Re: [galaxy-dev] Multiple select input error after update

] To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ [2] -- Alexandre Defelicibus Mestrando em Bioengenharia Programa de Pós-Graduação em Bioengenharia Universidade de São Paulo - USP -- Nicola Soranzo http://nsoranzo.altervista.org La mia

Re: [galaxy-dev] Question Regarding fetch_eggs c. vs pip

Hi Stephen and Nate, it seems that the problem with the WebError egg is now hitting also BioBlend TravisCI testing: https://travis-ci.org/galaxyproject/bioblend/builds/50391748 Both for Python 2.6 and 2.7, scripts/common_startup.sh fails with: WebError 0.8a couldn't be downloaded

Re: [galaxy-dev] problems splitting

Hi Roberto, I'm happy you solved your issue, thanks for sharing the solution! I'd suggest you open a pull request with the fixes at https://github.com/galaxyproject/galaxy . Cheers, Nicola Il 25.02.2015 15:07 Roberto Alonso CIPF ha scritto: Hello again :), I have found the problem, the

Re: [galaxy-dev] Galaxy for Natural Language Processing

Il 24.04.2015 03:18 Keith Suderman ha scritto: This can be done via the ToolShed. I assume your custom command interpreter is not different than python or perl as interpreter? One difference is that my interpreter is a Java program. I likely should have mentioned that little detail... anyone

Re: [galaxy-dev] Data Libraries

You may just use a different folder for each project inside a Sequencing library. Would that work? Nicola Il 24.04.2015 13:10 Ryan G ha scritto: This could work. In the long run though, after sequencing for a project, we'd like them people in the sequencing lab to be able to add the data to

Re: [galaxy-dev] trinity tool form not allowing None input for strand-specificity

Hi Christian, was the trinityrnaseq tool installed from the Tool Shed? Which repository? Just to check this is not a tool problem. Cheers, Nicola Il 08.05.2015 10:44 Christian Schudoma (TSL) ha scritto: Hi all, I have encountered a problem when trying to run trinityrnaseq (Galaxy Tool

Re: [galaxy-dev] trinity tool form not allowing None input for strand-specificity

.) Thanks Christian On 08/05/15 17:51, Nicola Soranzo wrote: Hi Christian, was the trinityrnaseq tool installed from the Tool Shed? Which repository? Just to check this is not a tool problem. Cheers, Nicola Il 08.05.2015 10:44 Christian Schudoma (TSL) ha scritto: Hi all, I

Re: [galaxy-dev] any working example of auth_conf.xml validating against openldap?

Hi Pablo, thanks for sharing your auth_conf.xml ! I think you may omit the dn from , it should be in the replacement dictionary automatically. I'll try to add something similar to auth_conf.xml.sample . Cheers, Nicola Il 20.05.2015 18:02 Pablo Escobar ha scritto: Hi I reply

Re: [galaxy-dev] package_bowtie_2_2_4 Executable Permissions - can't run bowtie as non-galaxy user

Hi David, can you open an issue at https://github.com/galaxyproject/docker-build ? Thanks, Nicola Il 18.06.2015 21:55 David Trudgian ha scritto: Installed bowtie2 from the toolshed, which brings in package_bowtie_2_2_4, which downloads bowtie binaries from depot.galaxyproject.org

Re: [galaxy-dev] functional tests / database lock

Hi Ryan, there is no know fix for this, apart from moving to PostgreSQL. Cheers, Nicola Il 12.06.2015 16:43 Ryan G ha scritto: Hi all - I'm running functional tests on a set of tools using 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and run the tool tests individually,

Re: [galaxy-dev] picard_MarkDuplicatesWithMateCigar functional test failure

Hi Ryan, please open a pull request at https://github.com/galaxyproject/tools-devteam The file is in tools/picard/ directory. Thanks, Nicola Il 12.06.2015 17:23 Ryan G ha scritto: The functional test for this tool fails. Looking at the XML wrapper, it looks like $comments is invalidit

Re: [galaxy-dev] Hey I got some problems using galaxy... could you help me?..

Hi Yoong, I think your tool is writing its logging messages on stderr, which causes Galaxy to mark the job as failed. I think that adding detect_errors="aggressive" to your should fix it, see https://github.com/galaxyproject/galaxy/pull/117 for details. Cheers, Nicola On 29/10/15 00:24,

Re: [galaxy-dev] Bismark installation dependencies error

Hi Jose, can you check that your release_15.07 is updated and contains git commit 197c7b21b209a7b6fbdb9a8a11c232a2b88523fc ( https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c232a2b88523fc )? Cheers, Nicola On 28/10/15 14:53, Jose Juan Almagro Armenteros wrote:

Re: [galaxy-dev] Bismark installation dependencies error

t;d...@bx.psu.edu <mailto:d...@bx.psu.edu>>: Yes, this is definitely related to the issue I fixed part of, and (I think) Nicola fixed the rest of. - Dave Bouvier http://galaxyproject.org http://usegalaxy.org On 10/28/2015 11:46 AM, Nicola Soranzo wrote:

[galaxy-dev] R: Planemo 0.19.0 testing tools that produce dataset collections

Hi Greg, in the inputs the param has name "input_gff", while in the test you are using name "input". Cheers, Nicola Von Kuster, Greg ha scritto >Hello Galaxy devs, > >I’m developing a tool that uses a multi-select list to accept any number of >input datasets. The tool works fine

Re: [galaxy-dev] atlas 3.10 IUC error

Peter is correct, can you open an issue at https://github.com/galaxyproject/tools-iuc/issues/new and ping @natefoo ? Thanks, Nicola On 03/11/15 18:23, Peter Cock wrote: On Tue, Nov 3, 2015 at 6:16 PM, wrote: Hi Nicola It is an i686. Is it a problem ? Cheers, Olivier

[galaxy-dev] R: Re: FASTQ Groomer tool

he service galaxy restart worked. > >Can you guys give me a small explanation please? > >Just for my understanding… > >  > >Cordialement / Regards, > >Edgar Fernandez > >  > >De : Nicola Soranzo [mailto:nicola.sora...@gmail.com] De la part de Nicola >

Re: [galaxy-dev] Puzzling error in program using Bioblend

Hi Mark, it seems that one dataset in the library (probably /usr/users/fr009/fernande/gal_exports/data/Intro Galaxy Training/Getting_started/NBARC/NB_domains.tabular ) is in 'error' state, so BioBlend, as a precaution, refuses to download it, even if it is possible to download it in Galaxy.

Re: [galaxy-dev] MS Active Directory Authentication

Hi Dwayne, see https://github.com/galaxyproject/galaxy/blob/dev/config/auth_conf.xml.sample ldap is equivalent to activedirectory Something like this may work for you: activedirectory False True ldap://dc1.example.com True

Re: [galaxy-dev] MS Active Directory Authentication

> > Dwayne > > From: Nicola Soranzo [mailto:nicola.sora...@gmail.com] On Behalf Of > Nicola Soranzo > Sent: Tuesday, October 13, 2015 1:44 PM > To: McCully, Dwayne (NIH/NIAMS) [C] <dmccu...@mail.nih.gov>; > galaxy-dev@lists.galaxyproject.org > Subject: Re: [galaxy-

Re: [galaxy-dev] LDAP Auto register - "username is None"

ts How is {username} in auth_config.xml set? Does it parse {email} to get it? Many thanks, Martin On 09/02/2015 03:38 PM, Nicola Soranzo wrote: > Hi Martin, > what LDAP server are you using? We have tested only OpenLDAP and > ActiveDirectory, but should work on any LDAP server. >

Re: [galaxy-dev] LDAP Auto register - "username is None"

he allow-register settings make/ask the user to provide a username rather than trying to auto generate it? or, is there a way to get the username out of the ldap server if it's not using uid to store it? > > Many thanks, > > Martin > > On 09/02/2015 06:09 PM, Nicola Soranzo wr

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

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 12:33 Peter Cock ha scritto: > Hi all, > > Is there a page on the wiki describing the

Re: [galaxy-dev] Renaming pages on the Galaxy wiki

Hi Peter, the wiki uses MoinMoin. As explained in https://moinmo.in/HelpOnProcessingInstructions#A.23redirect you can just create a new page with the old name containing only: #redirect NewWikiPageName I've already done that for the page you moved. Cheers, Nicola Il 02.09.2015 12:28 Peter

Re: [galaxy-dev] LDAP Auto register - "username is None"

Hi Martin, what LDAP server are you using? We have tested only OpenLDAP and ActiveDirectory, but should work on any LDAP server. If it is OpenLDAP, I think you should use: uid,mail ((mail={email})(uid={username})) {uid} More details in:

Re: [galaxy-dev] Galaxy on a Cluster -- Active Directory LDAP configuration

Hi Carlos, we are using Active Directory LDAP for user authentication, which works pretty well, but only the Galaxy user to submit jobs to the LSF cluster queue, so I can't help with the resource tracking. Cheers, Nicola On 21/09/15 20:19, Carlos Lijeron wrote: Everyone, We are setting up

Re: [galaxy-dev] Two instances on different server with only one postgres database ?

Hi Jean-Philippe, it's not clear to me what you are trying to do: are you trying to create a mirrored Galaxy server (same users, same data libraries, same tools, same histories for each user,...) or 2 different Galaxy servers using the same PostgreSQL database *server* as backend? If it's

Re: [galaxy-dev] Error installing tools from toolshed

... but I am still using the mercurial mirror, which says I'm up to date. Would this be a wise time, then, to change over to the Git repository directly? Thanks! Scott On Thu, Nov 19, 2015 at 8:15 PM, Nicola Soranzo <nsora...@tiscali.it <mailto:nsora...@tiscali.it>> wrote:

Re: [galaxy-dev] Error installing tools from toolshed

to:scott.b.szakony...@nd.edu>> wrote: Hi Nicola, Thank you, that's very helpful. I'll switch over to the GitHub repository and get the latest revision, then we'll see if that doesn't solve the problem. Best, Scott On Fri, Nov 20, 2015 at 9:33 AM, Nicola Sora

Re: [galaxy-dev] Error installing tools from toolshed

490.80 Safari/537.36" I'm not 100% sure these are in order... I have multiple web handlers running and the requests get spread out between them. I've tried to order them as best I can. Thanks! Scott On Fri, Nov 20, 2015 at 12:31 PM, Nicola Soranzo <nsora...@tiscali.it <mailto:nso

[galaxy-dev] R: Error installing tools from toolshed

Hi Scott, which Galaxy release are you using? This is a bug which should be fixed in an updated release_15.07 git branch. Cheers, Nicola Scott Szakonyi ha scritto >___ >Please keep all replies on the list by using "reply all"

Re: [galaxy-dev] LDAP authentification

s, Marija -Original Message----- From: Nicola Soranzo [mailto:nicola.sora...@gmail.com] On Behalf Of Nicola Soranzo Sent: Wednesday, June 01, 2016 4:21 PM To: Durdevic, Marija; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] LDAP authentification What is your LDAP server software

Re: [galaxy-dev] LDAP authentification

What is your LDAP server software? OpenLDAP or something else? Cheers, Nicola On 01/06/16 15:14, Durdevic, Marija wrote: No, I got the same error message :( -Original Message- From: Nicola Soranzo [mailto:nicola.sora...@gmail.com] On Behalf Of Nicola Soranzo Sent: Wednesday, June 01

Re: [galaxy-dev] LDAP authentification

ari/537.36" [pid: 23119|app: 0|req: 1/1] 10.17.16.180 () {54 vars in 1146 bytes} [Wed Jun 1 15:13:28 2016] POST /user/login?use_panels=False => generated 5018 bytes in 101 msecs (HTTP/1.1 200) 2 headers in 73 bytes (1 switches on core 0) -Original Message- From: Nicola Soranzo [

Re: [galaxy-dev] Loading or Upload Large datasets into Galaxy History

Hi Amos, please vote for the "Chunked file uploads" issue :) https://github.com/galaxyproject/galaxy/issues/573 Cheers, Nicola On 28/01/16 19:56, Raphenya, Amogelang wrote: Hi All, Is there a faster way to upload or load large datasets into galaxy history without using FTP? I tried

Re: [galaxy-dev] cleanup

Hi Philipp, if you are using Galaxy release 16.01, you should load the virtualenv before running the cleanup script, e.g.: $ cd GALAXY_HOME $ . .venv/bin/activate $ python scripts/cleanup_datasets/cleanup_datasets.py ... Cheers, Nicola On 23/02/16 15:07, Hans-Rudolf Hotz wrote: Hi Philipp

Re: [galaxy-dev] errors installing tool dependencies...

Hi Edgar, this smells like an old fixed bug, what version of Galaxy are you running? Cheers, Nicola On 25/01/16 14:22, Fernandez Edgar wrote: Hello Martin, Thank you! Your instructions for my problem with Perl package worked. For the URL of hmmer, it is wrong and I will report it like you

Re: [galaxy-dev] errors installing tool dependencies...

-343-6111 poste 16568//* *From:*Nicola Soranzo [mailto:nicola.sora...@gmail.com] *On Behalf Of *Nicola Soranzo *Sent:* January-25-16 12:05 PM *To:* Fernandez Edgar <edgar.fernan...@umontreal.ca>; Martin Čech <mar...@bx.psu.edu>; galaxy-...@bx.psu.edu *Subject:* Re: [galaxy-dev] error

Re: [galaxy-dev] Warning: Incorrect datetime value in Galaxy 16.01

Hi Fred, can you please check that you are on the latest commit of the release_16.01 branch? If yes, please open an issue at https://github.com/galaxyproject/galaxy/issues/new specifying which database server you are using and providing a complete traceback from the log file? Thanks a lot

Re: [galaxy-dev] File_path setting not working

Hi Scott, in which subdirectory of database/ are files being created? The only other relevant directive in galaxy.ini should be: #job_working_directory = database/job_working_directory Cheers, Nicola On 06/04/16 21:27, Scott Szakonyi wrote: Hello, I'm trying to set our Galaxy instance to

Re: [galaxy-dev] perl version 5.18.1 repository error

Hi Philipp, can you try to reinstall the tool dependency? Go to the Admin interface, "Manage installed tools", click on the "package_perl_xml_parser_expat_2_41", then from the "Repository Actions" menu select "Manage tool dependencies", select the dependency in error and "Uninstall", then

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

Hi Daniel, I've been using python27 from CentOS Software Collections for quite some time. It's a bit annoying because you have to remember to load it, but it is surely doable. Cheers, Nicola On 21/03/16 17:46, D K wrote: Hi Galaxy Devs, This may be premature but I read that for Galaxy

Re: [galaxy-dev] tmp directory

You can use tmpwatch on RedHat/CentOS/Fedora or tmpreaper on Debian/Ubuntu. Cheers, Nicola On 01/03/16 14:30, Raphenya, Amogelang wrote: Is there a script that is used to clean up database/tmp / / /*Amos Raphenya* / /Bioinformatics Software Developer/ /Department of Biochemistry &

Re: [galaxy-dev] Sandbox repository item says "This revision can be installed: False

Hi Bob, it seems that you uploaded a zip file, but only tar.gz and tar.bz2 archives are supported. Try to create one archive of these types and upload it to the existing repository with the default options. Cheers, Nicola On 01/04/16 18:04, rbrown1...@comcast.net wrote: Good afternoon, I

Re: [galaxy-dev] Tool shed tools, manual dep installation

Hi David, in the server I am administering I don't use the Tool Shed dependency resolver and is not much work if you are used to environment modules. For more information, see: https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html Cheers, Nicola On 13/04/16 16:42, Martin

Re: [galaxy-dev] LDAP not working release 16_01

Hi Mohamed, you need to install python-ldap in your Python virtual environment, e.g.: $ . .venv/bin/activate (.venv)$ pip install python-ldap Cheers, Nicola Mohamed Kassam ha scritto >___ >Please keep all replies on the list

Re: [galaxy-dev] Question: Cannot start local Galaxy after upgrade to v16.01

Hi Daniel, by looking at your traceback, it seems you have a file /opt/galaxy/lib/pkg_resources.py which has been removed in Galaxy 16.01 . To verify that you can execute git status which should print something like: On branch release_16.01 Your branch is up-to-date with

Re: [galaxy-dev] TestToolShed down?

Works for me now. Cheers, Nicola On 28/07/16 09:44, Peter Cock wrote: 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

Re: [galaxy-dev] Remote user auth and API

Hi Sarah! I guess that your problem is with an untrusted certificate, you can get one for free at https://letsencrypt.org/ You can disable certificate verification in bioblend as in the example below: import bioblend.galaxy gi = bioblend.galaxy.GalaxyInstance(url=my_server, key=my_key)

Re: [galaxy-dev] Possible bug in drmaa and Galaxy?

Hi Ray, I don't see anything strange in the Galaxy logs. The job on the cluster "finished normally" just means that it completed its execution without being killed by the cluster scheduler or for other external reasons. The second line in the logs is telling you that Galaxy has seen that the

Re: [galaxy-dev] package_cython_0_20_1

Hi Philipp, I have updated the package on the ToolShed, can you try to update it on your local Galaxy and reinstall the dependency? Cheers, Nicola On 15/07/16 12:24, Rathert, Philipp, Dr. wrote: package_cython_0_20_1 Dear all, I am trying to install package_cython_0_20_1 but I always get

Re: [galaxy-dev] Connecting LDAP with Galaxy

AP servers. On 2016-08-08 09:01, Nicola Soranzo wrote: Hi Miuki, the file config/auth_conf.xml.sample contains examples and documentation of possible values that you have to put in your config/auth_conf.xml , unfortunately a lot depends on what LDAP/Active Directory server you are usi

Re: [galaxy-dev] Connecting LDAP with Galaxy

nd explained myself poorly. >>>>> >>>>> This is actually a very serious problem if one wants to integrate >>>>> Galaxy >>>>> in an existing SSO environment based on LDAP. >>>>> >>>>> Tiago >>>>&g

Re: [galaxy-dev] view details not working

Hi Vincent, what release of Galaxy are you using? It should be fixed by https://github.com/galaxyproject/galaxy/pull/2312 , which is available in latest release_16.01 and following. Cheers, Nicola On 08/08/16 14:58, Vincent Cahais wrote: Dear all, I have a very strange bug on my galaxy

Re: [galaxy-dev] problems with 'action type="metadata" name="dbkey"' in tool xml

Hi Hans, see my comment below. On 16/08/16 09:51, Hans-Rudolf Hotz wrote: Dear All I am trying to move our Galaxy installation to new hardware and at the same time to a new version (the original is "15.10",minor version "2" via mercurial; the new is "16.04" via github): So far, I am

Re: [galaxy-dev] problems with 'action type="metadata" name="dbkey"' in tool xml

I've tested bowtie_wrapper on Galaxy release_16.04: type="from_data_table" name="bowtie_indexes" column="1" offset="0"> works fine for me. Cheers, Nicola On 16/08/16 11:42, Nicola Soranzo wrote: Forget about my previous comment, I should have read you

Re: [galaxy-dev] problems with 'action type="metadata" name="dbkey"' in tool xml

. Cheers, Nicola On 16/08/16 11:29, Nicola Soranzo wrote: Hi Hans, see my comment below. On 16/08/16 09:51, Hans-Rudolf Hotz wrote: Dear All I am trying to move our Galaxy installation to new hardware and at the same time to a new version (the original is "15.10",minor version "2

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

Hi Peter, adding version="1.0.1">galaxy_sequence_utils to each of these tools should solve the problem, there is a Bioconda package which provides the Python library: https://anaconda.org/bioconda/galaxy_sequence_utils Cheers, Nicola On 31/01/17 10:39, Peter Cock wrote: Hi all, A few of

Re: [galaxy-dev] Resource temporarily unavailable

Hi Marija, you can try to set retry_job_output_collection = 3 in your config/galaxy.ini file and see if that helps. Cheers, Nicola On 23/01/17 09:47, Durdevic, Marija wrote: Dear developers, From time to time I have issue on my Galaxy server. The problem is when job is done and results

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

Hi Mohamed, the lib/galaxy/auth/ folder is not new at all, there seems to be a problem in your config/auth_conf.xml , what do you have inside ? Cheers, Nicola On 24/02/17 08:56, Mohamed Kassam wrote: Dear Gildas, Thanks for your message. So I 've tried and it recretaed a new .venv.

Re: [galaxy-dev] my.galaxy/toolshed bioblend or install_tool_shed_tools swallows toolshed

Hi Ido, your analysis is correct, this is what the BioBlend documentation prescribes: https://bioblend.readthedocs.io/en/latest/api_docs/galaxy/all.html#bioblend.galaxy.GalaxyInstance Cheers, Nicola Tamir,Ido ha scritto >It only works when specifying the url like this (http +

Re: [galaxy-dev] Authentication issue

Hi Mohamed, - what Galaxy release are you using? - what LDAP server are you using? - how did you configured LDAP auth? remote user or using config/auth_conf.xml Cheers, Nicola On 15/09/16 18:27, Mohamed Kassam wrote: Dear all I have an issue today, with authentication in our galaxy instance.

Re: [galaxy-dev] planemo test with

I've also tried putting these files under galaxy-test/tool-data, test-data, etc... and that didn't help either. I'm not understanding what I'm doing wrong here. Any additional suggestions would be appreciated. Thanks! On Fri, Oct 7, 2016 at 3:26 AM, Nicola Soranzo <nsora...@tiscali

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

Hi Edgar, presently the Prokka wrapper requires some dependencies (in particular some Perl modules) to be installed separetely, see the README file at https://toolshed.g2.bx.psu.edu/view/crs4/prokka/ We are planning to release an updated Prokka wrapper which will use Conda dependencies, you

Re: [galaxy-dev] planemo test with

Hi D K, for a good example of how to test parameters from data tables, please see: https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers Your tool_data_table_conf.xml.test should be different from your .sample and contain: Please note the use of ${__HERE__} to

Re: [galaxy-dev] liftOver output database error

Hi Sarah, this problem has been fixed yesterday in release_16.04 and following with https://github.com/galaxyproject/galaxy/pull/2800 . Cheers, Nicola On 18/08/16 14:24, Sarah DIEHL wrote: Dear all, I just ran the liftOver tool that comes with Galaxy

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

Hi Peter, why not use BioBlend? 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 link there but it wasn't obvious to me. >Reading the

Re: [galaxy-dev] Install error of package_bioconductor_limma_3_28_10

Hi Alexandre, thanks for your email! Can you please open an issue for this at https://github.com/galaxyproject/tools-iuc/issues/new ? Cheers, Nicola On 03/10/16 15:37, Alexandre Defelicibus wrote: Hi all, I got this error when I tried to install the package

Re: [galaxy-dev] R dependency problems with readline libraries

I suppose this is the same as https://github.com/galaxyproject/tools-devteam/issues/100 , just for a different R version. Cheers, Nicola On 03/10/16 20:10, Nikolaos Tur wrote: Hi, installation of deseq2 1.10.0 causes next problem:

Re: [galaxy-dev] Cannot start Galaxy DistributionNotFound: Paste

Hi Hernán, the bitbucket repository has been abandoned and so the code you are using is not maintained any more, please get it with git from https://github.com/galaxyproject/galaxy More information are on the wiki: https://wiki.galaxyproject.org/Admin/GetGalaxy Cheers, Nicola On 27/10/16

Re: [galaxy-dev] galaxy venv problem

Hi, you can read extensive documentation about the Galaxy framework dependencies here: https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html As a general advice, I would recommend to keep the framework dependencies separated from the tool dependencies. For the tool

Re: [galaxy-dev] filter options

Hi Vincent, have you defined the dbindel table in config/tool_data_table_conf.xml ? Cheers, Nicola On 04/11/16 08:09, Vincent Cahais wrote: Dear All, I try to filter options for a param linked to a datatable. I want to keep only options with the same dbkey as my input file. But i cannot make

Re: [galaxy-dev] conda management of tools dependent on python3

Hi Wolfgang, I guess that the conda recipe should be updated to also specify - python >=3 in the requirements. Cheers, Nicola On 03/11/16 21:04, Wolfgang Maier wrote: I'm not quite sure if I understand you correctly, but let's see. The original tool wrapper stated python3 as a dependency.

Re: [galaxy-dev] Galaxy Security Vulnerability - Arbitrary code execution

Thanks David, the issue has been already reported, see https://github.com/galaxyproject/galaxy/issues/3332 , hopefully someone from the Galaxy Team will look into this soon. You can get the patch from GitHub in the mean time, it has been applied to all branches starting from release_14.10 .

Re: [galaxy-dev] openms python3 & print

Hi Matthias, I think you're using an old version of the tool, the one at https://toolshed.g2.bx.psu.edu/view/galaxyp/openms_decoydatabase/178e00cf12d7 doesn't use a Python wrapper. The development repository is at https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms

Re: [galaxy-dev] Issue with SLURM-DRMAA

Hi Gwen, thanks for reporting this issue! You are correct and similar problems have been reported frequently on the mailing list and on Gitter/IRC. If you go to https://galaxyproject.org/admin/config/performance/cluster/ and click on the "Edit" button, you can modify the page yourself on

Re: [galaxy-dev] Issue with GATK2 on Galaxy Repository.

Hi, which version of GATK are you using? From your email it seems you may be using GATK3, which is not supported by the Galaxy GATK2 wrappers. Cheers, Nicola On 31/05/17 04:36, OLABODE OLUWASEUN AJAYI wrote: Hi Dev, I am running a local instance Galaxy for developing a variant calling

Re: [galaxy-dev] AD Intergration

On 08/06/17 16:36, Hans-Rudolf Hotz wrote: Hi John I am trying to integrate AD with Galaxy. My auth_config.xml look like the below, but galaxy won't start with those setting. what error do you get in the log? activedirectory This should be "ldap", shouldn't-it? Actually

Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Hi Edgar, Frederic, if you are using Apache as proxy for your Galaxy server, then you should probably add |AllowEncodedSlashes NoDecode| to your Apache config, see https://galaxyproject.org/admin/config/apache-proxy/#allow-encoded-slashes-in-urls Cheers, Nicola On 15/06/17 15:35, SAPET,

Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

Soranzo [mailto:nicola.sora...@gmail.com] *On Behalf Of *Nicola Soranzo *Sent:* June 15, 2017 10:44 AM *To:* SAPET, Frederic <frederic.sa...@biogemma.com>; Fernandez Edgar <edgar.fernan...@umontreal.ca>; galaxy-...@bx.psu.edu *Subject:* Re: [galaxy-dev] new installation galaxy-17.0

Re: [galaxy-dev] new installation galaxy-17.05 - Uncaught error.

? I use the Apache proxy since a while without any problem, with previous versions of Galaxy. Regards, Fred *De :*Nicola Soranzo [mailto:nicola.sora...@gmail.com] *De la part de* Nicola Soranzo *Envoyé :* jeudi 15 juin 2017 16:44 *À :* SAPET, Frederic <frederic.sa...@biogemma.com>; Fer

Re: [galaxy-dev] the future of trackster - was: galaxy-dev Digest, Vol 136, Issue 8

According to the website, only UCSC Genome Browser and Blat require a commercial license. Cheers, Nicola On 17/10/17 15:50, Hans-Rudolf Hotz wrote: Hi Matthias No, the twobit-files are not mandatory for trackster. They are only required if you want to zoom into the nucleotide level. Also,

Re: [galaxy-dev] unipept visualization

On 31.08.2017 17:39, Nicola Soranzo wrote: Hi Matthias, that should be fixed on dev already by pull request: https://github.com/galaxyproject/galaxy/pull/4522 Cheers, Nicola On 31/08/17 16:30, Matthias Bernt wrote: Hi Sam, I tried on 17.05 and dev without any success. Any idea where I could

Re: [galaxy-dev] unipept visualization

Hi Matthias, that should be fixed on dev already by pull request: https://github.com/galaxyproject/galaxy/pull/4522 Cheers, Nicola On 31/08/17 16:30, Matthias Bernt wrote: Hi Sam, I tried on 17.05 and dev without any success. Any idea where I could start debugging? Best, Matthias On

Re: [galaxy-dev] Active Directory Authentication question

79-4201 halmabr...@sidra.org <mailto:halmabr...@sidra.org> *|*www.sidra.org <http://www.sidra.org/> Description: C:\Users\fgenevieve\AppData\Local\Microsoft\Windows\Temporary Internet Files\Content.Outlook\O53SYTUP\Sidra-Logo-Member of QF Short.PNG *From:*Nicola Soranzo [mai

Re: [galaxy-dev] Active Directory Authentication question

Hi Hakeem, a couple of suggestions: - allow-register should be False - I don't see a line with something like ldap://dc1.example.com , but I suppose you have omitted it - if your AD server doesn't allow anonymous searches (like in my case), you need to specify also:

Re: [galaxy-dev] Tool to download galaxy datasets locally

: Directory prefix cannot be empty Nicola Soranzo wrote: Hi Evan, you can have a look at https://toolshed.g2.bx.psu.edu/view/earlhaminst/export_to_cluster/ <https://toolshed.g2.bx.psu.edu/view/earlhaminst/export_to_cluster/b97775e9fe06> Hope that helps! Cheers, Nicola On 27/03/18 16:03

[galaxy-dev] ELIXIR Workshop for Galaxy training material and skills improvement

onsored by ELIXIR-UK and the ELIXIR Training Platform. Registration closes soon, hurry up! https://www.eiseverywhere.com/galaxy We look forward to seeing many of you in Norwich! Nicola -- Nicola Soranzo, Ph.D. Data Infrastructure & Algorithms group Earlham Institute Norwich Research Park, N

Re: [galaxy-dev] Galaxy Cleanup

See also: https://galaxyproject.github.io/training-material/topics/admin/tutorials/monitoring-maintenance/slides.html Cheers, Nicola On 27/04/18 15:05, Hans-Rudolf Hotz wrote: Hi Christopher It depends on the setting of "cleanup_job" ('always', 'onsuccess', 'never'), whether the temporary

Re: [galaxy-dev] problem with Visualization 'Scatterplot' in 18.05

Dear Hans-Rudolf, I think this is being worked on at https://github.com/galaxyproject/galaxy/pull/6297 . Cheers, Nicola On 08/06/18 14:57, Hans-Rudolf Hotz wrote: just adding a little bit more information:  - this problem happens independent of using paste or uwsgi  - as far as I have

Re: [galaxy-dev] bam_to_bigwig invalid syntax error

Hi Marco, this tool has not been updated recently and it still uses tool_dependencies.xml for its dependencies. You can choose among 3 options (in order of my personal preference): - add a new requirement for Python2 to the tool bam_to_bigwig.xml file:   python   and reinstall the Conda

Re: [galaxy-dev] Ballgown does not work

Hi Jochen, Theo also opened a pull request to submit it to IUC: https://github.com/galaxyproject/tools-iuc/pull/1366 but hasn't updated it after August 2017. Cheers, Nicola On 10/04/18 14:37, Jochen Bick wrote: Hej Peter, thanks for the quick reply. My galaxy is a release_17.05 I think the

Re: [galaxy-dev] fonts on headless compute nodes

Hi Matthias, if you add  'openjdk >8.0.121' to your conda command below, you should get openjdk from conda-forge. For an explanation, see: https://github.com/bioconda/bioconda-recipes/pull/8588 https://github.com/conda/conda/issues/6948#issuecomment-369360906 Cheers, Nicola On 25/04/18

Re: [galaxy-dev] Tool to download galaxy datasets locally

Hi Evan, you can have a look at https://toolshed.g2.bx.psu.edu/view/earlhaminst/export_to_cluster/ Hope that helps! Cheers, Nicola On 27/03/18 16:03, evan clark wrote: Has anyone attempted to write a tool that

Re: [galaxy-dev] Fastq.gz datatype not recognized on import to data library

Hi Christopher, can you please submit an issue for this at https://github.com/galaxyproject/galaxy/issues/ with the relevant logs and/or tracebacks? Cheers, Nicola On 03/12/2018 13:33, Previti wrote: Dear all, In my ongoing saga concerning our data libraries, I came across another issue

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

Hi Peter, if you open the page for data_manager_shapeit_reference in the test ToolShed you will see that revision 5 and 6 are not installable, they both have "*This revision can be installed:* False" . If you instead select revision 3 it is installable. Cheers, Nicola On 17/09/18 11:51,

[galaxy-dev] Re: galaxy not running after galaxy.yml changes

Hi Jochen, try with: make config-validate Cheers, Nicola On 10/05/2019 09:13, Jochen Bick wrote: > Hej Nate, > > thx for your email. We did not touch that file. Maybe we just have a > corrupted yml file? Is there a good way to check (lint) that file? > > Cheers Jochen > > On 09.05.19 19:56,