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

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

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

-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

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

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] Galaxy Blast

> 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

/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

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

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

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

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

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

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

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

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

Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

I'm glad you could solve this - thanks for letting us know and linking to the old email discussion which helped. Peter On Thu, Jul 7, 2016 at 4:35 PM, Katherine Beaulieu wrote: > Hi Peter, I ending up finding a solution to my problem using this forum > post: >

Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

Maybe sharing your tool XML file would be best - is it on GitHub? Peter On Wed, Jun 29, 2016 at 7:43 PM, Katherine Beaulieu wrote: > Ok, so I don't give the user the option to select the correct data type to > reduce the amount of stuff the user has to know when

Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

to galaxy. > > On Wed, Jun 29, 2016 at 10:45 AM, Peter Cock <p.j.a.c...@googlemail.com> > wrote: >> >> The auto-detection is only used when importing a >> file into Galaxy (e.g. by uploading it). >> >> If you are writing a tool which produces output i

Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

, Katherine Beaulieu <katherine.beaulieu...@gmail.com> wrote: > Hmm, I must have some sort of other logic error which is preventing the > detection of the format. Thanks for the information! > > On Wed, Jun 29, 2016 at 10:24 AM, Peter Cock <p.j.a.c...@googlemail.com> > wro

Re: [galaxy-dev] setting metadata externally failed for HistoryDatasetAssociation

Hi Anthony, The line numbers for binary.py don't match the current latest source, but I would bet this is due to the samtools binary not being on the path of the cluster nodes. Note Galaxy itself needs samtools for dealing with BAM files and this is expected to be on the $PATH (and it not

Re: [galaxy-dev] not sure what I can do about this...

Hi Edgar, Are your Galaxy server AND your cluster are all running Oracle Linux 6? If yes, my guess about the cluster using an older version of Linux compared to the Galaxy server is unrelated. Peter On Tue, May 24, 2016 at 7:47 PM, Fernandez Edgar wrote: > Hello

Re: [galaxy-dev] not sure what I can do about this...

Hi Fernandez, We saw something very like that with mixed versions of Linux, specifically our Galaxy head node where pysam was installed had CentOS 7, but the node where Galaxy was trying to run the metadata detection was CentOS 6. Unfortunately I do not have a record of the exact traceback - but

Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

On Tue, May 24, 2016 at 11:42 AM, Raymond Wan <rwan.w...@gmail.com> wrote: > Hi Peter, > > > On Tue, May 24, 2016 at 6:29 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: >> In case you didn't know, Galaxy likes to keep all BAM files in >> coordinate sorted or

Re: [galaxy-dev] Parallelism (job splitting) for ncbi_blast_plus running through CloudMan

On Tue, May 3, 2016 at 9:23 PM, David Kovalic wrote: > Peter, > > We made the modification to the config file, restarted galaxy and things > seem to be working from the galaxy end. We see sub-job directories being > created in /mnt/galaxy/tmp/job_working_directory. We think

Re: [galaxy-dev] Parallelism (job splitting) for ncbi_blast_plus running through CloudMan

Hi David, The NCBI BLAST+ wrappers have a tag setup, which becomes active if you have use_tasked_jobs = True in your config/galaxy.ini file (aka universe_wsgi.ini). Specifically, the wrappers use this: This is hard coded to break up the query FASTA file into batches of 1000 sequences (e.g.

Re: [galaxy-dev] init scripts version 16.01

We had something similar breaking when using run-as-real-user, where config/galaxy.ini setting external_chown_script which defaults to scripts/external_chown_script.py was being run on the cluster nodes using the system default Python. Here we created a wrapper shell script which invoked the

Re: [galaxy-dev] MySQL & ToolShed installs: 'latin-1' codec can't encode character

On Mon, Apr 4, 2016 at 2:30 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Hello all, > > We just ran into a Tool Shed installation problem under a test > installation of Galaxy v16.01, while trying to install the meme_fimo > tool. > > ... > > 'latin-1' code

[galaxy-dev] MySQL & ToolShed installs: 'latin-1' codec can't encode character

Hello all, We just ran into a Tool Shed installation problem under a test installation of Galaxy v16.01, while trying to install the meme_fimo tool. Clicking through the GUI takes me to the failed install of the perl_xml_parser_expat version 2.41 package (under

Re: [galaxy-dev] Toolshed Question, In reference to https://toolshed.g2.bx.psu.edu/view/youngkim/ezbamqc/caed0168f704

On Wed, Mar 30, 2016 at 9:46 PM, Molik, David wrote: > We're uploading a tool to the Galaxy Toolshed and were wondering about sample > files: > > Should .loc.sample files refer to sample data ( test-data ) > or should they be generalized for integration into other instances of

Re: [galaxy-dev] Python 2.7 vs 2.6 for galaxy after 16.01

On Wed, Mar 23, 2016 at 10:54 PM, D K wrote: > Great! thanks for the suggestions. I just tried using centos software > collections and that seems to work. I'll do some more testing but hopefully > it's as simple as that! Is there any reason that most of you who responded

Re: [galaxy-dev] automatic adding of a tab in a fastq header

Well done for solving this Fabien, with only a small hint from me. I'm glad to see your suggested fix has already been applied to the Galaxy repository so should be in the next stable release. Thank you! Peter (Also thank you Martin, Nicola, Dan, etc) On Tue, Mar 22, 2016 at 8:43 PM, Martin

Re: [galaxy-dev] shed_tool_conf.xml

I would try validating the broken XML file (e.g. using an online tool, or an XML aware editor). That might be enough to find the error and fix it by hand. I don't know if there is a clever way to regenerate the file instead... Peter On Tue, Mar 22, 2016 at 11:49 AM, Rathert, Philipp, Dr.

Re: [galaxy-dev] automatic adding of a tab in a fastq header

e two cases a tab was added. > > Fabien > > > Le 18/03/2016 17:04, Peter Cock a écrit : >> >> Hi Fabien, >> >> There is a Galaxy upload option to turn spaces into tabs, useful for >> tables of data. Is that being ticked by mistake? That would explain >> thi

Re: [galaxy-dev] automatic adding of a tab in a fastq header

Hi Fabien, There is a Galaxy upload option to turn spaces into tabs, useful for tables of data. Is that being ticked by mistake? That would explain this problem. Also I would check if the FASTQ file format is being detected automatically, or set explicitly (e.g. fastqsanger)? Doing that ought to

Re: [galaxy-dev] external_chown_script.py and the local job runner

On Mon, Jan 25, 2016 at 4:59 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Mon, Jan 25, 2016 at 4:44 PM, John Chilton <jmchil...@gmail.com> wrote: >> I think the problem is more that it is configured globally and not >> per-destination. The real user stuff sh

Re: [galaxy-dev] Problems uploading files to galaxy

On Tue, Mar 15, 2016 at 2:21 PM, John Chilton wrote: > If you are running jobs as "the real user" with drmaa (using the chown > script) - you will probably want to setup a separate job destination > using the local runner for upload jobs. The upload tool uses files > that

Re: [galaxy-dev] Python 2.7 six egg fetching issue

On Fri, Mar 4, 2016 at 3:13 PM, Yves Gagnon wrote: > Hi everyone, > > When I try to run galaxy using python 2.7 I get this error message while > fetching eggs. Under python 2.6 I do not have that issue: > > DistributionNotFound: six==1.9.0 > > The galaxy release I use is

Re: [galaxy-dev] error loading files into galaxy

Hello Hakeem, Did you ever solve this import problem? We suddenly started seeing this on our main (old) Galaxy server, which we have not intentionally changed recently: $ hg log | head changeset: 17125:e837a68e8d14 tag: tip parent: 17121:7a4e3a661a76 parent:

Re: [galaxy-dev] Python script can't can't import BioPython modules in Galaxy 16.01

On Thu, Mar 3, 2016 at 12:06 PM, Makis Ladoukakis wrote: > Hello everyone, > > I've recently upgraded to Galaxy 16.01 and i have some issues with a python > wrapper from a tool. When I run it via Galaxy I get the following error: > > Traceback (most recent call last): >

Re: [galaxy-dev] trouble with python packages after galaxy update

On Thu, Mar 3, 2016 at 9:14 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Thu, Mar 3, 2016 at 8:24 AM, Linda Bakker <linda.bak...@wur.nl> wrote: >> Hi Guys, >> So i updated my galaxy instance to release_16.01 >> I usually started galaxy in a venv and us

Re: [galaxy-dev] trouble with python packages after galaxy update

On Thu, Mar 3, 2016 at 8:24 AM, Linda Bakker wrote: > Hi Guys, > So i updated my galaxy instance to release_16.01 > I usually started galaxy in a venv and used pip to install any packages my > tool needed. (in this case, numpy and scipy) > > ... > >

Re: [galaxy-dev] Dependencies for sudo scripts/drmaa_external_runner.py ?

On Wed, Mar 2, 2016 at 5:27 PM, Nate Coraor <n...@bx.psu.edu> wrote: > On Wed, Mar 2, 2016 at 12:07 PM, Peter Cock <p.j.a.c...@googlemail.com> > wrote: >> >> On Wed, Mar 2, 2016 at 4:59 PM, Nate Coraor <n...@bx.psu.edu> wrote: >> > On Mon,

[galaxy-dev] Fwd: BOSC 2016 Call for Abstracts

ssed the earlier announcement last year, we finally got rid of the paper forms for OBF membership, see: http://news.open-bio.org/2015/12/10/online-membership-form/ -- Forwarded message -- From: Peter Cock <p.j.a.c...@googlemail.com> Date: Tue, Mar 1, 2016 at 5:56 PM Subject:

[galaxy-dev] Dependencies for sudo scripts/drmaa_external_runner.py ?

Hello all, QUESTION: When submitting jobs to the cluster as the real user, how should sudo scripts/drmaa_external_runner.py be told which Python to use, and how would it activate the venv if needed for the DRMAA dependency? BACKGROUND: We're currently trying Galaxy out on a new CentOS 6 VM,

Re: [galaxy-dev] Downgrade tool upload tool

Thanks for clarifying Makis, I think this change is likely due to changes in Galaxy rather than in the upload tool itself. On our (slightly out of date) Galaxy or the public server, that URL no longer loads the original tool form - you get the new drag-and-drop upload interface. I would guess

Re: [galaxy-dev] Downgrade tool upload tool

Hi Makis, The upload tool is a little special in that it is used internally by Galaxy and doesn't entirely behave like a normal tool. What are you trying to achieve by "downgrading" it? Peter On Mon, Feb 29, 2016 at 11:29 AM, Makis Ladoukakis wrote: > What about if I

[galaxy-dev] stage_data_in_history ValueError: No JSON object could be decoded

Hi all, Occasionally I've seen TravisCI tool tests fail with an exeception ValueError: No JSON object could be decoded, e.g. https://travis-ci.org/peterjc/galaxy_blast/jobs/107255016 ... galaxy.jobs INFO 2016-02-16 14:17:41,118 Collecting metrics for Job 139 galaxy.jobs DEBUG 2016-02-16

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

Good to know :) https://github.com/peterjc/galaxy_blast/pull/77 The pull request looks good - sadly distracted by TravisCI failures from Galaxy/planemo/dependency changes. Thanks, Peter On Tue, Feb 9, 2016 at 3:28 PM, Floreline TOUCHARD wrote: > Hi, > > sorry

Re: [galaxy-dev] Removing set_metadata_externally from wiki documentation?

On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Hello all, > > We're currently looking at changing our Galaxy setup to link user accounts > with Linux user accounts for better cluster integration (running jobs as the > actual user on SGE). A

[galaxy-dev] Python on cluster for setting metadata after jobs complete

On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Hello all, > > We're currently looking at changing our Galaxy setup to link user accounts > with Linux user accounts for better cluster integration (running jobs as the > actual user on SGE). A

[galaxy-dev] external_chown_script.py and the local job runner

On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Hello all, > > We're currently looking at changing our Galaxy setup to link user accounts > with Linux user accounts for better cluster integration (running jobs as the > actual user on SGE). A

Re: [galaxy-dev] external_chown_script.py and the local job runner

On Mon, Jan 25, 2016 at 4:44 PM, John Chilton wrote: > I think the problem is more that it is configured globally and not > per-destination. The real user stuff should all be per-destination and > not globally configured - since it should be possible to have like a >

[galaxy-dev] Creating cluster_files_directory (default database/pbs)

On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Hello all, > > We're currently looking at changing our Galaxy setup to link user accounts > with Linux user accounts for better cluster integration (running jobs as the > actual user on SGE). A

Re: [galaxy-dev] Python on cluster for setting metadata after jobs complete

Thanks John, On Mon, Jan 25, 2016 at 3:29 PM, John Chilton wrote: > The script generated to call Galaxy is here: > > https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/metadata.py#L838 > > The job template stuff that setups of the environment the job runs

Re: [galaxy-dev] Creating cluster_files_directory (default database/pbs)

this though, I would be happy to > merge this. The best place to ensure this directory exists is in the > drmaa runner where it is being used. > > -John > > > > On Mon, Jan 25, 2016 at 4:20 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: >> On Mon, Jan 25, 2016 at 11:

Re: [galaxy-dev] Python on cluster for setting metadata after jobs complete

On Mon, Jan 25, 2016 at 5:50 PM, John Chilton <jmchil...@gmail.com> wrote: > On Mon, Jan 25, 2016 at 3:44 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: >> Thanks John, >> >> On Mon, Jan 25, 2016 at 3:29 PM, John Chilton <jmchil...@gmail.com> wrote:

[galaxy-dev] Removing set_metadata_externally from wiki documentation?

Hello all, We're currently looking at changing our Galaxy setup to link user accounts with Linux user accounts for better cluster integration (running jobs as the actual user on SGE). As part of this, we've tried setting up a fresh installation on a new VM which has thrown up some issues. First

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

On Wed, Jan 20, 2016 at 2:43 PM, Gildas Le Corguillé wrote: > 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 Great - a pull request against

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

On Wed, Jan 20, 2016 at 9:19 AM, Floreline TOUCHARD wrote: > Hi, > > I would like to add some tools of the EMBOSS suite (6.6.0) to my Galaxy > instance. It seems that the only wrapper available for Galaxy is for the > 5.0.0 version >

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

On Wed, Jan 20, 2016 at 2:22 PM, Floreline TOUCHARD 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

Re: [galaxy-dev] RFC: new

On Friday, 1 January 2016, Björn Grüning wrote: > Hi Galaxy developers, > > this is a RFC to get the implementation details right for a new action > type in `tool_dependencies.xml`. > > Since years we try to save a very crucial sustainability problem: >

[galaxy-dev] samtools bam2fq --> samtools fastq / samtools fasta

Hello all, About a year ago I stated wrapping the "samtools bam2fq" command from samtools v1.1 for use in Galaxy: https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_bam2fq That uncovered a number of bugs in "samtools bam2fq" which have resulted in two new commands "samtools

Re: [galaxy-dev] (no subject)

Hi Justin, You are not alone! Galaxy has limited understanding of column headers in a # line, but there is room for improvement here certainly. I'm sure there are open issues on some/all of these points but Trello is being very slow and the only link I could find in my emails is:

Re: [galaxy-dev] wolfpsort

Hi Olivier, First of all, let's double check what kind of machine you are running, in case that gives us some clues: $ arch $ uname -a Let's double check which Perl you have, $ which perl $ perl -v $ /usr/bin/perl -v NOTE: You have to pipe the input file into this tool, it does not take the

Re: [galaxy-dev] wolfpsort

On Fri, Dec 4, 2015 at 11:19 AM, Olivier CLAUDE wrote: > Hi Peter, > Thanks for all. > > ... > >> >> What happens if you try to do this: >> >> $ cd /path/you/put/wolfpsort >> $ ./runWolfPsortSummary animal >> <~/repositories/pico_galaxy/test-data/four_human_proteins.fasta >>

Re: [galaxy-dev] wolfpsort

On Fri, Dec 4, 2015 at 2:16 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Fri, Dec 4, 2015 at 12:59 PM, Olivier CLAUDE <o.cla...@outlook.fr> wrote: >> Ok i did not saw it. >> I runned it with ./ and it worked fine. It gave me the same answer you gave &

Re: [galaxy-dev] wolfpsort

On Fri, Dec 4, 2015 at 12:59 PM, Olivier CLAUDE wrote: > Ok i did not saw it. > I runned it with ./ and it worked fine. It gave me the same answer you gave > me earlier. > > Olivier Excellent :) So, this matches what I found - as long as I changed to the Wolf PSORT

Re: [galaxy-dev] 3 questions

On Wed, Dec 2, 2015 at 5:07 PM, Olivier CLAUDE wrote: > Hello again, > > > > 1/ > > I managed to find WolfPsort on github. > You mean https://github.com/fmaguire/WoLFPSort ? I can see why Finlay Maguire did that although I'm not 100% sure that is within the licence. In

Re: [galaxy-dev] Unable to up Planemo against latest dev

wrote: > Hi Peter/ John > requirementx.txt already includes the latest version of nose > > nose==1.3.7 > > It is nose that is complaining it does not like the sys,args passed in by > FunctionalTest.py > > Christian > > ____ > F

Re: [galaxy-dev] Unable to up Planemo against latest dev

On Fri, Nov 20, 2015 at 9:59 AM, Christian Brenninkmeijer wrote: > Hi All, > > I am unable to run Planemo against the latest dev branch. > > 1. import twill error > > I was able to fix this by adding to requirements.txt > twill==1.8.0 > lxml==3.5.0 >

Re: [galaxy-dev] Bug when reading in tab seperated files

Hi Christian, I think the "cvs" datatype sniffer should be fixed not to accept tab separated files, to me a clear false positive given Galaxy has a separate "tabular" format for "tsv" files. Also surprisingly the "tabular" datatype does not seem to have a sniff method at all:

Re: [galaxy-dev] Planemo 0.20.0 and xunit

On Tue, Nov 17, 2015 at 2:48 PM, John Chilton wrote: > Thanks for the bug report. Somehow Galaxy isn't installing the > development wheels into the transient Galaxy's virtualenv, I've wiped > out my planemo caches and I can't reproduce this locally. Perhaps unrelated, but I

Re: [galaxy-dev] Tmhmm and signal P

On Fri, Nov 13, 2015 at 11:08 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Fri, Nov 13, 2015 at 10:40 AM, Olivier CLAUDE <o.cla...@outlook.fr> wrote: >> >> Do anybody knows where i can find WolFPSORT? The >> website semms to be down for a while

Re: [galaxy-dev] Tmhmm and signal P

On Fri, Nov 13, 2015 at 10:40 AM, Olivier CLAUDE wrote: > Hello, > > This is working! For signlaP and promoter at least. > Good. > I still got this weird error with tmhmm ("no output from tmhmm") and I can't > figure what's wrong . > The message "no output from tmhmm" is

Re: [galaxy-dev] Tmhmm and signal P

Hi Olivier, On Thu, Nov 12, 2015 at 1:03 PM, Olivier CLAUDE wrote: > Hi Björn! > > I do have signalP 3 , it's installed and on the path. Good. It is a shame that CBS use a proprietary license which forbids redistribution and packaging - otherwise I could have tried to

Re: [galaxy-dev] Tmhmm and signal P

On Thu, Nov 12, 2015 at 4:24 PM, Olivier CLAUDE wrote: > I followed the instuctions given by peter and signalp works with galaxy! > Thanks a lot! > Do I try the same for tmhmm2 and promoter2? > Thanks a lot again! > > Olivier Our notes from installing tmhmm2: TMHMM arrives

Re: [galaxy-dev] atlas 3.10 IUC error

On Tue, Nov 3, 2015 at 6:16 PM, wrote: > Hi Nicola > > It is an i686. Is it a problem ? > > Cheers, > Olivier Currently only for 64bit Linux are pre-compiled binaries used:

Re: [galaxy-dev] search paths for custom tools

The tools using Bioptyhon etc should declare a dependency, see e.g. https://github.com/biopython/galaxy_packages Use a repository_dependencies.xml file declaring this as a dependency, Also, in your tool XML file(s) you must include: biopython That should then trigger Galaxy to

Re: [galaxy-dev] search paths for custom tools

/view/peterjc/align_back_trans Peter On Mon, Oct 26, 2015 at 4:16 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > The tools using Bioptyhon etc should declare a dependency, see e.g. > > https://github.com/biopython/galaxy_packages > > Use a repository_dependenci

Re: [galaxy-dev] search paths for custom tools

On Mon, Oct 26, 2015 at 4:37 PM, Tony Schreiner wrote: > I take it the tool_dependencies.xml file goes in the same directory as the > custom tool xml files are. And as such applies to any of them in this > folder? > > Thanks > Tony They need to be in the same tar-ball

[galaxy-dev] Deleting / deprecating an empty Tool Shed repository?

Hi all, Following the Biopython 1.66 release, I will be creating: https://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_66/ https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_66/ Due to user error and a planemo bug [1], I accidentally created the following on the

Re: [galaxy-dev] Spaces in GenomeSpaces file URLs from genomespace_importer tool

ne of my failed jobs. > I also created a Trello bug submission. > > Regards, > > Marco > > On Wed, Oct 21, 2015 at 10:15 AM, Peter Cock <p.j.a.c...@googlemail.com> > wrote: >> >> Thanks Marco, >> >> OK, that seems to still be part of the Galaxy

Re: [galaxy-dev] Spaces in GenomeSpaces file URLs from genomespace_importer tool

Hi Marco, I'd lay money on the the tool parameter sanitization done in Cheetah intended to avoid any command insertion into the shell command. This can be configured within the tool definition using the tag set:

Re: [galaxy-dev] Developing package wrappers

On Tue, Oct 20, 2015 at 10:01 AM, Tiago Rodrigues Antao wrote: > Hi, > > I am afraid that I might be overlooking something obvious but... > > I am trying to add a few tools to the RAD-Seq portfolio of Galaxy. For > that effect I am designing a few package wrappers. My problem is

Re: [galaxy-dev] blast2html

Hi Juan, It does sounds like something in Galaxy's HTML security code could be to blame... Do you have any other HTML producing tools installed? It would be useful to see how their output behaves. e.g. The BLAST+ tools offer (very simple ugly) HTML output directly. Peter On Thu, Oct 8, 2015 at

Re: [galaxy-dev] Creating R galaxy wrapper where a function checks file extension

Creating symlinks with normal extensions is a common approach here where the Galaxy filenames won't work. Peter On Fri, Oct 2, 2015 at 10:57 AM, Martin Vickers wrote: > > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Hi all, > > I've been tasked with getting someone's R

Re: [galaxy-dev] Creating R galaxy wrapper where a function checks file extension

in action? Is it done > in the xml wrapper somewhere or do I need to write a script that does this > and then call the Rscript? > > Cheers, > > Martin > > On 10/02/2015 11:13 AM, Peter Cock wrote: >> Creating symlinks with normal extensions is a common >> approa

Re: [galaxy-dev] not sure what I can do about this...

On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar wrote: > Hello Björn, > > Thank you for answering! > When I installed Prokka from the Galaxy ToolShed, all the dependencies were > installed too. > tbl2asn is one of those dependencies... > How would I replace it? > >

Re: [galaxy-dev] Advice on Galaxy administration

On Tue, Sep 22, 2015 at 4:38 PM, Raymond Wan <rwan.w...@gmail.com> wrote: > Hi Peter, > > > On Tue, Sep 22, 2015 at 5:18 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: >> Hi Ray, >> >> You will absolutely need command line access to the Galaxy >

Re: [galaxy-dev] Advice on Galaxy administration

Hi Ray, You will absolutely need command line access to the Galaxy server for some of the administration tasks - the web admin controls and web report tool only let you do some of the likely tasks. During the initial setup admin (sudo) rights would be useful, at very least you'll need the sys

Re: [galaxy-dev] Subtleties of and escaping dollar signs

aybe Eric or Björn will find a > couple free hours some day to get that wiki information ported over > :). > > Thanks for the catch Peter, > John > > On Tue, Sep 1, 2015 at 11:43 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: >> Hello all, >> >> I've j

Re: [galaxy-dev] Wiki documentation for tool_dependencies.xml file

at 12:12 PM, Nicola Soranzo <nsora...@tiscali.it> wrote: > Hi Peter, > the page you are looking for is: > > https://wiki.galaxyproject.org/ToolDependenciesTagSets > > I think it should be better linked, I had to bookmark it! > > Cheers, > Nicola > > Il 02.09.2015 1

[galaxy-dev] Renaming pages on the Galaxy wiki

Hi all, I just renamed a page on the wiki to fix a typo: https://wiki.galaxyproject.org/ToolsWitDependenciesInSameRepository now: https://wiki.galaxyproject.org/ToolsWithDependenciesInSameRepository I didn't see any option about setting up a redirection from the old URL (for pages linked to

[galaxy-dev] Wiki documentation for tool_dependencies.xml file

Hi all, Is there a page on the wiki describing the tool_dependencies.xml file syntax? Searching finds pages with examples, e.g. https://wiki.galaxyproject.org/ToolsWithDependenciesInSameRepository https://wiki.galaxyproject.org/ComplexRepositoryDependencies What I am looking for is something

[galaxy-dev] Subtleties of and escaping dollar signs

Hello all, I've just noticed that dollar signs for accessing environment variables must be escaped in the XML tag, but must not be escaped in the tag: https://github.com/peterjc/pico_galaxy/commit/4613a08139a3dfa07c3b0411ac8a91f55deabb74 I presume this is because is parsed as a Cheetah

Re: [galaxy-dev] Switching history doesn't work with prefix

Hello Ping, I can confirm this bug. I noticed this some time back when the new history was in beta, but neglected to explore what was wrong. Apologies. When looking at: http://our_server_name/galaxy/history/view_multiple Via Firefox I can see the switch button is triggering a URL like:

Re: [galaxy-dev] Failure when preparing job on blastp

Hi Peter v H, Which version of Galaxy are you running? Which version of ncbi_blast_tools are you running? (ideally down to the ToolShed revision) My guess is that since this used to be .extra_files_path perhaps your Galaxy is too old for .files_path to work?

Re: [galaxy-dev] Failure when preparing job on blastp

no, its not an old Galaxy. On 21 July 2015 at 17:37, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Peter v H, Which version of Galaxy are you running? Which version of ncbi_blast_tools are you running? (ideally down to the ToolShed revision) My guess is that since this used

Re: [galaxy-dev] Failure when preparing job on blastp

, Peter van Heusden p...@sanbi.ac.za wrote: Previous revision of ncbi_blast_plus works like a charm, thanks. On 21 July 2015 at 19:57, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks Peter, Yes, you are using the latest release published to the Tool Shed, aka v0.1.03 (internal changes

Re: [galaxy-dev] Object-Store, setting filetypes crashes Galaxy

Hello all, This is resurrecting an old thread, but using $input.extra_files_path rather than $input.files_path explained an unfortunate regression in the BLAST+ wrappers reported earlier today: https://github.com/peterjc/galaxy_blast/issues/69 Thanks John for his detective work. Given

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