[galaxy-dev] Re: Daemon mode fail job submission

[Gildas Le Corguillé]

Hi,

There is at least one issue

   
   /media/vol1/gridengine/lib/linux-x64/libdrmaa.so


   
   /media/vol1/gridengine/lib/linux-x64/libdrmaa.so


I don’t know if it’s THE issue :/




Gildas


Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science): 
http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Co-leader of the IFB Core Cluster: 
https://www.france-bioinformatique.fr/en/cluster 
<https://www.france-bioinformatique.fr/fr/cluster>

Member of the Workflow4Metabolomics project: http://workflow4metabolomics.org 
<http://workflow4metabolomics.org/>

Station Biologique de Roscoff
Sorbonne Université / CNRS
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81



> Le 28 avr. 2020 à 17:32, Luc Cornet  a écrit :
> 
> Hi galaxy community,
> 
> I am quite new in galaxy but I would like to install a local instance on our 
> cluster (SGE).
> I have a problem with DRMAA :
> 
> When I activate the --daemon mode, the job don't pass in the queue system but 
> with no Damon, it pass (the log below)
> The second problem is that $GALAXY_SLOTS is not define, Could it be related 
> to the problem below ?
> Someone can help me, please ? (available at : 
> https://help.galaxyproject.org/t/job-submission-failed-when-daemon/351)
> 
> Thanks,
> Luc
> 
> ## with no daemon 
>galaxy.jobs.runners.drmaa DEBUG 2020-04-28 17:07:21,424 [p:32191,w:1,m:0] 
> [DRMAARunner.work_thread-1] (47) submitting file 
> /media/vol2/home/galaxy/galaxy/database/jobs_directory/000/47/galaxy_47.sh
>galaxy.jobs.runners.drmaa DEBUG 2020-04-28 17:07:21,425 [p:32191,w:1,m:0] 
> [DRMAARunner.work_thread-1] (47) native specification is: -q cassava.q -pe 
> snode 10
>galaxy.jobs.runners.drmaa INFO 2020-04-28 17:07:21,440 [p:32191,w:1,m:0] 
> [DRMAARunner.work_thread-1] (47) queued as 1007701
>galaxy.jobs DEBUG 2020-04-28 17:07:21,441 [p:32191,w:1,m:0] 
> [DRMAARunner.work_thread-1] (47) Persisting job destination (destination id: 
> big_jobs)
>galaxy.jobs.runners.drmaa DEBUG 2020-04-28 17:07:22,042 [p:32191,w:1,m:0] 
> [DRMAARunner.monitor_thread] (47/1007701) state change: job is queued and 
> active
> 
> ## with daemon
>galaxy.jobs.runners.drmaa DEBUG 2020-04-28 15:39:16,138 [p:26779,w:1,m:0] 
> [DRMAARunner.work_thread-1] (45) submitting file 
> /media/vol2/home/galaxy/galaxy/database/jobs_directory/000/45/galaxy_45.sh
>galaxy.jobs.runners.drmaa DEBUG 2020-04-28 15:39:16,138 [p:26779,w:1,m:0] 
> [DRMAARunner.work_thread-1] (45) native specification is: -q cassava.q -pe 
> snode 10
> 
> ## job_conf
> 
>
>
>
>
> load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
> load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
> id="drmaa_library_path">/media/vol1/gridengine/lib/linux-x64/libdrmaa.so
>
>
>
>
>-q cassava.q -pe snode 
> 10
>
>
>
>   
>   
>
>
> 
> 
> 
> 
> Luc Cornet, PhD
> Bio-informatician 
> Mycology and Aerobiology
> Sciensano
> ___
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[galaxy-dev] Re: conda not installing deps.

[Gildas Le Corguillé]

Hi Jochen,

Did you try to install the deps with the dedicated "Manage dependencies" and 
check the log ?
Is Conda installed in /opt/galaxy/tools/_conda/bin/conda ?

BTW, are you sure you need to enable this option? 
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/galaxy.yml.sample#L265-L271
 
<https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/galaxy.yml.sample#L265-L271>
 

Gildas

--------
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science): 
http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Co-leader of the IFB Core Cluster: 
https://www.france-bioinformatique.fr/en/cluster 
<https://www.france-bioinformatique.fr/fr/cluster>

Member of the Workflow4Metabolomics project: http://workflow4metabolomics.org 
<http://workflow4metabolomics.org/>

Station Biologique de Roscoff
Sorbonne Université / CNRS
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81



> Le 27 juil. 2019 à 11:06, Jochen Bick  a écrit :
> 
> Hej Björn,
> 
> We have activated all conda parameters in the yml. But when you install a 
> tool the deps are not installed. So every tool is installed with no deps.
> 
> Jochen
> 
> ⁣Get BlueMail for Android ​
> 
> On Jul 26, 2019, 21:07, at 21:07, "Björn Grüning"  
> wrote:
>> Hi Jochen,
>> 
>> what is not working? Do you have any error message.
>> 
>> Ciao,
>> Bjoern
>> 
>> Am 25.07.19 um 15:45 schrieb Jochen Bick:
>>> Hi
>>> 
>>> we have a new galaxy 19.01 instance and conda is somehow not running
>>> correctly:
>>> 
>>> galaxy.yml
>>> 
>>>   #dependency_resolvers_config_file:
>> config/dependency_resolvers_conf.xml
>>>   conda_prefix: /opt/galaxy/tools/_conda
>>>   #conda_exec: null
>>>   #conda_debug: false
>>>   #conda_ensure_channels: 'iuc,conda-forge,bioconda,defaults'
>>>   #conda_use_local: false
>>>   conda_auto_install: true
>>>   conda_auto_init: true
>>>   conda_copy_dependencies: true
>>> 
>>>   job_working_directory: /opt/galaxy/daten/jobs_directory
>>> 
>>> any ideas?
>>> 
>>> Thanks Jochen
>>> 
>>> 
>>> 
>>> 
>>> --
>>> ETH Zurich
>>> *Jochen Bick*
>>> Animal Physiology
>>> Institute of Agricultural Sciences
>>> Postal address: Universitätstrasse 2 / LFW B 58.1
>>> 8092 Zurich, Switzerland
>>> Office: Eschikon 27
>>> 8315 Lindau, Switzerland
>>> 
>>> Phone +41 52 354 92 06
>>> jochen.b...@usys.ethz.ch <mailto:jochen.b...@usys.ethz.ch>
>>> www.ap.ethz.ch
>>> 
>>> ___
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Re: [galaxy-dev] add labels to tools

[Gildas Le Corguillé]

It’s an attribute of the XML element 


gvk.bx.psu.edu:9009
column_maker
test
f06aa1bf1e8agvk.bx.psu.edu:9009/repos/test/column_maker/Add_a_column1/1.1.0
1.1.0



Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org <http://workflow4metabolomics.org/>

Station Biologique de Roscoff
Sorbonne Université / CNRS
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



> Le 4 févr. 2019 à 15:33, Jochen Bick  a écrit :
> 
> Thanks Gildas, for the quick reply! That looks like the right page... but I 
> don't see a concrete example. For example if I would like to add "new" to a 
> tool?
> 
> Cheers Jochen
> On 04.02.19 15:25, Gildas Le Corguillé wrote:
>> Hi Jochen,
>> 
>> Here is what you are looking for : 
>> https://galaxyproject.org/admin/tool-panel/#adding-labels-to-tools 
>> <https://galaxyproject.org/admin/tool-panel/#adding-labels-to-tools>
>> 
>> Cheers
>> 
>> Gildas
>> 
>> -
>> Gildas Le Corguillé - Bioinformatician/Bioanalyste
>> 
>> Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
>> http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>
>> 
>> Member of the Workflow4Metabolomics project
>> http://workflow4metabolomics.org <http://workflow4metabolomics.org/>
>> 
>> Station Biologique de Roscoff
>> Sorbonne Université / CNRS
>> Place Georges Teissier 29680 Roscoff FRANCE
>> tel: +33 2 98 29 23 81
>> --
>> 
>> 
>> 
>>> Le 4 févr. 2019 à 15:20, Jochen Bick >> <mailto:jochen.b...@usys.ethz.ch>> a écrit :
>>> 
>>> Hi,
>>> 
>>> I'm interested to add labels to tool such as shown on usegalaxy.org 
>>> <http://usegalaxy.org/> for example for the tool hifive 
>>> <https://usegalaxy.org/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fsauria%2Fhifive%2Fhifive%2F0.1.0>.
>>>  
>>> How can I add these labels.
>>> 
>>> Cheers Jochen
>>> -- 
>>> ETH Zurich
>>> *Jochen Bick*
>>> Animal Physiology
>>> Institute of Agricultural Sciences
>>> Postal address: Universitätstrasse 2 / LFW B 58.1
>>> 8092 Zurich, Switzerland
>>> Office: Eschikon 27
>>> 8315 Lindau, Switzerland
>>> 
>>> Phone +41 52 354 92 06
>>> jochen.b...@usys.ethz.ch <mailto:jochen.b...@usys.ethz.ch> 
>>> <mailto:jochen.b...@usys.ethz.ch> <mailto:jochen.b...@usys.ethz.ch>
>>> www.ap.ethz.ch <http://www.ap.ethz.ch/>
>>> ___
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>>> 
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>>>  http://galaxyproject.org/search/ <http://galaxyproject.org/search/>
> -- 
> ETH Zurich
> *Jochen Bick*
> Animal Physiology
> Institute of Agricultural Sciences
> Postal address: Universitätstrasse 2 / LFW B 58.1
> 8092 Zurich, Switzerland
> Office: Eschikon 27
> 8315 Lindau, Switzerland
> 
> Phone +41 52 354 92 06
> jochen.b...@usys.ethz.ch <mailto:jochen.b...@usys.ethz.ch> 
> <mailto:jochen.b...@usys.ethz.ch> <mailto:jochen.b...@usys.ethz.ch>
> www.ap.ethz.ch <http://www.ap.ethz.ch/>
> ___
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Re: [galaxy-dev] use or convert tool.xml file for database webpage

[Gildas Le Corguillé]

Hi Jochen,

Note that there are some projects which propose a layer, a web interface, over 
the Galaxy engine.
Those solutions are using the API (BioBlend) to display Galaxy objects from the 
history, and to launch jobs.

Here is two of them:
MetaGenSense: https://f1000research.com/articles/4-86/v3
https://ngphylogeny.fr


Cheers

Gildas

Le 06/02/2018 11:07, « galaxy-dev au nom de Jochen Bick » 
 
a écrit :

Hi Peter,

thanks for your quick reply.

> 
> Could you not provide a limited Galaxy instance instead?
> Just your tool and any other key functionality needed to
> use with it (importing files perhaps, maybe some plotting
> or filtering commands)?

hmm the problem is that I would like to use this for a publication and
also provide a galaxy tool which will then access the database webpage.
Right now I just have a tool that access the mysql database in our local
galaxy instance.
I guess a webpage would be nicer for non galaxy user.

Cheers Jochen
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Re: [galaxy-dev] external display and data editing

[Gildas Le Corguillé]

Salut Nils,

I think that you should take a look at the Galaxy Interactive Environment (GIE):
 - https://docs.galaxyproject.org/en/master/admin/interactive_environments.html 
<https://docs.galaxyproject.org/en/master/admin/interactive_environments.html> 
 - 
https://galaxyproject.github.io/training-material/topics/dev/tutorials/interactive-environments/slides.html
 
<https://galaxyproject.github.io/training-material/topics/dev/tutorials/interactive-environments/slides.html>
 

Cheers

Gildas

---------
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org <http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



> Le 15 nov. 2017 à 09:26, Nils Paulhe <nils.pau...@gmail.com> a écrit :
> 
> Dear list,
> 
> I'm working on data visualization / display in galaxy.
> I'm wondering if it's possible to save a resource edited from the viewer 
> plugin or an external display in the current history.
> In my opinion the easier / proper way is to use an external display to show / 
> edit the resources and upload the edited files in the current history using 
> galaxy API.
> 
> Does anyone have tried something similar?
> Cheers
> 
> Nils
> ___
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Re: [galaxy-dev] conda bash environment problem as real user

[Gildas Le Corguillé]

Hi,

workaround#2 : use the new admin interface "Manage Tool Dependencies" : 
https://galaxyproject.github.io/training-material/topics/dev/tutorials/conda/slides.html#18
 
<https://galaxyproject.github.io/training-material/topics/dev/tutorials/conda/slides.html#18>

It will allow you to create Conda environments and individual package with the 
user galaxy (and check if you miss some of them).

My 2 cents

Gildas

---------
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org <http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



> Le 11 oct. 2017 à 16:41, Matthias Bernt <m.be...@ufz.de> a écrit :
> 
> Dear list,
> 
> our galaxy runs jobs as real user and I get the following error for multiple 
> tools:
> 
> """
> Failed to activate conda environment! Error was: CondaEnvironmentError: 
> Environment error: Cannot activate environment bash. User does not have write 
> access for conda symlinks. Fatal error: Exit code 1 ()
> """
> 
> Does anyone have an idea where I could start digging? My workaround (run the 
> tool once as galaxy user) is to time consuming since I have to restart galaxy 
> 2x.
> 
> Thanks a lot.
> 
> Cheers,
> Matthias
> 
> P.S.: https://github.com/galaxyproject/galaxy/issues/4767
> 
> 
> 
> -- 
> 
> ---
> Matthias Bernt
> Bioinformatics Service
> Molekulare Systembiologie (MOLSYB)
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> Helmholtz Centre for Environmental Research GmbH - UFZ
> Permoserstraße 15, 04318 Leipzig, Germany
> Phone +49 341 235 482296,
> m.be...@ufz.de, www.ufz.de
> 
> Sitz der Gesellschaft/Registered Office: Leipzig
> Registergericht/Registration Office: Amtsgericht Leipzig
> Handelsregister Nr./Trade Register Nr.: B 4703
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> Wilfried Kraus
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> Prof. Dr. Dr. h.c. Georg Teutsch
> Administrative Geschäftsführerin/ Administrative Managing Director:
> Prof. Dr. Heike Graßmann
> ---
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Re: [galaxy-dev] Displaying tool select list according to user

[Gildas Le Corguillé]

As it was already mention, about the filtering we presented at Baltimore this 
project : https://github.com/abims-sbr/galaxy-blastprivate 
<https://github.com/abims-sbr/galaxy-blastprivate>

And about the report, we also have something about that 
:https://github.com/abims-sbr/galaxy-blastvisu 
<https://github.com/abims-sbr/galaxy-blastvisu>

But shame on us, there is a lot of dust on them.
Although, if we can build a little group around this project, we are stil 
interesting in. Our goal was also to drop out our W3Blast server. 

Gildas

---------
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org <http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



> Le 21 sept. 2017 à 13:50, SAPET, Frederic <frederic.sa...@biogemma.com> a 
> écrit :
> 
> Hi Peter,
> 
> Good idea, I will keep that in mind for other needs.
> I'm not sure that it will be suitable for what I want to do. Users will have 
> to first import database to their history (yet another step as they ask me 
> for less, even the upload process is sometimes one step they would like to 
> avoid !)
> 
> But it could be a way of achieving what I want, if Galaxy could get files (or 
> .loc files) from a data library, within the tool form itself !
> 
> Maybe I will create an issue on the Galaxy git in order to discuss about 
> that. I will be glad to help if something can be done.
> 
> Maybe some explanations about the fact that my users ask me for "less steps".
> I really want Galaxy to be the main tool of our analysis platform. 
> Right now I still maintain a plain old perl/php/CGI web interface. With a 
> blast tool (among a lot of others tools). This proprietary Blast interface is 
> really like you will find on NCBI or EBI sites. And you can quickly paste 
> your sequences, pick up a database, a Blast algorythm and then launch. Few 
> seconds later I have a 'htmlized' Blast report, with a nice picture.
> This use case (is this sequence a part of this database ?) is still faster on 
> this plain old interface. And I afraid that I will have to keep it until they 
> found Galaxy better than it...
> 
> Maybe it could be another (or two) idea(s)  : the user can drag and drop his 
> file within the tool form, Galaxy will handle the creation of this file 
> within the history and then launch the tool. Or user can copy/paste a 
> sequence within a text-area, and Galaxy will handle the creation of a file 
> from these data within the history and then launch the tool.
> This skips upload process.
> 
> thank you again for sharing your ideas, it helps!
> 
> Fred
> 
> -Message d'origine-
> De : Peter Cock [mailto:p.j.a.c...@googlemail.com] 
> Envoyé : mercredi 20 septembre 2017 12:37
> À : SAPET, Frederic <frederic.sa...@biogemma.com>
> Cc : Laure QUINTRIC <laure.quint...@ifremer.fr>; Galaxy-dev 
> <galaxy-dev@lists.galaxyproject.org>
> Objet : Re: [galaxy-dev] Displaying tool select list according to user
> 
> Have you tried creating the BLAST databases as files in your history (by 
> running makeblastdb within Galaxy), and then importing them into a shared 
> data library (which can then be configured with role based permissions)?
> 
> Peter
> 
> 
> On Wed, Sep 20, 2017 at 9:39 AM, SAPET, Frederic 
> <frederic.sa...@biogemma.com> wrote:
>> Hello Laure
>> 
>> 
>> 
>> this idea cannot be applied in my use case.
>> 
>> indeed I don’t want that users can choose which data to display. I 
>> want to hide some data based on their name/group/address (anything 
>> that can be useful to clasify my users).
>> 
>> 
>> 
>> Thank you for sharing your ideas :)
>> 
>> 
>> 
>> Fred
>> 
>> De : Laure QUINTRIC [mailto:laure.quint...@ifremer.fr]
>> Envoyé : mercredi 13 septembre 2017 13:54 À : Peter Cock 
>> <p.j.a.c...@googlemail.com>; SAPET, Frederic 
>> <frederic.sa...@biogemma.com>
>> 
>> 
>> Cc : Galaxy-dev <galaxy-dev@lists.galaxyproject.org>
>> Objet : Re: [galaxy-dev] Displaying tool select list according to user
>> 
>> 
>> 
>> A workaround would be to do this :
>> 
>> - first, create a tool which will output a tabular loc file with all 
>> the cust

Re: [galaxy-dev] migratting to Galaxy new realease error

[Gildas Le Corguillé]

Hi Mohamed,

Have you try to remove (and backup if you want) the whole .venn folder?
Galaxy will create a new one with all its needs.

Best

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org <http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



> Le 24 févr. 2017 à 09:42, Mohamed Kassam <k.mam...@gmail.com> a écrit :
> 
> Hello 
> i tried to install via root and maybe it works, 
> 
> However now the bash run.sh it is working, however my ldap is not working I 
> have password incorrect and I get this error in the terminal :
> 
> galaxy.auth.providers.ldap_ad ERROR 2017-02-24 10:52:24,672 LDAP 
> authenticate: search exception
> Traceback (most recent call last):
>   File "/home/galaxy/galaxy-dist/lib/galaxy/auth/providers/ldap_ad.py", line 
> 118, in authenticate
> ldap.set_option(*opt)
>   File 
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/ldap/functions.py",
>  line 135, in set_option
> return _ldap_function_call(None,_ldap.set_option,option,invalue)
>   File 
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/ldap/functions.py",
>  line 66, in _ldap_function_call
> result = func(*args,**kwargs)
> ValueError: option error
> 
> 
> Any idea ?
> 
> Thanks,
> 
> Mohamed
> 
> 2017-02-24 9:11 GMT+01:00 Mohamed Kassam <k.mam...@gmail.com 
> <mailto:k.mam...@gmail.com>>:
> Dear all,
> 
> I have migrate my old version of Galaxy to the new release V17.01, And I am 
> facing this error when I am running run.sh, any clue ?
> 
> Installing collected packages: python-ldap
>   Found existing installation: python-ldap 2.4.17
> DEPRECATION: Uninstalling a distutils installed project (python-ldap) has 
> been deprecated and will be removed in a future version. This is due to the 
> fact that uninstalling a distutils project will only partially uninstall the 
> project.
> Can't uninstall 'python-ldap'. No files were found to uninstall.
>   Can't roll back python-ldap; was not uninstalled
> Exception:
> Traceback (most recent call last):
>   File 
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/basecommand.py",
>  line 215, in main
> status = self.run(options, args)
>   File 
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/commands/install.py",
>  line 342, in run
> prefix=options.prefix_path,
>   File 
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_set.py",
>  line 784, in install
> **kwargs
>   File 
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_install.py",
>  line 851, in install
> self.move_wheel_files(self.source_dir, root=root, prefix=prefix)
>   File 
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/req/req_install.py",
>  line 1064, in move_wheel_files
> isolated=self.isolated,
>   File 
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/wheel.py", 
> line 345, in move_wheel_files
> clobber(source, lib_dir, True)
>   File 
> "/home/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/pip/wheel.py", 
> line 329, in clobber
> os.utime(destfile, (st.st_atime, st.st_mtime))
> OSError: [Errno 1] Operation not permitted: 
> '/home/galaxy/galaxy-dist/.venv/lib64/python2.7/site-packages/dsml.pyo'
> 
> 
> Thanks,
> 
> Mohamed
> 
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Re: [galaxy-dev] Blast db permission

[Gildas Le Corguillé]

Hello Mohamed,

Two years ago, we had exactly the same needs (actually, we still have) and took 
an internship to investigate and develop a solution to privatize blast databank 
through Galaxy.
As many projects, we didn’t find enough time to finalize that.

I have just push the different scripts we have if you want to test or just have 
a look: https://github.com/abims-sbr/galaxy-blastprivate 
<https://github.com/abims-sbr/galaxy-blastprivate>

Cheers

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org <http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



> Le 19 janv. 2017 à 14:53, Peter Cock <p.j.a.c...@googlemail.com> a écrit :
> 
> Hello Mohamed,
> 
> Right now this is not possible, and I can't think of any way to
> restrict access to system level BLAST databases listed in
> the blast*.loc files by user. However, since other Galaxy
> tools use *.loc files, someone else may have some ideas.
> 
> You might be able to try using a BLAST database in a
> shared data library (Galaxy has a role based permissions
> system you could use), but the user would first have to
> import the database into their current history.
> 
> I hope that helps,
> 
> Peter
> 
> On Thu, Jan 19, 2017 at 1:45 PM, Mohamed Kassam <k.mam...@gmail.com> wrote:
>> Dear all,
>> 
>> I would like to know if it is possible to put permission on the macro.xml
>> for ncbi-blast + database.
>> For example if I want to show the db to one user and not to all.
>> 
>> Best reagards,
>> 
>> Mohamed
>> 
>> ___
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Re: [galaxy-dev] Installation of packages failing

[Gildas Le Corguillé]

You can propose some updates (ie: URL) in this GitHub repo : 
https://github.com/galaxyproject/cargo-port 
<https://github.com/galaxyproject/cargo-port>

Cheers

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org <http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



> Le 19 déc. 2016 à 10:42, Peter Briggs <peter.bri...@manchester.ac.uk> a écrit 
> :
> 
> Hello James
> 
> I think this might be a general problem with depot.galaxyproject.org serving 
> packages, as I've been experiencing similar problems since Friday - attempts 
> to fetch e.g.
> 
> http://depot.galaxyproject.org/package/source/galaxy_sequence_utils/galaxy_sequence_utils-1.0.1-st.tgz
> 
> also fail with timeouts.
> 
> I guess it needs someone from the the Galaxy project to take a look,
> 
> Best wishes
> 
> Peter
> 
> On 18/12/16 20:25, James Mullan wrote:
>> Hello,*
>> *
>> * *  I am trying to install packages with dependencies from
>> Galaxy Main tool shed.
>> This worked Thursday and since Friday it no longer works for me.
>> It seems this url is no longer reachable. Examples of what I see in the
>> log during download are shown below.
>> 
>> Any help would be much appreciated.
>> 
>> package_bowtie_0_12_7
>> Error downloading from URL
>> http://depot.galaxyproject.org/package/linux/x86_64/bowtie/bowtie-0.12.7-linux-x86_64.tgz
>> 
>> package_samtools_0_1_19
>> Exception: Error downloading from URL
>> https://depot.galaxyproject.org/software/samtools/samtools_0.1.19_src_all.tar.bz2*
>> *
>> 
>> Regards
>> ​James
>> 
>> J P Mullan
>> 
>> 
>> ___
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>> 
> 
> -- 
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
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[galaxy-dev] Restart Galaxy without interruption

[Gildas Le Corguillé]

Hi,

Since Galaxy need to be restarted sometime (load datatype, add ressources in 
.loc, apply changes in the galaxy.ini), is anybody of you have solutions to 
restart it without interrupt the service?

We are now using nginx, uwsgi and supervisord.

My hope is to split the Galaxy process in two group (1 uwsgi and 2 job handlers 
per group). That way, we will be able to restart the group1 and then the group2.


I was planning to set the 2 uwsgi servers and delegate the load balancing to 
ngnix (https://www.nginx.com/resources/admin-guide/load-balancer/ 
<https://www.nginx.com/resources/admin-guide/load-balancer/>) 
But maybe, some of you already implemented that and can provide me some advices 
or warnings.

The job handler part seems easier to deal with 
--server-name=handler1_%(process_num)s
--server-name=handler2_%(process_num)s

Thanks by advance

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org <http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



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Re: [galaxy-dev] Tool needs a particular file extension -- now Datatype help

[Gildas Le Corguillé]

Hi Steve,

Galaxy try to sniff the data to guess the appropriate datatype.
For Binaries, if any datatype (sniffer) is found from 
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py 
<https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py>
 , you get this message "The binary uploaded file contains inappropriate 
content."

For your wave file, you will have to add a class 
(https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py#L1334
 
<https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py#L1334>)
  for the wave format and implement a sniffer 
(https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py#L1354
 
<https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py#L1354>)
 with a test if/else 
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py#L1358
 
<https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py#L1358>
 
Typically for Binary, you can get the first n bytes which used to be a text  
and check it’s equal to, i hope, "wave". There are bunch of example in the file.

And finally, a Pull Request on https://github.com/galaxyproject/galaxy 
<https://github.com/galaxyproject/galaxy> :)

Good luck

Gildas

---------
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org <http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



> Le 22 oct. 2016 à 12:36, Peter Cock <p.j.a.c...@googlemail.com> a écrit :
> 
> Hi Steve,
> 
> You are on the right track, but something in the WAV file has
> triggered one of Galaxy's security protections to try to block
> uploading of potentially dangerous files. There may be some
> settings here you can relax - I've not had to deal with this
> myself.
> 
> Peter
> 
> On Fri, Oct 21, 2016 at 8:55 PM, Steve Cassidy <steve.cass...@mq.edu.au> 
> wrote:
>> Thanks all,
>>  it seems that my real problem is that the audio file (.wav) is not being
>> identified as a valid datatype and ending up as a zero length text file. So,
>> I need to start to explore the world of datatypes.
>> 
>> Following the docs
>> (https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes) I can
>> modify datatypes_conf.xml in my Galaxy sources and add a new datatype for
>> wav files:
>> 
>>> display_in_upload="true" mimetype="audio/wav" subclass="True”/>
>> 
>> but, I get a message "The uploaded binary file contains inappropriate
>> content” and a zero length file just as I did before adding this - although
>> the datatype is now set to ‘wav’.
>> 
>> I didn’t add a sniffer for this and set the datatype explicitly on upload.
>> 
>> Also, this doesn’t seem like a modular way to add datatypes - how do I
>> include datatypes in my tool definition?  I can see from some other tools
>> that I include a datatypes_conf.xml in my tool folder.   When I try that and
>> test with planemo the new type isn’t found.
>> 
>> Pointers welcome.
>> 
>> Thanks,
>> 
>> Steve
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Re: [galaxy-dev] uploading multi-file archives and creation of potentially large collections

[Gildas Le Corguillé]

Hi Stephan,

I will only answer about uploading zip files. Since the release_16.04, a zip 
datatype is integrated within the Galaxy distribution. But without any sniffer, 
so your users will have to select, before the upload, the zip datatype manually.

I also want to write this kind of tool which will be able to extract a zip file 
and produce dataset collections. I would also like to add the possibility to 
create one dataset collection per folder (condition/phenotype). I start 
something like that last week but ...
Thus, in short term, I want to propose this tool to help my user to switch to 
dataset collections but I want this transition as smooth as possible (users are 
sometime stubborn)

Thanks to ask, I will follow this thread closely.


Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org <http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



> Le 4 août 2016 à 17:44, Stephan Oepen <o...@ifi.uio.no> a écrit :
> 
> colleagues,
> 
> in our adaptation of galaxy for large-scale natural language
> processing, a fairly common use pattern is to invoke a workflow on a
> potentially large number of text files.  hence, i am wondering about
> facilities for uploading an archive (in ‘.zip’ or ‘.tgz’ format, say)
> containing several files, where i would like the upload tool to
> extract the files from the archive, import each individually into my
> history, and (maybe optionally) create a list collection for the set
> of files.
> 
> in my current galaxy instance (running version 2015.03), when i upload
> a multi-file ‘.zip’ file, part of the above actually happens: however,
> the upload tool only imports the first file extracted from the archive
> (and helpfully shows a warning message on the corresponding history
> entry).  have there been relevant changes in this neighborhood in more
> recent galaxy releases?
> 
> related to the above, we have started to experiment with potentially
> large collections and are beginning to worry about the scalability of
> the collection mechanism.  in principle, we would like to operate on
> collections comprised of tens or hundreds of thousands of individual
> datasets.  what are common collection sizes (in the number of
> components, not so much in the aggregate file size) used in other
> galaxy instances to date?  what kind of gut reaction do galaxy
> developers have to the idea of a collection containing, say, a hundred
> thousand entries?
> 
> with thanks in advance,
> ___
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Re: [galaxy-dev] Returning BLAST datatypes and DB loc files to Galaxy core?

[Gildas Le Corguillé]

Hi all,

If indeed, datatypes return within the Galaxy distribution, can we imagine 
propose different datatypes_conf.xml?

Galaxy isn’t anymore dedicated to NGS purpose. It is use also for metabolomics, 
proteomics, … 

So it could be great to propose 1 "common" list of datatypes (text, tabular, 
png, pdf, …) and n specific datatypes lists for the n scientific areas to 
reduce this huge list of datatypes proposed to the users.
Maybe this selection should be based on edam ontology. As you know they are 
almost already annotated with edam_format and edam_data


Gildas

-----
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org <http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



> Le 1 août 2016 à 18:41, Peter Cock <p.j.a.c...@googlemail.com> a écrit :
> 
> I have a work-in-progress branch and pull request here,
> https://github.com/peterjc/galaxy/tree/blast_datatypes
> https://github.com/galaxyproject/galaxy/pull/2696
> 
> The Galaxy TravisCI tests looked fine.
> 
> Peter
> 
> On Mon, Aug 1, 2016 at 11:18 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> Dear all,
>> 
>> I ran this past the IUC first, and the only comments were
>> positive.
>> 
>> Although I wasn't at GCC2017 to discuss this in person,
>> I understand that the Galaxy Team now encourages
>> widely used datatypes to be included in the main Galaxy
>> repository, rather than distributed via the Tool Shed.
>> 
>> To that end, would a pull request returning the BLAST
>> datatypes and associated database *.loc files be welcome?
>> 
>> These are currently on my GitHub repository here:
>> https://github.com/peterjc/galaxy_blast/
>> 
>> And the datatypes are distributed via the Tool Shed here:
>> http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
>> 
>> Assuming this happens, we would need to phase out the
>> tool shed version (but it will still be needed while older
>> Galaxy instances are still running).
>> 
>> Are there any pitfalls to worry about if the datatypes are
>> already there with Galaxy and the tool shed version is
>> installed on top? Or the tool shed version was installed
>> but then Galaxy was updated to include the version
>> bundled with Galaxy?
>> 
>> Thanks,
>> 
>> Peter
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Re: [galaxy-dev] per-tool job resource defaults

[Gildas Le Corguillé]

Hi Stephan,

I will just quickly answer to your last question. Because, I’m not sure to 
understand the first part of your message or take the time to :P

> i am hoping i am overlooking something :-).  is there a way to define
> job resource defaults on a per-tool basis?

Perhaps, I didn’t understand your message at all:


In your tool wrapper, you can use "\${GALAXY_SLOTS:-8}" to dynamically set the 
ressource according to the setting in the job_conf.xml.
Here by default, the job will take 8 CPU (personally, I find that it’s a trap 
when the administrator/me miss this default value, I prefer to set the default 
value to 1)



 my_amazing_tool -query "$query" […] -num_threads "\${GALAXY_SLOTS:-8}" […]



In your job_conf.xml, you can set per tool a destination. Thus, you can specify 
the number of CPU/Slot, the memory needed, the queue, the nodes ...


 
   -V -w n -q galaxy.q -R y -pe thread 
4 -l mem_free=10G 
 


 



I hope it will help you

Cheers


Gildas

---------
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org <http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



> Le 12 mars 2016 à 10:36, Stephan Oepen <o...@ifi.uio.no> a écrit :
> 
> dear colleagues,
> 
> at the university of oslo, we develop a galaxy-based portal for
> natural language processing (LAP: Language Analysis Portal).  jobs are
> submitted to a compute cluster via DRMAA and SLURM.  current
> development is against the galaxy release of march 2015.
> 
> i am wondering about fine-grained control of job resources.  our goal
> is that most users need not look past the ‘Use default job resource
> parameters’ toggle in the job configuration dialogue.
> 
> as i understand it, i think we can populate the ‘nativeSpecification’
> parameter in ‘job_conf.xml’ with SLURM-specific command-line options
> to set defaults, for example the project, maximum run-time, number of
> cores, memory per core, and such.  i assume these defaults will be
> combined with and overwritten by ‘custom’ job resource parameters, in
> case any are specified in the job configuration dialogue?
> 
> i tried to track the flow of information from
> ‘lib/galaxy/jobs/runners/drmaa.py’ via
> ‘scripts/drmaa_external_runner.py’ into the drmaa-python egg, but i
> could not easily work out where the merging of ‘nativeSpecification’
> and custom resource parameters happens; presumably at about the same
> time as an actual job script file is created, for submission to SLURM?
> could someone point me in the right direction here?
> 
> —more importantly, maybe: we would like to establish per-tool resource
> defaults.  for example, some of our tools require substantially more
> memory per core than others.  i cannot easily find a way of
> associating resource default with individual tools.  i looked at the
> tool configuration syntax, ‘job_conf.xml.sample_advanced’, and
> ‘job_resource_params_conf.xml.sample’, as well as at the following
> documentation pages:
> 
>  https://wiki.galaxyproject.org/Admin/Config/Jobs
>  https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
> 
> i am hoping i am overlooking something :-).  is there a way to define
> job resource defaults on a per-tool basis?
> 
> with warmest thanks in advance, oe
> ___
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Re: [galaxy-dev] Problems with planemo functional tests

[Gildas Le Corguillé]

Hi,

Do you still have the config/galaxy.ini.sample file unchanged ?

We observed this message when some .sample are missing or were modified.

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org <http://workflow4metabolomics.org/>

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--



> Le 3 mars 2016 à 07:31, Léo Biscassi <leo.bisca...@gmail.com> a écrit :
> 
> Hi, the command that you suggested not working, the same output is presented. 
> I tested with the following commands:
> 
> sudo planemo test 
> /home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml 
> --galaxy_root=/home/leobiscassi/programs/galaxy
> 
> sudo planemo test 
> /home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml
> 
> What is the influence of xUnit file in the process? I did the question 
> because the warning message showing "Cannot locate xUnit report option for 
> tests - update Galaxy for more detailed breakdown".
> 
> P.S.: My Galaxy instance is the latest stable version.
> 
> Best regards,
> 
> On Thu, Mar 3, 2016 at 2:53 AM Björn Grüning <bjoern.gruen...@gmail.com 
> <mailto:bjoern.gruen...@gmail.com>> wrote:
> Hi,
> 
> maybe I'm mistaken something, its way to early here ... but you need to
> specify a path to the tool you want to test.
> 
> For example:
> 
> planemo test /foo/bar/foo.xml
> 
> or to a directory full of tools.
> 
> planemo test /foo/bar
> 
> Hope this helps,
> Bjoern
> 
> Am 03.03.2016 um 04:48 schrieb Léo Biscassi:
> > Hi Folks,
> > I tried follow this tutorial [1], but I have problems in execute the
> > command "planemo t --galaxy_root=/home/leobiscassi/programs/galaxy" for
> > perform functional tests, any suggestion?
> > Bellow some images about this problem:
> >
> > imagem1.jpg
> > *Figure 1: *Command
> >
> > imagem2.jpg
> > *Figure 2:* Error
> >
> > imagem3.jpg
> > *Figure 3: *Galaxy Path
> >
> > Planemo's version is 0.23.0.
> >
> > [1] https://planemo.readthedocs.org/en/latest/writing_standalone.html 
> > <https://planemo.readthedocs.org/en/latest/writing_standalone.html>
> >
> > P.S: The command is utilized for same tool presented in tutorial.
> >
> > Att.
> > --
> > *Léo Biscassi*
> > Facebook - https://pt-br.facebook.com/lbiscassi 
> > <https://pt-br.facebook.com/lbiscassi>
> > Linkedin - https://br.linkedin.com/in/leobiscassi 
> > <https://br.linkedin.com/in/leobiscassi>
> > Skype - biscassi.leo
> > Twitter - https://twitter.com/leobiscassi <https://twitter.com/leobiscassi>
> >
> >
> > ___
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >   https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/ 
> > <http://galaxyproject.org/search/mailinglists/>
> >
> -- 
> Léo Biscassi
> Facebook - https://pt-br.facebook.com/lbiscassi 
> <https://pt-br.facebook.com/lbiscassi>
> Linkedin - https://br.linkedin.com/in/leobiscassi 
> <https://br.linkedin.com/in/leobiscassi>
> Skype - biscassi.leo
> Twitter - https://twitter.com/leobiscassi 
> <https://twitter.com/leobiscassi>___
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Re: [galaxy-dev] packaging R scripts

[Gildas Le Corguillé]

Hi,

For me, three solutions :
 - You can find existing packages which will install your library 
(https://testtoolshed.g2.bx.psu.edu/view/jeltje/package_dnacopy_1_40_0/118417199f06
 
<https://testtoolshed.g2.bx.psu.edu/view/jeltje/package_dnacopy_1_40_0/118417199f06>).
 So you will just need to link a requirement 
(https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Crequirements.3E_tag_set
 
<https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Crequirements.3E_tag_set>)
 and a tool_dependencies.xml file
 - If not, you can write your own package. But thanks to Ross Lazarus, to deal 
with dependencies of dependencies of dependencies, there is a tool for that 
https://testtoolshed.g2.bx.psu.edu/view/fubar/biocdepgen_r_3_1_2/faafc60f3d6a 
<https://testtoolshed.g2.bx.psu.edu/view/fubar/biocdepgen_r_3_1_2/faafc60f3d6a>
 - If you lack of time, you install R and needed libraries on your serveur.

Unfortunately, I can’t explain you why you couldn’t install your library 
through your script because R use to allow installing in the user home.


Gildas

---------
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--



> Le 26 févr. 2016 à 09:03, Xianrong Wong <won...@gmail.com> a écrit :
> 
> Hi,
> I am trying to package an R script (that requires certain R packages) 
> into a galaxy tool.  Any advice would be deeply appreciated!  
> 
> I have tested it on planemo and it works.  When I tried the version I 
> uploaded onto the toolshed, I got an error saying that the R packages do not 
> exist.  I next added the following lines to the R script:
> 
> source("https://bioconductor.org/biocLite.R 
> <https://bioconductor.org/biocLite.R>")
> 
> biocLite()
> 
> biocLite(c("DNAcopy", "preprocessCore"))
> 
> and I got the following error when running the installed tool on galaxy:
> 
> 
> 
> Installing package(s) ‘DNAcopy’, ‘preprocessCore’
> Warning in install.packages(pkgs = doing, lib = lib, ...) :
>   'lib = "/usr/local/lib/R/site-library"' is not writable
> Error in install.packages(pkgs = doing, lib = lib, ...) : 
>   unable to install packages
> Calls: biocLite ... .biocLiteInstall -> .reposInstall -> install.packages
> Execution halted
> ___
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Re: [galaxy-dev] correctly installing to toolshed

[Gildas Le Corguillé]

Hi,

I think that you don’t need :

.$__tool_directory__/

rm_consecutive_sameScore.pl "$input1" 
"$output1"
seems enough if you join the script .pl with your wrapper .xml

Gildas

---------
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--



> Le 23 févr. 2016 à 17:46, Xianrong Wong <won...@gmail.com> a écrit :
> 
> 

___
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Re: [galaxy-dev] SUCCESS Re: Fwd: Rscript run under Tools Directory cannot see Datafile in History smaller email size

[Gildas Le Corguillé]

Can you attach your XML wrapper and R script or part of them ?

I will take a look on them.

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--



> Le 5 févr. 2016 à 17:30, rbrown1...@comcast.net a écrit :
> 
> Good morning Gildas,
> After moving  my   block below -- 
> this fixed worked
> FYI   the Rscript  in the same tool dir has issues with reading a dataset 
> from the directory.   Seems like permissions but isn't.
> Thank you
> Bob Brown
> - Original Message -----
> From: Gildas Le Corguillé <lecorgui...@sb-roscoff.fr>
> To: rbrown1...@comcast.net
> Cc: John Chilton <jmchil...@gmail.com>, galaxy-dev@lists.galaxyproject.org
> Sent: Fri, 05 Feb 2016 08:27:07 - (UTC)
> Subject: Re: [galaxy-dev] Fwd: Rscript run under Tools Directory cannot see 
> Datafile in History smaller email size
> Hi,
> Because R always return blabla in the standard error output (stderr), by 
> default Galaxy thinks that there is a problem. You need this following lines 
> in your wrapper xml : 
> 
>   
> 
> With that, Galaxy will use the code error (echo  $?) instead of the stderr to 
> detect an error.
> Another thing, you can use 
> Foo.R $inputFile1 . 
> If your script is in the same folder as your xml
> 
> Gildas
> -
> Gildas Le Corguillé - Bioinformatician/Bioanalyste
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)
> 
> Station Biologique de Roscoff - UPMC/CNRS - FR2424
> Place Georges Teissier 29680 Roscoff FRANCE
> tel: +33 2 98 29 23 81
> http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/>
> --
> 
> 
> Le 4 févr. 2016 à 21:25, rbrown1...@comcast.net 
> <mailto:rbrown1...@comcast.net> a écrit :
> 
> John,
> Thanks for the great info.  I got the R to work not the Rscript.
> However, my data files return RED even though there is data in them
> I am still getting R warning but no errors
> During startup - Warning messages:
> 1: Setting LC_CTYPE failed, using "C" 
> 2: Setting LC_COLLATE failed, using "C" 
> 3: Setting LC_TIME failed, using "C" 
> 4: Setting LC_MESSAGES failed, using "C" 
> 5: Setting LC_MONETARY failed, using "C" 
> 6: Setting LC_PAPER failed, using "C" 
> 7: Setting LC_MEASUREMENT failed, using "C" 
> Is there a flag I can set to igrore these warning and have Galaxy return 
> GREEN?
> thanks.
> bob
> - Original Message -
> From: John Chilton <jmchil...@gmail.com <mailto:jmchil...@gmail.com>>
> To: rbrown1...@comcast.net <mailto:rbrown1...@comcast.net>, 
> galaxy-dev@lists.galaxyproject.org <mailto:galaxy-dev@lists.galaxyproject.org>
> Sent: Thu, 04 Feb 2016 20:11:53 - (UTC)
> Subject: Re: [galaxy-dev] Fwd: Rscript run under Tools Directory cannot see 
> Datafile in History smaller email size
> Forgot to cc the mailing list.
> -John
> On Thu, Feb 4, 2016 at 8:11 PM, John Chilton <jmchil...@gmail.com 
> <mailto:jmchil...@gmail.com>> wrote:
> > Are you sure about the --file when calling Rscript?
> >
> > Here is the usage for my local version which does not expect an
> > argument named --file:
> >
> > Usage: /path/to/Rscript [--options] [-e expr] file [args]
> >
> > --options accepted are
> > --help Print usage and exit
> > --version Print version and exit
> > --verbose Print information on progress
> > --default-packages=list
> > Where 'list' is a comma-separated set
> > of package names, or 'NULL'
> > or options to R, in addition to --slave --no-restore, such as
> > --save Do save workspace at the end of the session
> > --no-environ Don't read the site and user environment files
> > --no-site-file Don't read the site-wide Rprofile
> > --no-init-file Don't read the user R profile
> > --restore Do restore previously saved objects at startup
> > --vanilla Combine --no-save, --no-restore, --no-site-file
> > --no-init-file and --no-environ
> >
> > 'file' may contain spaces but not shell metacharacters
> >
> > Also, instead of using $GALAXY_ROOT - I would use $__tool_directory__
> > if the tool XML file is located next to the RScript, like this:
> >
> > $__tool_directory__/F

Re: [galaxy-dev] Fwd: Rscript run under Tools Directory cannot see Datafile in History smaller email size

[Gildas Le Corguillé]

Hi,

Because R always return blabla in the standard error output (stderr), by 
default Galaxy thinks that there is a problem. You need this following lines in 
your wrapper xml : 

  

With that, Galaxy will use the code error (echo  $?) instead of the stderr to 
detect an error.


Another thing, you can use 
Foo.R $inputFile1 . 
If your script is in the same folder as your xml


Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--



> Le 4 févr. 2016 à 21:25, rbrown1...@comcast.net a écrit :
> 
> John,
> Thanks for the great info.  I got the R to work not the Rscript.
> However, my data files return RED even though there is data in them
> I am still getting R warning but no errors
> During startup - Warning messages:
> 1: Setting LC_CTYPE failed, using "C" 
> 2: Setting LC_COLLATE failed, using "C" 
> 3: Setting LC_TIME failed, using "C" 
> 4: Setting LC_MESSAGES failed, using "C" 
> 5: Setting LC_MONETARY failed, using "C" 
> 6: Setting LC_PAPER failed, using "C" 
> 7: Setting LC_MEASUREMENT failed, using "C" 
> Is there a flag I can set to igrore these warning and have Galaxy return 
> GREEN?
> thanks.
> bob
> - Original Message -
> From: John Chilton <jmchil...@gmail.com>
> To: rbrown1...@comcast.net, galaxy-dev@lists.galaxyproject.org
> Sent: Thu, 04 Feb 2016 20:11:53 - (UTC)
> Subject: Re: [galaxy-dev] Fwd: Rscript run under Tools Directory cannot see 
> Datafile in History smaller email size
> Forgot to cc the mailing list.
> -John
> On Thu, Feb 4, 2016 at 8:11 PM, John Chilton <jmchil...@gmail.com> wrote:
> > Are you sure about the --file when calling Rscript?
> >
> > Here is the usage for my local version which does not expect an
> > argument named --file:
> >
> > Usage: /path/to/Rscript [--options] [-e expr] file [args]
> >
> > --options accepted are
> > --help Print usage and exit
> > --version Print version and exit
> > --verbose Print information on progress
> > --default-packages=list
> > Where 'list' is a comma-separated set
> > of package names, or 'NULL'
> > or options to R, in addition to --slave --no-restore, such as
> > --save Do save workspace at the end of the session
> > --no-environ Don't read the site and user environment files
> > --no-site-file Don't read the site-wide Rprofile
> > --no-init-file Don't read the user R profile
> > --restore Do restore previously saved objects at startup
> > --vanilla Combine --no-save, --no-restore, --no-site-file
> > --no-init-file and --no-environ
> >
> > 'file' may contain spaces but not shell metacharacters
> >
> > Also, instead of using $GALAXY_ROOT - I would use $__tool_directory__
> > if the tool XML file is located next to the RScript, like this:
> >
> > $__tool_directory__/Foo.R
> >
> > -John
> >
> >
> > On Thu, Feb 4, 2016 at 7:05 PM, <rbrown1...@comcast.net> wrote:
> >> Good morning team,
> >> I have an Rscript tool that is trying to read a file I uploaded into the
> >> history beforehand. Galaxy is running with the same user and privileges as
> >> the dataset directory.
> >> Rscript --slave --vanilla
> >> --file=$GALAXY_ROOT_DIR/tools/Foo/Foo.R --args $inputFile1 . 
> >> Why would this be?
> >>
> >> Error in file(file, "rt") : cannot open the connection
> >> Calls: performDataOrdering -> read.table -> file
> >> In addition: Warning message:
> >> In file(file, "rt") :
> >> cannot open file
> >> '--file=/home/rbrown/hmgalaxy/database/files/000/dataset_162.dat': No such
> >> file or directory
> >> Execution halted
> >>
> >> When I try to run as R versus Rscript - I get a syntax error about
> >> unexpected '(' on function call that works fine in R window.
> >>
> >> Thanks
> >> Bob
> >>
> >>
> >> ___
> >> Please keep all replies on the list by using "reply all"
> >> in your mail client. To manage your subscriptions to this
> >> and other Galaxy lists, please use the interface at:
> >> https://lists.galaxyproject.org/
> >>
> >> To search Gal

Re: [galaxy-dev] Adding a5_pipeline.pl to galaxy

[Gildas Le Corguillé]

Hi,

When you use ${output}, Galaxy creates a file in 
database/file//dataset_YYY.dat.
Your script seem to need a directory or maybe a prefix like "output".

So when the script generate its output filename. You can use the from_work_dir 
attribute of 

 
So, I guess something like that:


> 
> 
>   assemble microbial fastQ to fatsA
> 
>   a5_pipeline.pl ${file1} ${file2} output 
> 
> 
>   
> 
> 
>   
> 
>  output.contigs.fasta  
> output.contigs.qvl  
> output.raw1.pe.sort.bam  
> output.tmplibs 
> output.assembly_stats.csv  
> output.contigs.fastq  
> output.ec.fastq.gz   
> output.raw1.pe.sort.bam.bai  
> output.s1  
> output.s2   
> -->
>  
>  from_work_dir="output.contigs.fasta" label=“A5 output fastA"/>
>  from_work_dir="output.contigs.fastq" label=“A5 output fastQ”/>
> 
> 
> 


Good luck

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--



> Le 22 janv. 2016 à 15:13, Raphenya, Amogelang <raphe...@mcmaster.ca> a écrit :
> 
> Hi All,
> 
> I have a problem getting all the outputs in galaxy.
> 
> My xml config file looks like this:
> 
> 
> 
>   assemble microbial fastQ to fatsA
> 
>   a5_pipeline.pl ${file1} ${file2} ${output} 
> 
> 
>   
> 
> 
>   
> 
>  output.contigs.fasta  
> output.contigs.qvl  
> output.raw1.pe.sort.bam  
> output.tmplibs 
> output.assembly_stats.csv  
> output.contigs.fastq  
> output.ec.fastq.gz   
> output.raw1.pe.sort.bam.bai  
> output.s1  
> output.s2   
> -->
>  
> 
> 
> 
> 
> 
> 
> I get the following error when running the tool:
> 
> ../database/files/000/dataset_733.dat already exists and is not a directory.
> Please specify a new file path for a base name after the library file or 
> FastQ files.
> 
> Any ideas on how to get all the output or some output?
> 
> Cheers.
> 
> 
> Amos Raphenya 
> Bioinformatics Software Developer
> Department of Biochemistry & Biomedical Sciences
> McMaster University, MDCL 2317
> p: (905) 525-9140 ext: 22787
> a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1
> e:  raphe...@mcmaster.ca <mailto:raphe...@mcmaster.ca> 
> skype: amos_raphenya
> 
> ___
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> 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] EMBOSS 6.6.0 + NCBI-BLAST+ integration

[Gildas Le Corguillé]

Hi,

A long time ago, in a far far svn repo, we did this "multiple=true" on Peter 
wrappers.

I will try to propose it quickly :)

Gildas

-----
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--



> Le 20 janv. 2016 à 15:37, Peter Cock <p.j.a.c...@googlemail.com> a écrit :
> 
> On Wed, Jan 20, 2016 at 2:22 PM, Floreline TOUCHARD
> <floreline.touch...@gmail.com> wrote:
>> Thanks for the answer !
>> 
>> I compared the two versions of tools. It does not seem to be any major
>> differences indeed. I added these tools to my instance successfully.
> 
> Great :)
> 
>> Additional options in version 6 are not to be integrate to my Galaxy
>> instance immediately. I will update my XML file later if need arises. The
>> old wrappers are perfect for the moment.
> 
> If you have any feedback on the IUC work, please comment on the
> GitHub issue.
> 
>> For the NCBI BLAST+ suite I would like to select multiple databases only
>> from the *.loc files. There is no spaces in the paths in my *.loc files
>> (however there is spaces in the names of these databases, but I guess this
>> is not a problem). I thought I just have to add a tag "multiple=true" in the
>> XML file but it seems a bit more complex. Am I missing something ?
> 
> As far as I know, the multiple="true" tag only works on input datasets
> from your history. But that would make sense... I don't think I have
> ever tried this.
> 
> Even if that worked, the  tag would also need modifying
> to account for the multiple values from db_opts.database.
> 
> Another potential option is to extend makeblastdb which can in
> principle combine multiple FASTA and pre-existing databases...
> 
> Peter
> ___
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Re: [galaxy-dev] Extract features : error loading field data in usegalaxy

[Gildas Le Corguillé]

Hi,

Sorry for this UP.

Since this issue is also on usegalaxy.org <http://usegalaxy.org/>, I insist.

To get this error, you just need to add the tool "Extract features" on the 
workflow canevas.
You will get a red message "error loading field data" 


Gildas

---------
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--



> Le 13 nov. 2015 à 16:01, Gildas Le Corguillé <lecorgui...@sb-roscoff.fr> a 
> écrit :
> 
> Hi,
> 
> One of my user wanted to import a workflow using the tool "Extract features" 
> provided in the galaxy distrib : tools/filters/gff/extract_GFF_Features.xml
> 
> 
> On my instance, in the workflow canevas, I get this in red "error loading 
> field data"
> 
> On usegalaxy.org, I happy to observe that it's the same ... Sorry :)
> 
> Any idea ?
> 
> Gildas
> 
> -- 
> -
> Gildas Le Corguillé - Bioinformatician/Bioanalyste
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)
> 
> Station Biologique de Roscoff - UPMC/CNRS - FR2424
> Place Georges Teissier 29680 Roscoff FRANCE
> tel: +33 2 98 29 23 81
> http://abims.sb-roscoff.fr
> --
> 
> ___
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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Gildas Le Corguillé]

Hi All,

I have some knowledges about RADSeq ... at least about the 
bioinformatics part. This technology is growing up in my lab (marine 
science) and I'm involve in few of those projects.


So I'm in!

Gildas



Le 23/11/2015 20:59, Tiago Antao a écrit :

On Mon, 23 Nov 2015 18:03:05 +
John Chilton <jmchil...@gmail.com> wrote:


Someone should create an tools-iuc issue for this, I will certainly
participate also. I don't know anything RADSeq (or really much about
any kind of Seq) but I suspect I can find a way to help if there is a
TODO or ideas list that is tracked on github.


I am surrounded by RADSeq specialists (including some of the people
that developed the technology).
I will contact them to get a list of things needed (TODO) and probably
try to convince one of them to introduce the technology.
Unfortunately the geekiest of them all is not a big Galaxy fan, I am
afraid.

Tiago
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--
---------
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--

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Re: [galaxy-dev] API key change manually

[Gildas Le Corguillé]

Hello,

I don't know your constraints but you can easily generate a new one:
 - User
 - API Keys
 - Generate a new key now

Gildas


Le 17/11/2015 13:11, Mic a écrit :

Hello,
After I migrated Galaxy installation to Postgresql my API key got 
lost. I still know it and would like to add it to the database, but I 
am not quite sure how to do it.


How is it possible to add an API key to the database.

Thank you in advance.

Mic


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--
-----
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--

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[galaxy-dev] Extract features : error loading field data in usegalaxy

[Gildas Le Corguillé]

Hi,

One of my user wanted to import a workflow using the tool "Extract 
features" provided in the galaxy distrib : 
tools/filters/gff/extract_GFF_Features.xml



On my instance, in the workflow canevas, I get this in red "error 
loading field data"


On usegalaxy.org, I happy to observe that it's the same ... Sorry :)

Any idea ?

Gildas

--
---------
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--

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Re: [galaxy-dev] Hey, I got some problem using galaxy, If you have a time, I hope your help..!!

[Gildas Le Corguillé]

Hello Yoong,

I quickly see 3 mistakes :
 - you use interpreter="python" but if so, you need to put your scripts 
in the same directory of your .xml. If you really want to use the full 
absolute path, delete the interpreter argument.
 - you don't need $alignments.files_path in your command. $alignments 
seems enough.
 - you describe many outputs although you just use one of them 
($alignments). So, try to comment the others.


Some clues for you :)

Gildas


Le 28/10/2015 12:27, Greg Von Kuster a écrit :

Hello Yoong,

The best place to ask questions like this is the Galaxy Dev mailing 
list (galaxy-dev@lists.galaxyproject.org 
).  There are many 
developers that support this mailing list, so you  will undoutedly 
receive optimal answers to any of your questions.  I’ve forwarded your 
current questions to the mailing list.


Regards,

Greg Von Kuster

On Oct 28, 2015, at 12:56 AM, 홍윤지 > wrote:


hey, my name is yoong in korean student .
i'd like to run the program name Mapsplice2, so i made a xml file, 
and submit that


this is my xml file..




MapSplice2 Description


/home/yoong/galaxy/tools/MapSplice-v2.1.9/mapsplice.py -o 
$alignments.files_path -p 20 --qual-scale phred33 --bam --fusion -c 
/home/yoong/1_reference/hg19 -x /home/yoong/1_reference/BowtieIndex 
-1 $input_reads_1 -2 $input_reads_2











label="fusions_candidates.txt"/>







Help



and, look at the report error, there is no special error... what's 
was the problom..? Do I something wrong ?...

plz help me...!! Thank you ...




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