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

2015-10-28 Thread 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.

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

2015-11-13 Thread Gildas Le Corguillé
, 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 -

Re: [galaxy-dev] API key change manually

2015-11-17 Thread Gildas Le Corguillé
anage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- ----- Gildas Le

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

2016-01-08 Thread Gildas Le Corguillé
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

Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

2015-11-24 Thread Gildas Le Corguillé
h Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- --------- Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateforme ABiMS (Analyses and Bioinformatics for Marine Science) Station Biolo

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

2016-02-08 Thread 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

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

2016-02-05 Thread Gildas Le Corguillé
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

Re: [galaxy-dev] correctly installing to toolshed

2016-02-23 Thread 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 - Bioinfor

Re: [galaxy-dev] packaging R scripts

2016-02-26 Thread Gildas Le Corguillé
stall 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 - Bioinforma

Re: [galaxy-dev] correctly installing to toolshed

2016-02-25 Thread Gildas Le Corguillé
-Gildas Le Corguillé - Bioinformatician/BioanalystePlateforme ABiMS (Analyses and Bioinformatics for Marine Science)Station Biologique de Roscoff - UPMC/CNRS - FR2424Place Georges Teissier 29680 Roscoff FRANCEtel: +33 2 98 29 23 81http://abims.sb-roscoff.fr

Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

2016-01-20 Thread 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

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

2016-01-22 Thread Gildas Le Corguillé
t;/> > 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 Biolo

Re: [galaxy-dev] per-tool job resource defaults

2016-03-13 Thread Gildas Le Corguillé
es ... -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 Bio

Re: [galaxy-dev] Problems with planemo functional tests

2016-03-03 Thread 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

Re: [galaxy-dev] Trying to understand python dependencies

2016-07-27 Thread Gildas Le Corguillé
I forgot to say that Galaxy installs those dependencies (tool_dependencies or conda) beside your host system. That will not interfere with your host libraries, binaries ... Gildas - Gildas Le Corguillé - Bioinformatician

Re: [galaxy-dev] Returning BLAST datatypes and DB loc files to Galaxy core?

2016-08-01 Thread Gildas Le Corguillé
a 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://workflow4metabo

Re: [galaxy-dev] uploading multi-file archives and creation of potentially large collections

2016-08-05 Thread Gildas Le Corguillé
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

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

2017-02-24 Thread 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

Re: [galaxy-dev] Blast db permission

2017-01-20 Thread Gildas Le Corguillé
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

Re: [galaxy-dev] upload data error

2016-10-24 Thread Gildas Le Corguillé
- 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

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

2016-10-24 Thread Gildas Le Corguillé
uot;. 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/Bioanal

[galaxy-dev] Restart Galaxy without interruption

2016-11-14 Thread Gildas Le Corguillé
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://workflow4metabolomi

Re: [galaxy-dev] Installation of packages failing

2016-12-19 Thread 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 Pla

Re: [galaxy-dev] Displaying tool select list according to user

2017-09-21 Thread Gildas Le Corguillé
er. 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://work

Re: [galaxy-dev] conda bash environment problem as real user

2017-10-11 Thread Gildas Le Corguillé
ow 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 Bioinform