Re: [galaxy-dev] No legal value defined in a planemo test for param type="select" and options="from_file"

2018-01-17 Thread Peter Cock
It sounds like it could be this issue?: https://github.com/galaxyproject/planemo/issues/530 If so, the good news is there is a workaround (see issue discussion). Peter On Wed, Jan 17, 2018 at 4:24 PM, Olivier Inizan wrote: > Dear list, > > I am trying to write a test

Re: [galaxy-dev] contribute to tools without github

2017-10-20 Thread Peter Cock
I infer you are talking about this Tool Shed repository: https://toolshed.g2.bx.psu.edu/view/fabad/sparql_uniprot/ Sadly there is no README file and no copyright statements. The only clue to the author is one comment is written appears to be written in Spanish. Based on

Re: [galaxy-dev] Problems with BlastDB.loc

2017-10-18 Thread Peter Cock
What does your config/tool_data_table_conf.xml[.sample] file have? Can you turn on the debugging as this will will give more information about the *.loc files. e.g. https://github.com/galaxyproject/galaxy/pull/3095 https://github.com/galaxyproject/galaxy/pull/3099 Peter On Wed, Oct 18, 2017 at

Re: [galaxy-dev] upload file format is data - type not recognized in galaxy

2017-09-22 Thread Peter Cock
That's a shame - I don't see anything in the log either at first reading - it was hoping to see problems with missing datatypes or sniffers, which might explain this. Sorry, I am out of ideas. Peter On Fri, Sep 22, 2017 at 2:41 PM, Pavel Fibich wrote: > Hi Hans-Rudolf

Re: [galaxy-dev] upload file format is data - type not recognized in galaxy

2017-09-22 Thread Peter Cock
My first thought would be to double check the Galaxy startup logs (which normally tell you about the datatypes as they are setup). That ought to give some clues. Also check the XML files where the datatypes are defined are all still fine - do you have any of these and do they look fine?

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

2017-09-21 Thread Peter Cock
On Thu, Sep 21, 2017 at 12:50 PM, SAPET, Frederic < frederic.sa...@biogemma.com> wrote: > 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

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

2017-09-20 Thread Peter Cock
gt; > > > 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&

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

2017-09-12 Thread Peter Cock
; > > Fred > > > > *De :* galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] *De > la part de* Peter Cock > *Envoyé :* mardi 12 septembre 2017 14:56 > *À :* Laure QUINTRIC <laure.quint...@ifremer.fr> > *Cc :* Galaxy-dev <galaxy-dev@lists.galaxyp

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

2017-09-12 Thread Peter Cock
Hi Laure, I don't think there is any easy to use mechanism for this in Galaxy. Unfortunately Galaxy loads all the *.loc files at startup and treats them as global values available to all users equally. I can't find the email thread, but I recall someone previously trying to do something with a

Re: [galaxy-dev] Samtools problem in Docker

2017-08-14 Thread Peter Cock
Galaxy itself uses samtools for many operations, which is different from when samtools is called as a dependency of a tool run by the Galaxy user. However, the Docker image ought to take care of that - can you give more details of which Docker image you are using (URL, version, etc)? Thanks,

Re: [galaxy-dev] Data manager for ncbi_blast_plus in the main tool shed?

2017-08-11 Thread Peter Cock
Hi David, Daniel Blankenberg wrote one (CC'd): https://github.com/peterjc/galaxy_blast/tree/master/data_managers/ncbi_blastdb http://testtoolshed.g2.bx.psu.edu/view/blankenberg/data_manager_example_blastdb_ncbi_update_blastdb I've never used it in production and don't have enough understanding

Re: [galaxy-dev] Image in tool XML "help" section only renders when installed from toolshed?

2017-08-09 Thread Peter Cock
e fast response. From reading around elsewhere I'd understood > that using $PATH_TO_IMAGES was now deprecated? I think I tried it anyway and > it didn't seem to help. But I might have missed something, so I'd be > interested to know if it works for you. > > Best wishes > > Peter

Re: [galaxy-dev] Image in tool XML "help" section only renders when installed from toolshed?

2017-08-09 Thread Peter Cock
It looks like something important is not showing in the best practise website, special variable $PATH_TO_IMAGES as per the linked example: .. image:: $PATH_TO_IMAGES/slop-glyph.png Let me look into this, Peter On Wed, Aug 9, 2017 at 2:52 PM, Peter Briggs wrote:

Re: [galaxy-dev] Venn diagram example data

2017-07-27 Thread Peter Cock
helps. > > Thanks > Sam > > On Thu, Jul 27, 2017 at 11:33 AM, Peter Cock <p.j.a.c...@googlemail.com> > wrote: >> >> Hi Steven, >> >> Just in case, you're not talking about my older simpler Galaxy Tool >> for drawing simple Venn Diagrams, ar

Re: [galaxy-dev] Venn diagram example data

2017-07-27 Thread Peter Cock
Hi Steven, Just in case, you're not talking about my older simpler Galaxy Tool for drawing simple Venn Diagrams, are you? https://toolshed.g2.bx.psu.edu/view/peterjc/venn_list https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list This reminds me that I ought to update that tool to

Re: [galaxy-dev] tool and planemo problems

2017-07-12 Thread Peter Cock
And mere minutes later that change has been accepted, and will be part of the next release of Planemo. Thanks for the constructive feedback Matthias! Peter On Wed, Jul 12, 2017 at 4:24 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Good idea, pull request submitted: > > htt

Re: [galaxy-dev] tool and planemo problems

2017-07-12 Thread Peter Cock
with planemo command --help. > > Best, > Matthias > > > On 12.07.2017 16:57, Peter Cock wrote: >> >> Try: >> >> planemo lint --fail_level error sleepwaste.xml >> >> The default is to fail if there are warnings. >> >> Peter >> >

Re: [galaxy-dev] tool and planemo problems

2017-07-12 Thread Peter Cock
Try: planemo lint --fail_level error sleepwaste.xml The default is to fail if there are warnings. Peter On Wed, Jul 12, 2017 at 3:55 PM, Matthias Bernt <m.be...@ufz.de> wrote: > Hi Peter, > > I just call planemo l sleepwaste.xml > > Best, > Matthias > > > On 1

Re: [galaxy-dev] tool and planemo problems

2017-07-12 Thread Peter Cock
How are you running planemo lint - in particular is it set to fail if there are any warnings present (like your missing citation warning)? Peter On Wed, Jul 12, 2017 at 3:52 PM, Matthias Bernt wrote: > Dear list, > > In order to test the job resubmission feature I wrote a little

Re: [galaxy-dev] Issue with job_name, UnicodeDecodeError in drmaa

2017-05-29 Thread Peter Cock
if self.restrict_job_name_length: > job_name = job_name[:self.restrict_job_name_length] > return job_name > > -Raj > >> On May 29, 2017, at 11:33 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: >> >> Thanks Saravanaraj, >> &g

Re: [galaxy-dev] Issue with job_name, UnicodeDecodeError in drmaa

2017-05-29 Thread Peter Cock
915" > LC_TELEPHONE="en_US.iso885915" > LC_MEASUREMENT="en_US.iso885915" > LC_IDENTIFICATION="en_US.iso885915" > LC_ALL= > > I will talk to our sysadmin and see if I can change the locale to en_US.UTF-8. > > Thank you very much. > -Raj

Re: [galaxy-dev] Issue with job_name, UnicodeDecodeError in drmaa

2017-05-29 Thread Peter Cock
ob_name ) > File > "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", > line 400, in > job_name = ''.join( x if x in ( string.letters + string.digits + '_' ) > else '_' for x in job_name ) > UnicodeDecodeError: 'ascii' code

Re: [galaxy-dev] Issue with job_name, UnicodeDecodeError in drmaa

2017-05-29 Thread Peter Cock
Time for more debugging, try inserting something like this inserted the line above into /panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py (having backed up the file): log.debug( 'Making job_name, tag was %r, plan to use %r with underscores replacements' %

Re: [galaxy-dev] Running jobs as real user and extra_file_path

2017-04-28 Thread Peter Cock
On Wed, Mar 20, 2013 at 3:51 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Mon, Apr 30, 2012 at 4:47 PM, Nate Coraor <n...@bx.psu.edu> wrote: >> On Apr 25, 2012, at 9:39 AM, Louise-Amélie Schmitt wrote: >> >>> Hi everyone, >>> >>> I

Re: [galaxy-dev] atlas version 3.10.2 installation error

2017-04-19 Thread Peter Cock
+ 2.5.0. Peter On Wed, Apr 19, 2017 at 1:17 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > I've emailed the rest of the IUC for their input - adding the old versions > in bioconda should work, or adding the recent Biopython releases as packages > on the Tool Shed. > > Fo

Re: [galaxy-dev] atlas version 3.10.2 installation error

2017-04-19 Thread Peter Cock
be no good idea because of backward > compatibility? > > Cheers, > Matthias > > > > > > On 19.04.2017 13:50, Peter Cock wrote: > > Just lucky timing, could you try blast_rbh v0.1.11, > > > > https://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh/d8d9a9

Re: [galaxy-dev] atlas version 3.10.2 installation error

2017-04-19 Thread Peter Cock
be great to get the update, but since I have a > method that is working for the moment there is no need to hurry. > > Best, > Matthias > > > > On 19.04.2017 12:57, Peter Cock wrote: >> >> Oh right - I've just been updating ncbi_blast_plus this morning >> to tr

Re: [galaxy-dev] atlas version 3.10.2 installation error

2017-04-19 Thread Peter Cock
Oh right - I've just been updating ncbi_blast_plus this morning to transition to BLAST+ 2.5.0 via either bioconda or the older legacy Tool Shed. I can try to update blast_rbh next, which may solve this by letting you use bioconda. Peter On Wed, Apr 19, 2017 at 11:52 AM, Matthias Bernt

Re: [galaxy-dev] Testing updated NCBI BLAST+ wrappers for version 2.5.0

2017-04-19 Thread Peter Cock
This just went live on the main tool shed: https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ You can report issues here or on GitHub at: https://github.com/peterjc/galaxy_blast/issues Thanks, Peter On Thu, Dec 8, 2016 at 11:35 AM, Peter Cock <p.j.a.c...@googlemail.com>

Re: [galaxy-dev] GCC2107 Update: Oral presentation abstracts due 15 April

2017-04-13 Thread Peter Cock
bioinformatics software development and open science in the biological research community (like the Galaxy Community Conference). http://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/ https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md Regards, Peter (Dr Peter Cock, OBF

Re: [galaxy-dev] [Bosc] BOSC 2017: Call for Abstracts

2017-04-10 Thread Peter Cock
2017 at 18:05, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Dear all, > > Recent BOSC meetings have had a strong Galaxy presence, so please do > consider submitting an abstract and/or attending BOSC 2017 in Prague. > > Thank you, > > Peter > > Dr. Peter Cock, &g

Re: [galaxy-dev] cluster access

2017-04-10 Thread Peter Cock
ng up email > aliases? I would need to ask our cluster admins if they could realize this. > > Best, > Matthias > > > > On 10.04.2017 16:39, Peter Cock wrote: >> >> This may depend on the cluster setup, and how Galaxy accesses it. >> What are you using? >>

Re: [galaxy-dev] cluster access

2017-04-10 Thread Peter Cock
This may depend on the cluster setup, and how Galaxy accesses it. What are you using? We use SGE (actually Univa Grid Engine) via DRMAA, and had to setup usern...@example.org email aliases just for this. Peter On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt wrote: > Dear list,

Re: [galaxy-dev] git clone 16.10 bwa 0.7.15 data manager

2017-04-10 Thread Peter Cock
Hi Bryan, I suspect the missing dependency BWA may reflect the switch away from Galaxy's home-grown packaging system to using Conda - enabled by default since v17.01, https://docs.galaxyproject.org/en/master/admin/conda_faq.html Newer dependencies will likely next get an old fashioned package

[galaxy-dev] Fwd: [Bosc] BOSC 2017: Call for Abstracts

2017-03-08 Thread Peter Cock
Dear all, Recent BOSC meetings have had a strong Galaxy presence, so please do consider submitting an abstract and/or attending BOSC 2017 in Prague. Thank you, Peter Dr. Peter Cock, Bioinformatician at The James Hutton Institute; Open Bioinformatics Foundation, board of directors, treasurer

Re: [galaxy-dev] Rg: Galaxy Version

2017-03-08 Thread Peter Cock
.com/api/version` to learn the release of Galaxy you have. > > Thanks for using Galaxy, > > Martin > > On Wed, Mar 8, 2017 at 7:39 AM Peter Cock <p.j.a.c...@googlemail.com> wrote: >> >> Galaxy was originally distributed via the mercurial (hg) version >> contr

Re: [galaxy-dev] Rg: Galaxy Version

2017-03-08 Thread Peter Cock
Galaxy was originally distributed via the mercurial (hg) version control system, later the git version control system. Try this (which will work on a very old Galaxy using hg), $ hg log | head changeset: 17125:e837a68e8d14 tag: tip parent: 17121:7a4e3a661a76 parent:

Re: [galaxy-dev] Execute command once job has completed

2017-02-28 Thread Peter Cock
d writing it will > automatically run the convert to bigwig command > > > Peter Cock > February 28, 2017 12:21 PM > It depends on what you mean by automatic. You could > create a Galaxy Workflow where a tool is run which > generates the bedgraph file, and then as the next

Re: [galaxy-dev] Execute command once job has completed

2017-02-28 Thread Peter Cock
It depends on what you mean by automatic. You could create a Galaxy Workflow where a tool is run which generates the bedgraph file, and then as the next step it is converted to bigwig. For this specific task, it might be possible to exploit the Galaxy datatype definition for bedgraph to allow

Re: [galaxy-dev] Tools using Galaxy's Python library?

2017-02-13 Thread Peter Cock
t 11:20 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > This went smoother today, and has served to refresh some of the > details of how the Galaxy's venv etc all work. > > In my TravisCI setup for tool testing I currently "manually" install > the tool dependencies

Re: [galaxy-dev] ImportError and Project life cycle

2017-02-13 Thread Peter Cock
On Mon, Feb 13, 2017 at 9:17 AM, Matthias Bernt wrote: > Dear Martin, > > Thanks for your input. Before answering the raised questions I would like to > add some more information that I just found: > > I've noticed something odd (to me) which is maybe the source of the problem. >

Re: [galaxy-dev] ImportError and Project life cycle

2017-02-10 Thread Peter Cock
On Fri, Feb 10, 2017 at 3:26 PM, Matthias Bernt wrote: > Dear galaxy-dev list, > > I'm currently trying to introduce myself to the galaxy server, i.e., > learning how to use and administer a galaxy server. > > I have installed galaxy following this excellent tutorial: > >

Re: [galaxy-dev] Create a new datatype svg

2017-02-09 Thread Peter Cock
Hmm. I wonder if a composite datatype would work here? https://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes Peter On Thu, Feb 9, 2017 at 9:25 AM, Jochen Bick wrote: > Hi Dan, > > I understand the option with this specific flag. What I mean is that for

Re: [galaxy-dev] Peter Cock <p.j.a.c...@googlemail.com>

2017-02-01 Thread Peter Cock
t and let yo know how it goes. > > Thank you > > Eduardo > > On 01/02/2017 10:10, "Peter Cock" <p.j.a.c...@googlemail.com> wrote: > > > Hi Eduardo, > > > Certainly when Luobin Yang submitted the early work on the > PSI BLAST wrapper we need the P

Re: [galaxy-dev] Tools using Galaxy's Python library?

2017-02-01 Thread Peter Cock
Wed, Feb 1, 2017 at 9:46 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Thanks John - that could explain what's going wrong and offers > another approach to fixing my TravisCI testing - setting: > > preserve_python_environment = legacy_and_local > > or: > &

Re: [galaxy-dev] psiblast

2017-02-01 Thread Peter Cock
akeprofiledb. Does that allow you to remove psiblast from blacklist in > your repository? > > https://github.com/peterjc/galaxy_blast/blob/13d5b6deca0663d7f1301428574720 > b19aea1380/.tt_blacklist > > > Thank you > > Eduardo > > > On Tue, Feb 5, 2013 at 4:28 PM, Peter

Re: [galaxy-dev] Tools using Galaxy's Python library?

2017-02-01 Thread Peter Cock
rted - there is a config option that is documented > pretty well in the PR but I missed named it in the sample (fixing it with > https://github.com/galaxyproject/galaxy/pull/3521/files). > > Hopefully this helps and thanks for the bug report! > > -John > > > On Tue, Jan 31, 2

Re: [galaxy-dev] Tools using Galaxy's Python library?

2017-01-31 Thread Peter Cock
brary: > > https://anaconda.org/bioconda/galaxy_sequence_utils > > Cheers, > Nicola > > > On 31/01/17 10:39, Peter Cock wrote: >> >> Hi all, >> >> A few of my tools have for a long time used Galaxy's own parsing >> functionality in order to avoid an extern

[galaxy-dev] Tools using Galaxy's Python library?

2017-01-31 Thread Peter Cock
Hi all, A few of my tools have for a long time used Galaxy's own parsing functionality in order to avoid an external dependency. Lately this has stopped working on my TravisCI testing with planemo using the Galaxy dev branch (the stable master branch is fine): e.g.

Re: [galaxy-dev] Check running jobs

2017-01-27 Thread Peter Cock
Ah - I assumed you meant from the user-facing UI, or the reports page. I would suggest exploring the advance job metrics options, see e.g. https://github.com/galaxyproject/galaxy/blob/dev/config/job_metrics_conf.xml.sample I've never used it, but perhaps the backend using Collectl

Re: [galaxy-dev] Check running jobs

2017-01-27 Thread Peter Cock
Hi Katherine, I don't think Galaxy itself will tell you this, in part because the details would be dependent on the Cluster being used. I would do that via whatever cluster management system you are running (e.g. qstat or qmon if using SGE). By default all the jobs will be submitted by the

Re: [galaxy-dev] Blast db permission

2017-01-19 Thread Peter Cock
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

[galaxy-dev] Testing updated NCBI BLAST+ wrappers for version 2.5.0

2016-12-08 Thread Peter Cock
Hello all, I have updated the NCBI BLAST+ wrappers on the Test Tool Shed, the wrapper is now at v0.2.00: https://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ The main changes is this now depends on BLAST+ 2.5.0, and that is available via either BioConda or the Tool Shed:

Re: [galaxy-dev] Unable to upload bam files as links to my local galaxy instance - please help!

2016-12-05 Thread Peter Cock
Galaxy itself needs samtools, and this is not handled via the Tool Shed which only does dependencies of Galaxy Tools. I don't think the website is clear enough about this, https://wiki.galaxyproject.org/Admin/GetGalaxy just points at https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies

Re: [galaxy-dev] Moving Galaxy Install From One Server To Another

2016-11-23 Thread Peter Cock
On Wed, Nov 23, 2016 at 10:49 AM, Peter Briggs wrote: > Hello Evan, Hans-Rudolf > > I'm just in the middle of doing a similar migration for our local production > server, and Hans-Rudolf's advice seems sound to me. Definitely moving the > core Galaxy server has been

Re: [galaxy-dev] Code File Execution

2016-11-21 Thread Peter Cock
Are you asking how Galaxy takes the user-entered parameters (requested in the tool XML file with tags) and builds a command line string using the Cheetah-format template defined in the tag? At least part of the answer to that is the ToolEvaluator object:

Re: [galaxy-dev] Reporting issues for the wiki? e.g. universe_wgsi.ini still widely used

2016-11-15 Thread Peter Cock
thub.com/galaxyproject/galaxy-site. > > -Dannon > > On Tue, Nov 15, 2016 at 10:06 AM, Peter Cock <p.j.a.c...@googlemail.com> > wrote: >> >> Hello all, >> >> Is there a specific issue tracker for the wiki? It seems wrong to >> open an issue on the

[galaxy-dev] Reporting issues for the wiki? e.g. universe_wgsi.ini still widely used

2016-11-15 Thread Peter Cock
Hello all, Is there a specific issue tracker for the wiki? It seems wrong to open an issue on the main GitHub code repository... e.g. Many of the documentation pages still refer to the legacy configuration filename universe_wgsi.ini rather than the new name of config/galaxy.ini Problem pages

Re: [galaxy-dev] Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown

2016-11-03 Thread Peter Cock
xml file. > > version="" /> > > This tool is not the one trying to be installed. > > Thanks, > Miuki > On Nov 3, 2016, at 10:28 AM, Peter Cock > <p.j.a.c...@googlemail.com<mailto:p.j.a.c...@googlemail.com>> wrote: > > I think you may have hit the sa

Re: [galaxy-dev] Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown

2016-11-03 Thread Peter Cock
I think you may have hit the same bug I found recently: https://github.com/galaxyproject/galaxy/issues/3084 What is line 44 of your integrated_tool_panel.xml file? Peter On Thu, Nov 3, 2016 at 2:16 PM, Yip, Miu ki wrote: > Hi all, > > While trying to install tools from the

Re: [galaxy-dev] odose

2016-10-25 Thread Peter Cock
You might find this work useful for fetching bacteria from the NCBI: https://github.com/kblin/ncbi-genome-download Peter On Tue, Oct 25, 2016 at 12:54 PM, Vos, Michiel wrote: > > > Dear Galaxy developers, > > > > We hereby want to ask if anyone is interested in helping out

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

2016-10-22 Thread Peter Cock
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

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

2016-10-21 Thread Peter Cock
Using a soft link for this is a common pattern, and should be followed with && (ideally using XML CDATA to avoid escaping everything like etc), and quote the filenames just in case there are any spaces. e.g.

Re: [galaxy-dev] Tool.xml : correct way to define an environment_variable ?

2016-10-20 Thread Peter Cock
Hi Pierre, The first example looks OK, very similar to this one of mine for example, so I am not sure what is breaking: https://github.com/peterjc/pico_galaxy/blob/133aea82c02adf5509134c415565ada99c519312/tools/effectiveT3/tool_dependencies.xml I would try adding more shell actions to debug

Re: [galaxy-dev] galaxy - prokka - tbl2asn

2016-10-19 Thread Peter Cock
This is an annoyance from the NCBI team, and dealing with the expired tbl2asn tool is a regular question from Prokka users, eg: https://github.com/tseemann/prokka/issues/96 https://github.com/tseemann/prokka/issues/139 The Tool Shed package for Prokka will need updating - but luckily Nicola is

Re: [galaxy-dev] Python ValueError: too many values to unpack

2016-10-18 Thread Peter Cock
I just found this old email by a very similar exception logged as: https://github.com/galaxyproject/galaxy/issues/2987 There do seem to be some corner cases where missing default values are not handled nicely. Peter On Tue, Jan 26, 2016 at 2:38 PM, Matthias De Smet

Re: [galaxy-dev] planemo test with

2016-10-07 Thread Peter Cock
the command I'm using to run planemo: > . galaxy_test/.venv/bin/activate > planemo test --test_data /home/galaxy-functional-testdata --galaxy_root > galaxy-test/ --skip_venv test.xml > > I'm getting no errors when using the planemo lint tool. > > Thanks! > > On Fri, O

Re: [galaxy-dev] planemo test with

2016-10-07 Thread Peter Cock
Hi DK, Looking at your XML that looks OK. It might not be important, but how exactly are you running planemo test? I'm asking because currently it will not create tool-data/twobit.loc for you from your sample file - although in that case I would have expected a different error message:

Re: [galaxy-dev] [galaxy-iuc] GMAP tool_dependencies.xml package for ToolShed

2016-09-27 Thread Peter Cock
into the Galaxy core, under Galaxy's open source licence: Academic Free License version 3.0 https://github.com/galaxyproject/galaxy/blob/dev/LICENSE.txt Thanks, Peter On Tue, Sep 20, 2016 at 2:51 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Thanks JJ, > > That's great. We'r

Re: [galaxy-dev] [galaxy-iuc] GMAP tool_dependencies.xml package for ToolShed

2016-09-20 Thread Peter Cock
/jjohnson/package_gmap_2013_05_09/ > https://testtoolshed.g2.bx.psu.edu/view/jjohnson/gmap/ > > https://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_gmap_2013_05_09/ > > These can be copied to the iuc owned repositories and I could deprecate > those under my name. > &g

Re: [galaxy-dev] Send repeat parameter to code file for multiple select list

2016-09-01 Thread Peter Cock
e tag works: >> https://wiki.galaxyproject.org/Admin/Tools/Custom%20Code >> Thanks, >> Katherine >> >> On Thu, Sep 1, 2016 at 8:23 AM, Peter Cock <p.j.a.c...@googlemail.com> >> wrote: >>> >>> I'm not quite sure what you mean by a "code f

Re: [galaxy-dev] Send repeat parameter to code file for multiple select list

2016-09-01 Thread Peter Cock
I'm not quite sure what you mean by a "code file", but if you mean using the tag, here's an example: https://github.com/peterjc/galaxy_mira/blob/master/tools/mira4_0/mira4_de_novo.xml I am using a Cheetah syntax for loop to access each entry in a repeat parameter. Peter On Thu, Sep 1, 2016 at

Re: [galaxy-dev] how to create users through Galaxy API?

2016-08-30 Thread Peter Cock
>> https://bioblend.readthedocs.io/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.users >> >> Cheers, >> Nicola >> >> Peter Cock ha scritto >> >>> Thanks Hans-Rudolf, >>> >>> Yes - you are right. The wiki does li

Re: [galaxy-dev] how to create users through Galaxy API?

2016-08-29 Thread Peter Cock
gt; > Regards, Hans-Rudolf > > On 08/29/2016 05:27 PM, Peter Cock wrote: >> >> Hi Martin, >> >> I'd like to look into creating new users via the API (where we can >> control the email address and username format for integration with our >> cluster), and ha

Re: [galaxy-dev] how to create users through Galaxy API?

2016-08-29 Thread Peter Cock
Hi Martin, I'd like to look into creating new users via the API (where we can control the email address and username format for integration with our cluster), and have the web-interface forbid users from self-registration. The read-the-docs site you mentioned in this old email (below) doesn't

Re: [galaxy-dev] Introducing Conda as a new standard for Galaxy tool dependencies

2016-08-29 Thread Peter Cock
That's great Bjoern, I was thinking we should mention this on the wiki (with a link to the documentation rather than duplicating it). There are some existing pages about the tool_dependencies.xml system - but no obvious top level introduction that I saw?

Re: [galaxy-dev] Workflow Compatibility

2016-08-26 Thread Peter Cock
Hi Katherine, Are you asking about compatibility staying on the same Galaxy instance, or the harder problem of compatibility sharing workflows between Galaxy servers? Taking data from input Galaxy datasets should be fine, anything else may not be portable. Even the relatively simple case of

Re: [galaxy-dev] Doubled arguments from loc files in tests

2016-08-10 Thread Peter Cock
On Tue, Aug 9, 2016 at 6:33 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Hello all, > > Recently I've been debugging various problems with my Galaxy tool TravisCI > tests as part of moving to using "planemo test" rather than the fragile system > I first create

[galaxy-dev] Doubled arguments from loc files in tests

2016-08-09 Thread Peter Cock
Hello all, Recently I've been debugging various problems with my Galaxy tool TravisCI tests as part of moving to using "planemo test" rather than the fragile system I first created which mimicked a pre-ToolShed manual install:

Re: [galaxy-dev] Adding packages to depot.galaxyproject.org

2016-08-08 Thread Peter Cock
On Mon, Aug 8, 2016 at 3:27 PM, Björn Grüning <bjoern.gruen...@gmail.com> wrote: > Hi Peter, > > Am 08.08.2016 um 15:54 schrieb Peter Cock: >> On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche <e...@tamu.edu> wrote: >>> Hi Peter, >>> >>> The c

Re: [galaxy-dev] Adding packages to depot.galaxyproject.org

2016-08-08 Thread Peter Cock
On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche wrote: > Hi Peter, > > The cargo port is the ideal place for this, however it does not support > manual uploads of files. > Thanks Eric, You mean https://github.com/galaxyproject/cargo-port Is that something which might be addressed in

[galaxy-dev] Adding packages to depot.galaxyproject.org

2016-08-08 Thread Peter Cock
Hello all, How do tool wrapper developers/packagers go about adding entries to the Galaxy depot? There isn't a GitHub repository for this is there? Specifically I want to upload some older MIRA releases, e.g. these URLs have broken, but I have the original files and checksums:

Re: [galaxy-dev] Galaxy Blast

2016-08-02 Thread Peter Cock
-August/024696.html https://github.com/galaxyproject/galaxy/pull/2696 Peter On Wed, Jul 27, 2016 at 9:34 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Thank Dan, that's what I thought. > > So databases can added to any of the multiple blastdb.loc > files which Galaxy ought to

Re: [galaxy-dev] Add url in help of tool xml

2016-08-02 Thread Peter Cock
Great - I'm glad it was an easy fix. Peter On Tue, Aug 2, 2016 at 10:36 AM, Mohamed Kassam <k.mam...@gmail.com> wrote: > Hell Peter > The CDATA works perfectly thanks again. > > Mohamed > > 2016-08-02 11:31 GMT+02:00 Peter Cock <p.j.a.c...@googlemail.com>:

Re: [galaxy-dev] Add url in help of tool xml

2016-08-02 Thread Peter Cock
This could be as simple as the & needing to be escaped as or better escaping the whole help text using CDATA: https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#help-tag Can you show us your tool XML file? Is it on GitHub? Peter On Tue, Aug 2, 2016 at 10:26 AM,

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

2016-08-01 Thread Peter Cock
Hi Gildas, When datatypes were moved to the Tool Shed, I think the idea was to eventually have only a core set of topic-neutral datatypes (plain text, tabular, etc) in Galaxy itself. That does seem sensible. I'm not quite sure why policy has returned to a larger centralised set - but limitations

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

2016-08-01 Thread Peter Cock
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: >

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

2016-08-01 Thread Peter Cock
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.

Re: [galaxy-dev] TestToolShed down?

2016-07-28 Thread Peter Cock
For me too, thanks! Peter On Thu, Jul 28, 2016 at 11:06 AM, Nicola Soranzo <nsora...@tiscali.it> wrote: > Works for me now. > > Cheers, > Nicola > > > On 28/07/16 09:44, Peter Cock wrote: >> >> Hello all, >> >> The main Tool Shed

[galaxy-dev] TestToolShed down?

2016-07-28 Thread Peter Cock
Hello all, The main Tool Shed seems fine, but the Test Tool Shed is not: https://testtoolshed.g2.bx.psu.edu/ > Galaxy > > The Tool Shed could not be reached > > You are seeing this message because a request to the > Tool Shed timed out or was refused. This may be a temporary > issue which could

Re: [galaxy-dev] Galaxy Blast

2016-07-27 Thread Peter Cock
> was created during their installation. > > Please let me know if I can provide additional clarification. > > > > Thanks for using Galaxy, > > Dan > > >> On Jul 26, 2016, at 6:08 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: >> >> Hello all,

[galaxy-dev] Fwd: Galaxy Blast

2016-07-26 Thread Peter Cock
/tool_data_table_conf.xml.sample Can any of the Galaxy Data Manager expects advise please? Thanks, Peter -- Forwarded message -- From: Harry Wright <harry.wri...@moredun.ac.uk> Date: Tue, Jul 26, 2016 at 9:25 AM Subject: RE: Galaxy Blast To: Peter Cock <p.j.a.c...@googlemail.

Re: [galaxy-dev] Loading tool config file

2016-07-22 Thread Peter Cock
Sorry, I know relatively little about how Galaxy loads the tool XML files and turns this into the HTML pages. I've mostly searched the codebase with grep at the command line (also searching directly on GitHub works pretty well) trying to trace functionality when I was debugging something.

Re: [galaxy-dev] Loading tool config file

2016-07-22 Thread Peter Cock
Hi Katherine, Are you asking about the XML files which described Galaxy Tools by listing all the options to show the user, any help text to show the user, and instructions for how to turn the options picked into a command line to be executed:

Re: [galaxy-dev] Papers that cite Galaxy workflows

2016-07-22 Thread Peter Cock
Hi Steve, This isn't a very strong example, as it is self-reuse and self-citing, but anyway - we described some workflows in this book chapter: Cock and Pritchard (2014) Galaxy as a Platform for Identifying Candidate Pathogen Effectors. http://dx.doi.org/10.1007/978-1-62703-986-4_1 We re-used a

Re: [galaxy-dev] BLAST only using single core

2016-07-21 Thread Peter Cock
On Thu, Jul 21, 2016 at 10:35 AM, Shane Sturrock wrote: > > I’m just using the drmaa plugin so I’m guessing I need to either specify a > job runner for BLAST which sets GALAXY_SLOTS. The documentation isn’t > entirely clear although it seems I need to create a job_conf.xml

Re: [galaxy-dev] BLAST only using single core

2016-07-21 Thread Peter Cock
Hi Shane, We've not touched anything on the BLAST+ wrapper here for a while - the command line is always built using: -num_threads "\${GALAXY_SLOTS:-8}" That means use the environment variable $GALAXY_SLOTS if set, defaulting to 8 threads if not. See:

Re: [galaxy-dev] New galaxy parameter type

2016-07-15 Thread Peter Cock
Did you mean parameter as in input field shown to the user? Like a combobox or text field? Since this happened to come up earlier today, here's a rejected pull request which added a password parameter - that ought to give you a rough idea: https://github.com/galaxyproject/galaxy/pull/393 Peter

Re: [galaxy-dev] Get the username and password of a user

2016-07-15 Thread Peter Cock
Hi Mohamed, See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax which explains the $__user_id__ and $__user_email__ tokens which can be used in the definition of a tool wrapper XML file. From a security point of view, I don't think any tool should have access to the user's Galaxy

Re: [galaxy-dev] hide password xml tag

2016-07-15 Thread Peter Cock
This has been suggested before (with code to do it), but rejected on security grounds, see: https://github.com/galaxyproject/galaxy/pull/393 What would you do with the password when calling your tool? If you use it directly in the command line string then it will appear in the Galaxy logs, but

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