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

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:

[galaxy-dev] Re: conda not installing deps.

fig/sample/galaxy.yml.sample#L265-L271 <https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/config/sample/galaxy.yml.sample#L265-L271> Gildas -------- Gil

Re: [galaxy-dev] add labels to tools

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

Re: [galaxy-dev] use or convert tool.xml file for database webpage

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:

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

hub.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

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

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

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

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] migratting to Galaxy new realease error

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

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] Installation of packages failing

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

[galaxy-dev] Restart Galaxy without interruption

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] Tool needs a particular file extension -- now Datatype help

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

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

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] Returning BLAST datatypes and DB loc files to Galaxy core?

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] per-tool job resource defaults

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

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] packaging R scripts

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

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

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

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] Adding a5_pipeline.pl to galaxy

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] EMBOSS 6.6.0 + NCBI-BLAST+ integration

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] Extract features : error loading field data in usegalaxy

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

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] API key change manually

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

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

, 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] Hey, I got some problem using galaxy, If you have a time, I hope your help..!!

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.