Re: [galaxy-dev] Get Data and 'xlsx'

2018-10-15 Thread Peter Cock
is surely wrong. > > I created an issue for it here: > https://github.com/galaxyproject/galaxy/issues/6849 > > M. > > > > On Wed, Oct 10, 2018 at 2:11 PM D K wrote: >> >> Sure, I've attached a sample xlsx file and my datatypes_conf.xml file >> >&g

Re: [galaxy-dev] Get Data and 'xlsx'

2018-10-10 Thread Peter Cock
That sounds very strange - could you share the test file (ideally publicly, but at least by private email)? Modern MS files do use XML but I don't understand how it would be recognised as BLAST XML... It may also be useful to see your Galaxy data types configuration file. Peter On Wed, 10 Oct

Re: [galaxy-dev] tool data confusion

2018-10-02 Thread Peter Cock
epos/bgruening/diamond/64be1ac21109/tool_data_table_conf.xml > -> > tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/diamond_database.loc > > Best, > Matthias > > > On 02.10.2018 11:22, Peter Cock wrote: > > Personally I tend to work with $GALAXY/tool

Re: [galaxy-dev] tool data confusion

2018-10-02 Thread Peter Cock
Personally I tend to work with $GALAXY/tool-data/*.loc (and ignore the tool shed installed copies in their cryptically named folders) but this reflects in part the fact that this used to be the only copy of the file, and that's just what I always did. If you use a data manager, I don't know which

Re: [galaxy-dev] "Merging tabular data tables with non-matching columns is not allowed"

2018-09-18 Thread Peter Cock
Hi Peter vH, I wonder if adding columns is not supported - because some tools would define the table without the extra column? You might have to define a new data table instead (with largely the same content). But to be clear, I am not an expert in this area of Galaxy. However, it does seem the

Re: [galaxy-dev] collections with more than 25,000 items

2018-08-30 Thread Peter Cock
also very big? I tested this on the first 10 sequences and it took > about 10mins. But maybe this is still not faster than running all at once? > How many cores would you give such a job? > > Cheers Jochen > > On 30.08.2018 16:44, Peter Cock wrote: > > If there are any limits, it woul

Re: [galaxy-dev] collections with more than 25,000 items

2018-08-30 Thread Peter Cock
If there are any limits, it would be down to the Galaxy Admin's job settings - something generic with collections. Personally I've not done this - I tend to concatenate FASTA files to make large files with multiple sequences instead. (And then we have the optional task splitting enabled so that

Re: [galaxy-dev] tool datatypes

2018-08-17 Thread Peter Cock
to use the extra_files_path mechanism (which seems to > be the simplest for me) > > In any of these cases my next question would be how to create a test using > such a data as input and output (for output I have seen an example > somewhere). > > Cheers, > Matthias > > > >

Re: [galaxy-dev] tool datatypes

2018-08-17 Thread Peter Cock
xml file? > > Best, > Matthias > > > > Am 16/08/18 18:32 schrieb Peter Cock : > > Defining 20 different text-based formats does not look ideal (if that > is what you are doing). > > Do you have sample output in the repository? Perhaps at least some of > these ca

Re: [galaxy-dev] tool datatypes

2018-08-16 Thread Peter Cock
n I can pass the folder to > downstream tools (and can check for proper input). I hope that subclassing > txt or tabular will be sufficient. > > Cheers, > Matthias > > > > On 16.08.2018 17:02, Peter Cock wrote: >> >> More details might help - are you just de

Re: [galaxy-dev] tool datatypes

2018-08-16 Thread Peter Cock
More details might help - are you just defining the new datatype as a subclass in the XML, or do you need to include Python code (e.g. for a sniffer)? If you want to see some examples of datatypes using Python code which are available via the Tool Shed, here are two:

Re: [galaxy-dev] Expose Command Line in Galaxy

2018-07-11 Thread Peter Cock
You may have found a new Galaxy bug then :( Could you log an issue here: https://github.com/galaxyproject/galaxy/issues (From what you've said, I don't think that this is a problem in the BLAST+ wrappers themselves) Peter On Wed, Jul 11, 2018 at 3:20 PM, Matthias Enders <

Re: [galaxy-dev] Expose Command Line in Galaxy

2018-07-11 Thread Peter Cock
Good. So is everything resolved now? Peter On Wed, Jul 11, 2018 at 3:08 PM, Matthias Enders < m.end...@german-seed-alliance.de> wrote: > Dear Peter, > > > > yes we did reload the Blast *.loc files using the admin interface. Our > Version is 18.05 (based on the Galaxy – Docker image). > > > >

Re: [galaxy-dev] Expose Command Line in Galaxy

2018-07-11 Thread Peter Cock
Is there anything in the Admin's interface to let you reload the BLAST *.loc files? If yes, did you try it but it didn't work? What version of Galaxy do you have? Peter On Tue, Jul 10, 2018 at 3:11 PM, Matthias Enders < m.end...@german-seed-alliance.de> wrote: > Dear Peter, > > > > up to our

Re: [galaxy-dev] Expose Command Line in Galaxy

2018-07-10 Thread Peter Cock
Thanks for getting back to us - this was actually my guess from the original email - that it was not a blastn error message, but a Galaxy message before ever calling BLAST. My guess is you are seeing this issue, or something like it, with having to restart Galaxy to reload the *.loc files?

Re: [galaxy-dev] Expose Command Line in Galaxy

2018-07-10 Thread Peter Cock
There is a setting to enable showing the command line string and full paths on disk via the "i" icon from a history entry, see https://docs.galaxyproject.org/en/master/admin/options.html#expose-dataset-path # This option allows users to see the full path of datasets via the # "View Details"

Re: [galaxy-dev] Conda problem

2018-05-25 Thread Peter Cock
er I deleted these directories > the error messages disappeared and tools are running again. > > > Cheers, David > > ____ > From: Peter Cock <p.j.a.c...@googlemail.com> > Sent: 24 May 2018 14:22:40 > To: David Lee > Cc: galaxy-dev

Re: [galaxy-dev] Conda problem

2018-05-24 Thread Peter Cock
On Thu, May 24, 2018 at 2:14 PM, David Lee wrote: > Hi, > > > I hope somebody can help me with this. I've been maintaining a Galaxy > installation for the past few months that has suddenly developed a problem > that I can't undo. Which version of Galaxy? Can you tell

Re: [galaxy-dev] Ballgown does not work

2018-04-10 Thread Peter Cock
On Tue, Apr 10, 2018 at 3:28 PM, Jochen Bick wrote: > Hi Peter, > > >> >> https://github.com/CollardT/Ballgown-Wrapper > > I can contact report the issue on github. I think that would be best. > It looks like its looking for > a variable called dataset with is not

Re: [galaxy-dev] Ballgown does not work

2018-04-10 Thread Peter Cock
galaxy is a release_17.05 > > I think the xml is also broken. > > Cheers Jochen > > On 10.04.2018 15:28, Peter Cock wrote: >> Are you trying to install this? >> >> https://toolshed.g2.bx.psu.edu/view/theo.collard/ballgown_wrapper/05977e96375b >> >> If so,

Re: [galaxy-dev] Ballgown does not work

2018-04-10 Thread Peter Cock
Are you trying to install this? https://toolshed.g2.bx.psu.edu/view/theo.collard/ballgown_wrapper/05977e96375b If so, it does set out its requirements: bioconductor-ballgown r-dplyr r-optparse However, your Galaxy would have to be using BioConda to do this.

Re: [galaxy-dev] Error during FASTQ preview

2018-03-13 Thread Peter Cock
This could be a special character unicode issue, but my guess is something has gone wrong with compression. Can you identify the file on disk (easy via the history "i" for information icon if this option is enabled; by default Galaxy does not tell you the file path)? Then try the Unix command

Re: [galaxy-dev] Ensuring Python 2.7 when resolving conda dependencies for tool

2018-03-05 Thread Peter Cock
u can use pip in a conda environemnt to do this manually). > > Hope that helps, > Marius > > On 5 March 2018 at 17:51, Peter Cock <p.j.a.c...@googlemail.com> wrote: >> >> I stand corrected. Looking closer, there are conda packages >> for both Python 2 and

Re: [galaxy-dev] Ensuring Python 2.7 when resolving conda dependencies for tool

2018-03-05 Thread Peter Cock
2 conda-forge > tk: 8.6.7-0 conda-forge > wheel: 0.30.0-py27_2conda-forge > zlib:1.2.11-0 conda-forge > ``` > > So given a recent conda (latest version should work) and the correct channel > ord

Re: [galaxy-dev] Ensuring Python 2.7 when resolving conda dependencies for tool

2018-03-05 Thread Peter Cock
Tricky, as I understand it the conda python packages are specific to the conda version of Python - in this case Python 3 not 2. It might actually be simpler to fix pal_finder/pal_filter.py to cope with Python 3 - is the code online somewhere, I could probably cast an eye over it. Peter On Mon,

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

2018-02-06 Thread Peter Cock
Hi Jochen, I think you will find this very difficult without including a large chunk of the Galaxy code in your project for turning a tool XML file into an object representation. Although the main features of the tool XML provide a quite neutral tool description (list of arguments, output

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

2018-01-18 Thread Peter Cock
Domaine de Vilvert > 78352 Jouy-en-Josas > > Le 17 janv. 2018 à 17:39, Peter Cock <p.j.a.c...@googlemail.com> a écrit : > > It sounds like it could be this issue?: > > https://github.com/galaxyproject/planemo/issues/530 > > If so, the good news is there is a workaroun

Re: [galaxy-dev] Cluster Install Path Errors

2018-01-18 Thread Peter Cock
I *think* this is a problem with your copy of Python 2.7 and a standard library (hashlib) normally present. Do you know how this Python was installed? If it was compiled from source, then it may have been missing a few dependencies, and thus you have ended up with missing a few normally present

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] 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] 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] 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] 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

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