM, John Chilton  wrote:

> Is this going to work? I get that this would be a better design if
> done from the beginning, but what happens if you install an emboss
> repository upgrade (on an existing install) that brings in conflicting
> types from other repositories that already exist and have been
> previously installed? Does the tool shed have a mechanism to handle
> that?
> 
> -John
> 
> On Wed, Jul 16, 2014 at 9:20 AM, Björn Grüning
>  wrote:
>> Hi Eric,
>> 
>> 
>>> Forgive me, I'm not 100% clear on the custom plugin system used by galaxy,
>>> but if I "subclass" from the text data type, will sniffers I implement
>>> override text's and function? The lack of being able to add an entry to the
>>> sniffer section (unlike with the tabular example) led me to believe my
>>> genbank datatype wouldn't be sniffed.
>> 
>> 
>> Thats true, if you want to override functions, you need to subclass it on a
>> python level not on the XML level.
>> 
>> 
>>> Additionally, I'd still like to be able to add completely new datatypes,
>>> do you know of any working examples of this? As mentioned in my original
>>> post, duplicating an existing datatype and changing names on it surprisingly
>>> doesn't work.
>> 
>> 
>> https://github.com/bgruening/galaxytools/tree/master/datatypes/msa_datatypes
>> https://github.com/bgruening/galaxytools/blob/master/chemicaltoolbox/datatypes/datatypes_conf.xml
>> 
>> Is that enough, to get started?
>> 
>> 
>>> I'd be lovely to have the emboss datatypes split out.
>> 
>> 
>> Ok, than lets start :)
>> I will try to fork emboss into my galaxytools/datatypes repository and try
>> to split them. You will get commit access and can improve your genbank
>> datatype (and a few more ;)). Finally, we will talk to the devteam to
>> rewrite EMBOSS to depend on our separate data type repositories. OK?
>> 
>> Ciao,
>> Bjoenr
>> 
>>> Cheers,
>>> Eric
>>> 
>>> On July 16, 2014 8:34:55 AM CDT, Peter Cock 
>>> wrote:
 
 Indeed - ideally (once working) we can upload under the IUC ToolShed as
 a
 community maintained resource rather than under a personal account
 which
 becomes a single point of failure (the bus factor).
 
 We (the ICU) have previously discussed doing this so that the EMBOSS
 datatypes could become more of a meta-entry depending on other smaller
 specific datatype defining ToolShed repositories. But it hasn't reached
 the
 top of my personal TODO list yet ;)
 
 Peter
 
 On Wed, Jul 16, 2014 at 1:47 PM, Björn Grüning
  wrote:
> 
> Hi Eric,
> 
> please have a look at:
> 
> 
 
 https://github.com/bgruening/galaxytools/blob/master/datatypes/msa_datatypes/datatypes_conf.xml
> 
> 
> You need somthing like:
>  subclass="True" />
> 
> Lets try to split the EMBOSS datatypes a little bit into small
 
 chunks. E.g.
> 
> sequences_datatypes, msa_datatypes ... and so on ...
> 
> Cheers,
> Bjoern
> 
> 
> Am 14.07.2014 20:31, schrieb Eric Rasche:
> 
>> -BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>> 
>> I'm trying to add a new datatype to my galaxy instance for genbank
>> files, however I'm running into various issues. I've followed the
>> tutorial
>> (https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes)
>> 
>> however that example subclasses tabular, and I'd like to subclass
 
 Text
>> 
>> as they're plain text files, and I'd like to be able to define a
 
 sniffer
>> 
>> for them (not possible if your type=galaxy.datatypes.data:Text)
>> 
>> I figured the call ought to be something like
>> 
>> > subclass="True" />
>> 
>> however, everything I try fails with
>> 
>>> Error importing datatype module galaxy.datatypes.data: 'module'
 
 object
>>> 
>>> has no attribute 'Genbank'
>> 
>> 
>

Re: [galaxy-dev] writing datatypes

[John Chilton]

Is this going to work? I get that this would be a better design if
done from the beginning, but what happens if you install an emboss
repository upgrade (on an existing install) that brings in conflicting
types from other repositories that already exist and have been
previously installed? Does the tool shed have a mechanism to handle
that?

-John

On Wed, Jul 16, 2014 at 9:20 AM, Björn Grüning
 wrote:
> Hi Eric,
>
>
>> Forgive me, I'm not 100% clear on the custom plugin system used by galaxy,
>> but if I "subclass" from the text data type, will sniffers I implement
>> override text's and function? The lack of being able to add an entry to the
>> sniffer section (unlike with the tabular example) led me to believe my
>> genbank datatype wouldn't be sniffed.
>
>
> Thats true, if you want to override functions, you need to subclass it on a
> python level not on the XML level.
>
>
>> Additionally, I'd still like to be able to add completely new datatypes,
>> do you know of any working examples of this? As mentioned in my original
>> post, duplicating an existing datatype and changing names on it surprisingly
>> doesn't work.
>
>
> https://github.com/bgruening/galaxytools/tree/master/datatypes/msa_datatypes
> https://github.com/bgruening/galaxytools/blob/master/chemicaltoolbox/datatypes/datatypes_conf.xml
>
> Is that enough, to get started?
>
>
>> I'd be lovely to have the emboss datatypes split out.
>
>
> Ok, than lets start :)
> I will try to fork emboss into my galaxytools/datatypes repository and try
> to split them. You will get commit access and can improve your genbank
> datatype (and a few more ;)). Finally, we will talk to the devteam to
> rewrite EMBOSS to depend on our separate data type repositories. OK?
>
> Ciao,
> Bjoenr
>
>> Cheers,
>> Eric
>>
>> On July 16, 2014 8:34:55 AM CDT, Peter Cock 
>> wrote:
>>>
>>> Indeed - ideally (once working) we can upload under the IUC ToolShed as
>>> a
>>> community maintained resource rather than under a personal account
>>> which
>>> becomes a single point of failure (the bus factor).
>>>
>>> We (the ICU) have previously discussed doing this so that the EMBOSS
>>> datatypes could become more of a meta-entry depending on other smaller
>>> specific datatype defining ToolShed repositories. But it hasn't reached
>>> the
>>> top of my personal TODO list yet ;)
>>>
>>> Peter
>>>
>>> On Wed, Jul 16, 2014 at 1:47 PM, Björn Grüning
>>>  wrote:

 Hi Eric,

 please have a look at:


>>>
>>> https://github.com/bgruening/galaxytools/blob/master/datatypes/msa_datatypes/datatypes_conf.xml


 You need somthing like:
 >>> subclass="True" />

 Lets try to split the EMBOSS datatypes a little bit into small
>>>
>>> chunks. E.g.

 sequences_datatypes, msa_datatypes ... and so on ...

 Cheers,
 Bjoern


 Am 14.07.2014 20:31, schrieb Eric Rasche:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> I'm trying to add a new datatype to my galaxy instance for genbank
> files, however I'm running into various issues. I've followed the
> tutorial
> (https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes)
>
> however that example subclasses tabular, and I'd like to subclass
>>>
>>> Text
>
> as they're plain text files, and I'd like to be able to define a
>>>
>>> sniffer
>
> for them (not possible if your type=galaxy.datatypes.data:Text)
>
> I figured the call ought to be something like
>
>  subclass="True" />
>
> however, everything I try fails with
>
>> Error importing datatype module galaxy.datatypes.data: 'module'
>>>
>>> object
>>
>> has no attribute 'Genbank'
>
>
>
> To avoid this particular issue, I tried writing a separate datatype
>>>
>>> just
>
> for genbank files (type="galaxy.datatypes.genbank:Genbank"), however
> that fails with the same error:
>
>> galaxy.datatypes.registry ERROR 2014-07-14 13:23:23,100 Error
>>>
>>> importing
>>
>> datatype module galaxy.datatypes.genbank: 'module' object has no
>>>
>>> attribute
>>
>> 'genbank'
>> Traceback (most recent call last):
>> File
>>>
>>> "/home/hxr/work/galaxy-central/lib/galaxy/datatypes/registry.py",
>>
>> line 206, in load_datatypes
>>   module = getattr( module, mod )
>> AttributeError: 'module' object has no attribute 'genbank'
>
>
>
> Here's my lib/galaxy/datatypes/genbank.py looks like:
>
>> import pkg_resources
>> pkg_resources.require( "bx-python" )
>> import logging
>> from galaxy.datatypes import data
>> log = logging.getLogger(__name__)
>>
>> class Genbank( data.Text ):
>>   file_ext = "gb"
>>
>>   def sniff( self, filename ):
>>   header = open(filename).read(5)
>>   return header == 'LOCUS'
>
>
>
> To debug this, I've tried copying the tabula

Re: [galaxy-dev] Workflow with many inputs

[John Chilton]

I just want to clarify - do you have a tool with a multiple input data
parameter (e.g.  wrote:
> Hi all,
>
> I have a tool that receives multiple inputs, and it is working fine if I run
> it stand alone. However, I want to create a workflow where this tool receive
> as an input the output of other tools.
>
> I can connect the output from the other tools in the input of this tool, but
> the tool receives only one input.
>
> Is there a way to set multiple inputs to a tool in a workflow? I've found
> several similar questions like mine, but I haven't found an answer.
>
> I appreciate your help.
>
> Best regards,
>
> --
> Alexandre Defelicibus
> Mestrando em Bioengenharia
> Programa de Pós-Graduação em Bioengenharia
> Universidade de São Paulo - USP
>
> ___
> 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:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/

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Re: [galaxy-dev] API v/s twill based testing

[Peter Cock]

On Wed, Jul 16, 2014 at 7:44 PM, Saket Choudhary  wrote:
> Thanks Peter, I guess I should then rely on API based tests.
>

If it is just the order, make sure the order of the output files in the 
is consistent with that in the  and it make be OK with Twill...
I wonder if I filed a Trello card on this, or just an email?

Peter
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Re: [galaxy-dev] API v/s twill based testing

[Saket Choudhary]

Thanks Peter, I guess I should then rely on API based tests.


On 15 July 2014 14:18, Peter Cock  wrote:

> Hi Saket,
>
> From memory the Twill tests are fragile with the output file order in the
> XML.
>
> John was discussing switching the default from the Twill to API backend,
> not sure when that is happening though...
>
> Peter
>
> On Tue, Jul 15, 2014 at 9:31 AM, Saket Choudhary 
> wrote:
> > I recently updated tests for one of my wrappers and came across this
> strange
> > behaviour:
> >
> > The twill based testing reports a failure:
> > https://travis-ci.org/saketkc/galaxy_tools/jobs/29956682#L1463
> >
> > whereas, the API based testing shows success:
> > https://travis-ci.org/saketkc/galaxy_tools/jobs/29956683
> >
> > Unfortunately I cannot run these tests locally since I am behind a system
> > proxy [Refer:
> >
> http://dev.list.galaxyproject.org/Functional-Tests-and-ftype-td4664233.html
> ]
> > and have to rely on travis..
> >
> > The place where twii tests fails shows that  it is trying to compare the
> > diff between 'chasm_output_genes.tabular'  and
> > 'chasm_output_variants.tabular' instead of  'chasm_output_genes.tabular'.
> > [See : https://travis-ci.org/saketkc/galaxy_tools/jobs/29956682#L1469]
> >
> > I tried running my tools locally and I did not come across any case where
> > the 'variants' output gets replaced by the 'genes' output, thus possibly
> > ruling out unexpected behavior from the tool's server end.
> >
> > Is this a possible bug or am I missing something?
> >
> > Saket
> >
> > ___
> > 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:
> >   http://lists.bx.psu.edu/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/
>
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Re: [galaxy-dev] Updated Freebayes Wrapper - Bugs

[Nicola Soranzo]

Il 2014-06-30 18:40 Anton Nekrutenko ha scritto:

Lance:

Here is github URL:

https://github.com/nekrut/freebayes [3]

 On Wed, Jun 25, 2014 at 2:40 PM, Lance Parsons
 wrote:


Thanks for the major update of the Freebayes wrapper, excellent!

I've run into two issues, however.

1) When using "set allelic scope" I get the following error:

Fatal error: Exit code 1 ()
freebayes: unrecognized option `--min-repeat-length'
did you mean --min-repeat-size ?


This bug (and other 2) would be fixed by this pull request:

https://github.com/nekrut/freebayes/pull/1

Best,
Nicola


2) When using a vcf file as input I get the following error:

Fatal error: Exit code 1 ()
open: No such file or directory
[bgzf_check_bgzf] failed to open the file: input_variant_vcf.vcf.gz
[tabix++] was bgzip used to compress this file?
input_variant_vcf.vcf.gz

I'd be happy to help resolve these.  Is there a bitbucket repo
somewhere to submit pull requests?

--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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--

Anton Nekrutenko
Associate Professor
Dept. of Biochemistry and Molecular Biology
http://nekrut.bx.psu.edu [5]
 (814) 826-3051

Links:
--
[1] http://lists.bx.psu.edu/
[2] http://galaxyproject.org/search/mailinglists/
[3] https://github.com/nekrut/freebayes
[4] mailto:lpars...@princeton.edu
[5] http://nekrut.bx.psu.edu


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Re: [galaxy-dev] Multiple output tools in Workflow

[Peter Cock]

On Wed, Jul 16, 2014 at 5:28 PM, Calogero Zarbo  wrote:
> Hello to everybody
>
> I'm developing my own tool that need to switch the numbers of output files
> according to a parameter selected by the user from a list in the 
> tag.
> How can I do such thing?
>
> Here is the XML code:
> 
>  format="showelab-dataset,fbk-svm-dataset"/>
> 
>
> 
> ".fbk-svm-dataset" Format
> ".showelab-dataset"
> Format
> 
> 
> 
> 
> 
>
> 
> 
>  label="Training Dataset extracted from ${input_dataset.name}">
> format_options == "showelab"
> 
>  label="Validation Dataset extracted from ${input_dataset.name}">
> format_options == "showelab"
> 
>  label="Training Dataset extracted from ${input_dataset.name}">
> format_options == "fbk"
> 
> 
> format_options == "fbk"
> 
>  label="Validation Dataset extracted from ${input_dataset.name}">
> format_options == "fbk"
> 
> 
> format_options == "fbk"
> 
>
> 
>
>
> Basically I would like to have in the Workflow Canvas that the outputs
> displayed in the interface will change according to the format_options
> select parameter.
>
> Thanks in advance.

Hi Calogero,

I think this tool of mine would serve as a working example:
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id

Peter
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[galaxy-dev] Multiple output tools in Workflow

[Calogero Zarbo]

Hello to everybody

I'm developing my own tool that need to switch the numbers of output files
according to a parameter selected by the user from a list in the 
tag.
How can I do such thing?

Here is the XML code:





".fbk-svm-dataset" Format
".showelab-dataset" Format









format_options == "showelab"


format_options == "showelab"


format_options == "fbk"


format_options == "fbk"


format_options == "fbk"


format_options == "fbk"





Basically I would like to have in the Workflow Canvas that the outputs
displayed in the interface will change according to the format_options
select parameter.

Thanks in advance.




-- 
Calogero Zarbo


FBK - Fondazione Bruno Kessler
Center for Information Technology
Mpba - Predictive Models for Biomedicine & Environment
Via Sommarive, 18- 38123 Povo (Trento) IT
e-mail: za...@fbk.eu

phone: +39 0461 314 674
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Re: [galaxy-dev] writing datatypes

[Eric Rasche]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Björn,

On 07/16/2014 09:20 AM, Björn Grüning wrote:
> Hi Eric,
> 
>> Forgive me, I'm not 100% clear on the custom plugin system used by
>> galaxy, but if I "subclass" from the text data type, will sniffers I
>> implement override text's and function? The lack of being able to add
>> an entry to the sniffer section (unlike with the tabular example) led
>> me to believe my genbank datatype wouldn't be sniffed.
> 
> Thats true, if you want to override functions, you need to subclass it
> on a python level not on the XML level.

Okay, good, as I figured then.

>> Additionally, I'd still like to be able to add completely new
>> datatypes, do you know of any working examples of this? As mentioned
>> in my original post, duplicating an existing datatype and changing
>> names on it surprisingly doesn't work.
> 
> https://github.com/bgruening/galaxytools/tree/master/datatypes/msa_datatypes
> 
> https://github.com/bgruening/galaxytools/blob/master/chemicaltoolbox/datatypes/datatypes_conf.xml

Those absolutely should be, thank you.

I'll probably strip them down and post a minimal working example, and
code to the wiki as well, for future reference.

> Is that enough, to get started?
> 
>> I'd be lovely to have the emboss datatypes split out.
> 
> Ok, than lets start :)
> I will try to fork emboss into my galaxytools/datatypes repository and
> try to split them. You will get commit access and can improve your
> genbank datatype (and a few more ;)). Finally, we will talk to the
> devteam to rewrite EMBOSS to depend on our separate data type
> repositories. OK?

Ja, sounds good! Happy to help.

> 
> Ciao,
> Bjoenr
> 
>> Cheers,
>> Eric
>>
>> On July 16, 2014 8:34:55 AM CDT, Peter Cock
>>  wrote:
>>> Indeed - ideally (once working) we can upload under the IUC ToolShed as
>>> a
>>> community maintained resource rather than under a personal account
>>> which
>>> becomes a single point of failure (the bus factor).
>>>
>>> We (the ICU) have previously discussed doing this so that the EMBOSS
>>> datatypes could become more of a meta-entry depending on other smaller
>>> specific datatype defining ToolShed repositories. But it hasn't reached
>>> the
>>> top of my personal TODO list yet ;)
>>>
>>> Peter
>>>
>>> On Wed, Jul 16, 2014 at 1:47 PM, Björn Grüning
>>>  wrote:
 Hi Eric,

 please have a look at:


>>> https://github.com/bgruening/galaxytools/blob/master/datatypes/msa_datatypes/datatypes_conf.xml
>>>

 You need somthing like:
 >>> subclass="True" />

 Lets try to split the EMBOSS datatypes a little bit into small
>>> chunks. E.g.
 sequences_datatypes, msa_datatypes ... and so on ...

 Cheers,
 Bjoern


 Am 14.07.2014 20:31, schrieb Eric Rasche:

> I'm trying to add a new datatype to my galaxy instance for genbank
> files, however I'm running into various issues. I've followed the
> tutorial
> (https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes)
> 
> however that example subclasses tabular, and I'd like to subclass
 Text
> as they're plain text files, and I'd like to be able to define a
 sniffer
> for them (not possible if your type=galaxy.datatypes.data:Text)
> 
> I figured the call ought to be something like
> 
>  subclass="True" />
> 
> however, everything I try fails with
> 
>>> Error importing datatype module galaxy.datatypes.data: 'module'
 object
>>> has no attribute 'Genbank'
> 
> 
> To avoid this particular issue, I tried writing a separate datatype
 just
> for genbank files (type="galaxy.datatypes.genbank:Genbank"), however
> that fails with the same error:
> 
>>> galaxy.datatypes.registry ERROR 2014-07-14 13:23:23,100 Error
 importing
>>> datatype module galaxy.datatypes.genbank: 'module' object has no
 attribute
>>> 'genbank'
>>> Traceback (most recent call last):
>>> File
 "/home/hxr/work/galaxy-central/lib/galaxy/datatypes/registry.py",
>>> line 206, in load_datatypes
>>>   module = getattr( module, mod )
>>> AttributeError: 'module' object has no attribute 'genbank'
> 
> 
> Here's my lib/galaxy/datatypes/genbank.py looks like:
> 
>>> import pkg_resources
>>> pkg_resources.require( "bx-python" )
>>> import logging
>>> from galaxy.datatypes import data
>>> log = logging.getLogger(__name__)
>>>
>>> class Genbank( data.Text ):
>>>   file_ext = "gb"
>>>
>>>   def sniff( self, filename ):
>>>   header = open(filename).read(5)
>>>   return header == 'LOCUS'
> 
> 
> To debug this, I've tried copying the tabular data type completely,
> removed all the classes other than Tabular, and renamed it
 "Genbank",
> however this fails too with the same error.
> 
> Can anyone offer some insight?
> 
> Cheers,
> Eric
> ___
> Please keep all replies on the list by using "reply all"

Re: [galaxy-dev] writing datatypes

[Björn Grüning]

Hi Eric,


Forgive me, I'm not 100% clear on the custom plugin system used by galaxy, but if I 
"subclass" from the text data type, will sniffers I implement override text's 
and function? The lack of being able to add an entry to the sniffer section (unlike with 
the tabular example) led me to believe my genbank datatype wouldn't be sniffed.


Thats true, if you want to override functions, you need to subclass it 
on a python level not on the XML level.



Additionally, I'd still like to be able to add completely new datatypes, do you 
know of any working examples of this? As mentioned in my original post, 
duplicating an existing datatype and changing names on it surprisingly doesn't 
work.


https://github.com/bgruening/galaxytools/tree/master/datatypes/msa_datatypes
https://github.com/bgruening/galaxytools/blob/master/chemicaltoolbox/datatypes/datatypes_conf.xml

Is that enough, to get started?


I'd be lovely to have the emboss datatypes split out.


Ok, than lets start :)
I will try to fork emboss into my galaxytools/datatypes repository and 
try to split them. You will get commit access and can improve your 
genbank datatype (and a few more ;)). Finally, we will talk to the 
devteam to rewrite EMBOSS to depend on our separate data type 
repositories. OK?


Ciao,
Bjoenr


Cheers,
Eric

On July 16, 2014 8:34:55 AM CDT, Peter Cock  wrote:

Indeed - ideally (once working) we can upload under the IUC ToolShed as
a
community maintained resource rather than under a personal account
which
becomes a single point of failure (the bus factor).

We (the ICU) have previously discussed doing this so that the EMBOSS
datatypes could become more of a meta-entry depending on other smaller
specific datatype defining ToolShed repositories. But it hasn't reached
the
top of my personal TODO list yet ;)

Peter

On Wed, Jul 16, 2014 at 1:47 PM, Björn Grüning
 wrote:

Hi Eric,

please have a look at:



https://github.com/bgruening/galaxytools/blob/master/datatypes/msa_datatypes/datatypes_conf.xml


You need somthing like:


Lets try to split the EMBOSS datatypes a little bit into small

chunks. E.g.

sequences_datatypes, msa_datatypes ... and so on ...

Cheers,
Bjoern


Am 14.07.2014 20:31, schrieb Eric Rasche:


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

I'm trying to add a new datatype to my galaxy instance for genbank
files, however I'm running into various issues. I've followed the
tutorial
(https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes)

however that example subclasses tabular, and I'd like to subclass

Text

as they're plain text files, and I'd like to be able to define a

sniffer

for them (not possible if your type=galaxy.datatypes.data:Text)

I figured the call ought to be something like



however, everything I try fails with


Error importing datatype module galaxy.datatypes.data: 'module'

object

has no attribute 'Genbank'



To avoid this particular issue, I tried writing a separate datatype

just

for genbank files (type="galaxy.datatypes.genbank:Genbank"), however
that fails with the same error:


galaxy.datatypes.registry ERROR 2014-07-14 13:23:23,100 Error

importing

datatype module galaxy.datatypes.genbank: 'module' object has no

attribute

'genbank'
Traceback (most recent call last):
File

"/home/hxr/work/galaxy-central/lib/galaxy/datatypes/registry.py",

line 206, in load_datatypes
  module = getattr( module, mod )
AttributeError: 'module' object has no attribute 'genbank'



Here's my lib/galaxy/datatypes/genbank.py looks like:


import pkg_resources
pkg_resources.require( "bx-python" )
import logging
from galaxy.datatypes import data
log = logging.getLogger(__name__)

class Genbank( data.Text ):
  file_ext = "gb"

  def sniff( self, filename ):
  header = open(filename).read(5)
  return header == 'LOCUS'



To debug this, I've tried copying the tabular data type completely,
removed all the classes other than Tabular, and renamed it

"Genbank",

however this fails too with the same error.

Can anyone offer some insight?

Cheers,
Eric
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___
Please keep all replies on the l

Re: [galaxy-dev] writing datatypes

[Eric Rasche]

Forgive me, I'm not 100% clear on the custom plugin system used by galaxy, but 
if I "subclass" from the text data type, will sniffers I implement override 
text's and function? The lack of being able to add an entry to the sniffer 
section (unlike with the tabular example) led me to believe my genbank datatype 
wouldn't be sniffed.

Additionally, I'd still like to be able to add completely new datatypes, do you 
know of any working examples of this? As mentioned in my original post, 
duplicating an existing datatype and changing names on it surprisingly doesn't 
work.

I'd be lovely to have the emboss datatypes split out.

Cheers,
Eric

On July 16, 2014 8:34:55 AM CDT, Peter Cock  wrote:
>Indeed - ideally (once working) we can upload under the IUC ToolShed as
>a
>community maintained resource rather than under a personal account
>which
>becomes a single point of failure (the bus factor).
>
>We (the ICU) have previously discussed doing this so that the EMBOSS
>datatypes could become more of a meta-entry depending on other smaller
>specific datatype defining ToolShed repositories. But it hasn't reached
>the
>top of my personal TODO list yet ;)
>
>Peter
>
>On Wed, Jul 16, 2014 at 1:47 PM, Björn Grüning
> wrote:
>> Hi Eric,
>>
>> please have a look at:
>>
>>
>https://github.com/bgruening/galaxytools/blob/master/datatypes/msa_datatypes/datatypes_conf.xml
>>
>> You need somthing like:
>> > subclass="True" />
>>
>> Lets try to split the EMBOSS datatypes a little bit into small
>chunks. E.g.
>> sequences_datatypes, msa_datatypes ... and so on ...
>>
>> Cheers,
>> Bjoern
>>
>>
>> Am 14.07.2014 20:31, schrieb Eric Rasche:
>>
>>> -BEGIN PGP SIGNED MESSAGE-
>>> Hash: SHA1
>>>
>>> I'm trying to add a new datatype to my galaxy instance for genbank
>>> files, however I'm running into various issues. I've followed the
>>> tutorial
>>> (https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes)
>>>
>>> however that example subclasses tabular, and I'd like to subclass
>Text
>>> as they're plain text files, and I'd like to be able to define a
>sniffer
>>> for them (not possible if your type=galaxy.datatypes.data:Text)
>>>
>>> I figured the call ought to be something like
>>>
>>> >> subclass="True" />
>>>
>>> however, everything I try fails with
>>>
 Error importing datatype module galaxy.datatypes.data: 'module'
>object
 has no attribute 'Genbank'
>>>
>>>
>>> To avoid this particular issue, I tried writing a separate datatype
>just
>>> for genbank files (type="galaxy.datatypes.genbank:Genbank"), however
>>> that fails with the same error:
>>>
 galaxy.datatypes.registry ERROR 2014-07-14 13:23:23,100 Error
>importing
 datatype module galaxy.datatypes.genbank: 'module' object has no
>attribute
 'genbank'
 Traceback (most recent call last):
File
>"/home/hxr/work/galaxy-central/lib/galaxy/datatypes/registry.py",
 line 206, in load_datatypes
  module = getattr( module, mod )
 AttributeError: 'module' object has no attribute 'genbank'
>>>
>>>
>>> Here's my lib/galaxy/datatypes/genbank.py looks like:
>>>
 import pkg_resources
 pkg_resources.require( "bx-python" )
 import logging
 from galaxy.datatypes import data
 log = logging.getLogger(__name__)

 class Genbank( data.Text ):
  file_ext = "gb"

  def sniff( self, filename ):
  header = open(filename).read(5)
  return header == 'LOCUS'
>>>
>>>
>>> To debug this, I've tried copying the tabular data type completely,
>>> removed all the classes other than Tabular, and renamed it
>"Genbank",
>>> however this fails too with the same error.
>>>
>>> Can anyone offer some insight?
>>>
>>> Cheers,
>>> Eric
>>> -BEGIN PGP SIGNATURE-
>>> Version: GnuPG v2.0.22 (GNU/Linux)
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>>> =4m2j
>>> -END PGP SIGNATURE-
>>> ___
>>> 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:
>>>http://lists.bx.psu.edu/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>http://galaxyproject.o

Re: [galaxy-dev] writing datatypes

[Peter Cock]

Indeed - ideally (once working) we can upload under the IUC ToolShed as a
community maintained resource rather than under a personal account which
becomes a single point of failure (the bus factor).

We (the ICU) have previously discussed doing this so that the EMBOSS
datatypes could become more of a meta-entry depending on other smaller
specific datatype defining ToolShed repositories. But it hasn't reached the
top of my personal TODO list yet ;)

Peter

On Wed, Jul 16, 2014 at 1:47 PM, Björn Grüning
 wrote:
> Hi Eric,
>
> please have a look at:
>
> https://github.com/bgruening/galaxytools/blob/master/datatypes/msa_datatypes/datatypes_conf.xml
>
> You need somthing like:
>  subclass="True" />
>
> Lets try to split the EMBOSS datatypes a little bit into small chunks. E.g.
> sequences_datatypes, msa_datatypes ... and so on ...
>
> Cheers,
> Bjoern
>
>
> Am 14.07.2014 20:31, schrieb Eric Rasche:
>
>> -BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>>
>> I'm trying to add a new datatype to my galaxy instance for genbank
>> files, however I'm running into various issues. I've followed the
>> tutorial
>> (https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes)
>>
>> however that example subclasses tabular, and I'd like to subclass Text
>> as they're plain text files, and I'd like to be able to define a sniffer
>> for them (not possible if your type=galaxy.datatypes.data:Text)
>>
>> I figured the call ought to be something like
>>
>> > subclass="True" />
>>
>> however, everything I try fails with
>>
>>> Error importing datatype module galaxy.datatypes.data: 'module' object
>>> has no attribute 'Genbank'
>>
>>
>> To avoid this particular issue, I tried writing a separate datatype just
>> for genbank files (type="galaxy.datatypes.genbank:Genbank"), however
>> that fails with the same error:
>>
>>> galaxy.datatypes.registry ERROR 2014-07-14 13:23:23,100 Error importing
>>> datatype module galaxy.datatypes.genbank: 'module' object has no attribute
>>> 'genbank'
>>> Traceback (most recent call last):
>>>File "/home/hxr/work/galaxy-central/lib/galaxy/datatypes/registry.py",
>>> line 206, in load_datatypes
>>>  module = getattr( module, mod )
>>> AttributeError: 'module' object has no attribute 'genbank'
>>
>>
>> Here's my lib/galaxy/datatypes/genbank.py looks like:
>>
>>> import pkg_resources
>>> pkg_resources.require( "bx-python" )
>>> import logging
>>> from galaxy.datatypes import data
>>> log = logging.getLogger(__name__)
>>>
>>> class Genbank( data.Text ):
>>>  file_ext = "gb"
>>>
>>>  def sniff( self, filename ):
>>>  header = open(filename).read(5)
>>>  return header == 'LOCUS'
>>
>>
>> To debug this, I've tried copying the tabular data type completely,
>> removed all the classes other than Tabular, and renamed it "Genbank",
>> however this fails too with the same error.
>>
>> Can anyone offer some insight?
>>
>> Cheers,
>> Eric
>> -BEGIN PGP SIGNATURE-
>> Version: GnuPG v2.0.22 (GNU/Linux)
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>> dLiw3ddVm+BFmczJzRpt
>> =4m2j
>> -END PGP SIGNATURE-
>> ___
>> 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:
>>http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>http://galaxyproject.org/search/mailinglists/
>>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] writing datatypes

[Björn Grüning]

Hi Eric,

please have a look at:

https://github.com/bgruening/galaxytools/blob/master/datatypes/msa_datatypes/datatypes_conf.xml

You need somthing like:
subclass="True" />


Lets try to split the EMBOSS datatypes a little bit into small chunks. 
E.g. sequences_datatypes, msa_datatypes ... and so on ...


Cheers,
Bjoern


Am 14.07.2014 20:31, schrieb Eric Rasche:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

I'm trying to add a new datatype to my galaxy instance for genbank
files, however I'm running into various issues. I've followed the
tutorial (https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes)

however that example subclasses tabular, and I'd like to subclass Text
as they're plain text files, and I'd like to be able to define a sniffer
for them (not possible if your type=galaxy.datatypes.data:Text)

I figured the call ought to be something like



however, everything I try fails with


Error importing datatype module galaxy.datatypes.data: 'module' object has no 
attribute 'Genbank'


To avoid this particular issue, I tried writing a separate datatype just
for genbank files (type="galaxy.datatypes.genbank:Genbank"), however
that fails with the same error:


galaxy.datatypes.registry ERROR 2014-07-14 13:23:23,100 Error importing 
datatype module galaxy.datatypes.genbank: 'module' object has no attribute 
'genbank'
Traceback (most recent call last):
   File "/home/hxr/work/galaxy-central/lib/galaxy/datatypes/registry.py", line 
206, in load_datatypes
 module = getattr( module, mod )
AttributeError: 'module' object has no attribute 'genbank'


Here's my lib/galaxy/datatypes/genbank.py looks like:


import pkg_resources
pkg_resources.require( "bx-python" )
import logging
from galaxy.datatypes import data
log = logging.getLogger(__name__)

class Genbank( data.Text ):
 file_ext = "gb"

 def sniff( self, filename ):
 header = open(filename).read(5)
 return header == 'LOCUS'


To debug this, I've tried copying the tabular data type completely,
removed all the classes other than Tabular, and renamed it "Genbank",
however this fails too with the same error.

Can anyone offer some insight?

Cheers,
Eric
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Re: [galaxy-dev] Download URL needs user to be logged in first

[John Chilton]

I am not really sure what link you are referring to - can you tell me
how you found this link? "History -> Export to file" or is it via the
API?

Regardless, if you trust your users and want to disable security
mechanisms I believe (and I could be wrong) you should be able to by
finding the relevant controllers in Galaxy and changing either the
decorator to allow anonymous access or changing the checks on the
histories/datasets to disable checking if the supplied user is
authorized. Though this will make everyones data available to everyone
else (or the world if this is a publicly accessible Galaxy instance).

-John

On Wed, Jul 16, 2014 at 5:43 AM,   wrote:
> Hi,
>galaxy provides a download_url to download zipped up files. However, the
> user must first log into Galaxy to commence the download. Is there a way to
> turn this feature off, so that users can click on the link and download the
> data without first login
>
> Thanks
> Neil
>
> ___
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Re: [galaxy-dev] Uploading Multiple files

[John Chilton]

The traditional upload tool cannot take in multiple files - but there
is a new upload widget that can be used to upload a large number of
files simultaneously. The upload widget can be launched by clicking on
the upload icon in the tools menu header (to the right of the word
tools).

I hope this helps.

-John


On Tue, Jul 15, 2014 at 11:33 PM,   wrote:
> Hi,
>
> It was suggested recently that Galaxy would soon be providing the
> ability to upload multiple files rather than single files. Does anyone know
> when this might be available in Galaxy? I’ve downloaded the most recent
> version of Galaxy but as yet it is not present in the “stable” version
>
>
>
> Thanks for any information
>
> Neil
>
>
>
>
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>
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[galaxy-dev] Download URL needs user to be logged in first

[Neil.Burdett]

Hi,
   galaxy provides a download_url to download zipped up files. However, the 
user must first log into Galaxy to commence the download. Is there a way to 
turn this feature off, so that users can click on the link and download the 
data without first login

Thanks
Neil
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Re: [galaxy-dev] How to configure galaxy with a cluster

[Björn Grüning]

Hi Ben,

that is not possible at the moment. The idea is to keep the 
user-inferface as easy as possible for the user. You, as admin, can 
decide which resource a specific tool with a specific input will use. 
You will never see any options like that in a tool, but you can write a 
tool by yourself if you like, or "enhance" the megablast tool.


Cheers,
Bjoern


Am 16.07.2014 09:43, schrieb 王渭巍:

Thanks a lot, Thomas! It really helps, I added tools section followed your 
suggestion...

here is my job_conf.xml ( I am using Torque,  I have 3 servers. One for galaxy 
server, two for cluster computing.  )










walltime=72:00:00,nodes=1:ppn=8
128







and still no cluster options in "megablast" item.  How can I see cluster 
options in the page, for example, the page will let me choose to use local server or a 
cluster.

Ben



From: Thomas Bellembois
Date: 2014-07-15 17:41
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] How to configure galaxy with a cluster
Hello Ben,

you can configure your Galaxy instance to use your cluster in the
job_conf.xml file:

https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster

You can set up your instance to use your cluster by default for all jobs
or only for specific jobs.

Here is a part of my job_conf.xml for example:

 

 

 
 
 

 
 
 
 

 
 
 
   -r yes -b n -cwd -S /bin/bash
-V -pe galaxy 1
 
 
   -r yes -b n -cwd -S /bin/bash
-V -pe galaxy 12
 

 

 
 
 
 
 
 
 
 
 
 
 
 


Moreover you Galaxy user and Galaxy server must be allowed to submit
jobs to your scheduler.

Hope it  helps,

Thomas




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Re: [galaxy-dev] How to configure galaxy with a cluster

[Ross]

>and still no cluster options in "megablast" item.  How can I see cluster
options in the page, for example, the page will let me choose to use local
server or a cluster.

Users can't control destinations for tool execution through any interface
at present AFAIK - tool destinations are automated although you can have
complex plugins which might help. One obvious if slightly painful way to
make them user selectable is to (eg) in tool_conf.xml, include a suitably
cloned version megablast for each of the two destinations - each with a new
id (eg) "megablast_local" is always sent the local queue and the
"megablast_cluster" tool always goes to the cluster in your job conf.

Ugly but possible - I hope this helps.


On Wed, Jul 16, 2014 at 5:43 PM, 王渭巍  wrote:

> Thanks a lot, Thomas! It really helps, I added tools section followed your
> suggestion...
>
> here is my job_conf.xml ( I am using Torque,  I have 3 servers. One for
> galaxy server, two for cluster computing.  )
>
>
> 
> 
> 
>  load="galaxy.jobs.runners.pbs:PBSJobRunner"/>
> 
> 
> 
> 
> 
> walltime=72:00:00,nodes=1:ppn=8
> 128
> 
> 
> 
> 
> 
> 
>
> and still no cluster options in "megablast" item.  How can I see cluster
> options in the page, for example, the page will let me choose to use local
> server or a cluster.
>
> Ben
>
>
>
> *From:* Thomas Bellembois 
> *Date:* 2014-07-15 17:41
> *To:* galaxy-dev@lists.bx.psu.edu
> *Subject:* Re: [galaxy-dev] How to configure galaxy with a cluster
> Hello Ben,
>
> you can configure your Galaxy instance to use your cluster in the
> job_conf.xml file:
>
> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
>
> You can set up your instance to use your cluster by default for all jobs
> or only for specific jobs.
>
> Here is a part of my job_conf.xml for example:
>
> 
>  
>  load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
>
> 
>  load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
> 
>
> 
> 
> 
> 
>
> 
> 
> 
>   -r yes -b n -cwd -S /bin/bash
> -V -pe galaxy 1
> 
> 
>   -r yes -b n -cwd -S /bin/bash
> -V -pe galaxy 12
> 
>
> 
>
> 
> 
>  id="toolshed.g2.bx.psu.edu/repos/bhaas/trinityrnaseq/trinityrnaseq/0.0.1"
> destination="sge_big"/>
> 
> 
>  id="
> toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.1.00
> "
> destination="sge_big"/>
>  id="
> toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.1.00
> "
> destination="sge_big"/>
>  id="
> toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.00
> "
> destination="sge_big"/>
>  id="
> toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00
> "
> destination="sge_big"/>
>  id="
> toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.1.00
> "
> destination="sge_big"/>
>  id="
> toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.1.00
> "
> destination="sge_big"/>
>  id="
> toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.1.00
> "
> destination="sge_big"/>
> 
>
> Moreover you Galaxy user and Galaxy server must be allowed to submit
> jobs to your scheduler.
>
> Hope it  helps,
>
> Thomas
>
> --
> Thomas Bellembois, Network and System Administrator
> ENS-Lyon/IGFL - FRANCE
> +33 4 26 73 13 67
>
> .The IGFL is a member of the "portail-labos" project
> (https://portail-labos.ens-lyon.fr/site/).
> .IGFL IT documentation: http://itdoc.igfl.ens-lyon.fr/itdoc
>
> On 15/07/2014 11:22, 王渭巍 wrote:
> > Hello, everyone,
> > I am new here, and I am trying to configure galaxy with a
> cluster.
> > I have 3 servers. One for galaxy server, two for cluster
> computing. And I followed "Running Galaxy Tools on a Cluster" done the
> configuration.
> > Now I have 2 questions:
> > 1. How to vertify whether I have configured the galaxy cluster
> successfully? For example, I don't see there is any cluster options in "NGS
> mapping (bowtie2)  ", but I see cluster options in a web galaxy.
> > 2. And any other work I should do for configuring galaxy with a
> cluster?
> > Thank you for any help.
> >
> > Ben
> >
> >
> >
> > ___
> > 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:
> >   http://lists.bx.psu.edu/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/
> >
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  

Re: [galaxy-dev] How to configure galaxy with a cluster

[Thomas Bellembois]

Hello,

I am not a megablast expert but the
"tools/metag_tools/megablast_wrapper.xml" may help you to understand how
the program is run. You may want to tune the parameters.

Regards,

Thomas

On 16/07/2014 09:43, 王渭巍 wrote:
> Thanks a lot, Thomas! It really helps, I added tools section followed your 
> suggestion...
> 
> here is my job_conf.xml ( I am using Torque,  I have 3 servers. One for 
> galaxy server, two for cluster computing.  )
> 
>  
>  
>  
>  
>  
>  
>  
>  
>  
> walltime=72:00:00,nodes=1:ppn=8 
> 128 
>  
>  
>  
>  
>  
> 
> 
> and still no cluster options in "megablast" item.  How can I see cluster 
> options in the page, for example, the page will let me choose to use local 
> server or a cluster. 
> 
> Ben
> 
> 
>  
> From: Thomas Bellembois
> Date: 2014-07-15 17:41
> To: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] How to configure galaxy with a cluster
> Hello Ben,
>  
> you can configure your Galaxy instance to use your cluster in the
> job_conf.xml file:
>  
> https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
>  
> You can set up your instance to use your cluster by default for all jobs
> or only for specific jobs.
>  
> Here is a part of my job_conf.xml for example:
>  
> 
> 
>  load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
>  
> 
>  load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
> 
>  
> 
> 
> 
> 
>  
> 
> 
> 
>   -r yes -b n -cwd -S /bin/bash
> -V -pe galaxy 1
> 
> 
>   -r yes -b n -cwd -S /bin/bash
> -V -pe galaxy 12
> 
>  
> 
>  
> 
> 
>  id="toolshed.g2.bx.psu.edu/repos/bhaas/trinityrnaseq/trinityrnaseq/0.0.1" 
> destination="sge_big"/>
> 
> 
>  id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.1.00"
> destination="sge_big"/>
>  id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.1.00"
> destination="sge_big"/>
>  id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.00"
> destination="sge_big"/>
>  id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.00"
> destination="sge_big"/>
>  id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.1.00"
> destination="sge_big"/>
>  id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.1.00"
> destination="sge_big"/>
>  id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.1.00"
> destination="sge_big"/>
> 
>  
> Moreover you Galaxy user and Galaxy server must be allowed to submit
> jobs to your scheduler.
>  
> Hope it  helps,
>  
> Thomas
>  
> 


-- 
Thomas Bellembois, Network and System Administrator
ENS-Lyon/IGFL - FRANCE
+33 4 26 73 13 67

.The IGFL is a member of the "portail-labos" project
(https://portail-labos.ens-lyon.fr/site/).
.IGFL IT documentation: http://itdoc.igfl.ens-lyon.fr/itdoc
___
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] How to configure galaxy with a cluster

[王渭巍]

Thanks a lot, Thomas! It really helps, I added tools section followed your 
suggestion...

here is my job_conf.xml ( I am using Torque,  I have 3 servers. One for galaxy 
server, two for cluster computing.  )

 
 
 
 
 
 
 
 
 
walltime=72:00:00,nodes=1:ppn=8 
128 
 
 
 
 
 


and still no cluster options in "megablast" item.  How can I see cluster 
options in the page, for example, the page will let me choose to use local 
server or a cluster. 

Ben


 
From: Thomas Bellembois
Date: 2014-07-15 17:41
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] How to configure galaxy with a cluster
Hello Ben,
 
you can configure your Galaxy instance to use your cluster in the
job_conf.xml file:
 
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
 
You can set up your instance to use your cluster by default for all jobs
or only for specific jobs.
 
Here is a part of my job_conf.xml for example:
 



 



 




 



  -r yes -b n -cwd -S /bin/bash
-V -pe galaxy 1


  -r yes -b n -cwd -S /bin/bash
-V -pe galaxy 12

 

 













 
Moreover you Galaxy user and Galaxy server must be allowed to submit
jobs to your scheduler.
 
Hope it  helps,
 
Thomas
 
-- 
Thomas Bellembois, Network and System Administrator
ENS-Lyon/IGFL - FRANCE
+33 4 26 73 13 67
 
.The IGFL is a member of the "portail-labos" project
(https://portail-labos.ens-lyon.fr/site/).
.IGFL IT documentation: http://itdoc.igfl.ens-lyon.fr/itdoc
 
On 15/07/2014 11:22, 王渭巍 wrote:
> Hello, everyone, 
> I am new here, and I am trying to configure galaxy with a cluster. 
> I have 3 servers. One for galaxy server, two for cluster computing. 
> And I followed "Running Galaxy Tools on a Cluster" done the configuration. 
> Now I have 2 questions:
> 1. How to vertify whether I have configured the galaxy cluster 
> successfully? For example, I don't see there is any cluster options in "NGS 
> mapping (bowtie2)  ", but I see cluster options in a web galaxy. 
> 2. And any other work I should do for configuring galaxy with a 
> cluster?
> Thank you for any help.
> 
> Ben 
> 
> 
> 
> ___
> 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:
>   http://lists.bx.psu.edu/
> 
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
> 
 
 
 
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/
 
To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/