Re: [galaxy-dev] Tool Tests failing with Exception: History in error state.

2015-01-30 Thread Nicola Soranzo
Hi Peter, I was also getting Exception: History in error state errors with BioBlend continuous integration testing, but those seem to be fixed with latest Dannon's commit 3618b7a91e23096ecf7ce5842c1e16c749251a4d . Nicola Il 30.01.2015 17:36 Peter Cock ha scritto: Retitling thread, On

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

2015-01-15 Thread Nicola Soranzo
] 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

2015-02-12 Thread Nicola Soranzo
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

2015-02-13 Thread Nicola Soranzo
Il 13.02.2015 03:17 Peter Cock ha scritto: Hi Roberto, It looks like this is a known issue with FASTQ splitting, https://trello.com/c/qRHLFSzd/1522-issues-with-tasked-jobs-parallelism I originally broke it during a refactor, but it looks like the discussion died about that that method was

Re: [galaxy-dev] problem with latest toolshed devteam cuffmerge wrapper multi-select

2015-02-20 Thread Nicola Soranzo
Hi Nikhil, I would suggest to open an issue on https://github.com/galaxyproject/tools-devteam/issues Best, Nicola Il 20.02.2015 10:28 Nikhil Joshi ha scritto: So I am doing some debugging and it looks like in the from_html function in the SelectToolParameter class, it gets the legal values

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

2015-02-12 Thread Nicola Soranzo
/) is what was causing the weird egg fetching errors.  Newer versions of pkg_resources create a mangled distribution string for some eggs with nonstandard version identifiers. On Thu Feb 12 2015 at 6:44:29 AM Nicola Soranzo nsora...@tiscali.it wrote: Hi Stephen and Nate, it seems

Re: [galaxy-dev] problems splitting

2015-02-25 Thread Nicola Soranzo
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] tophat error

2015-02-24 Thread Nicola Soranzo
Il 24.02.2015 10:19 Björn Grüning ha scritto: Am 24.02.2015 um 10:03 schrieb Peter Cock: On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon wrote: The main problem for me was that I was not aware that the tophat tool had a dependency on a command line tool outside of galaxy installation. I see

Re: [galaxy-dev] Importing file via FTP can silently fail, [Errno ftp error] 550

2015-02-26 Thread Nicola Soranzo
Il 26.02.2015 15:57 Peter Cock ha scritto: On Thu, Feb 26, 2015 at 2:24 PM, John Chilton wrote: Yeah - that is unfortunate - I agree completely that the resulting datasets should be red. I have created a Trello card here: https://trello.com/c/A6LrdjUU [1] -John Thanks John, Does the new

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

2015-04-24 Thread Nicola Soranzo
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

2015-04-24 Thread Nicola Soranzo
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

2015-05-08 Thread Nicola Soranzo
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

2015-05-08 Thread Nicola Soranzo
.) 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?

2015-05-20 Thread Nicola Soranzo
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

2015-06-19 Thread Nicola Soranzo
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] Login problem with Galaxy instance

2015-06-16 Thread Nicola Soranzo
Hi Efthymios, have you tried to delete the cookies in the browser? That may fix the problem. Cheers, Nicola Il 16.06.2015 17:46 Makis Ladoukakis ha scritto: Hi I have some experience with setting up Galaxy instances but I came across a very peculiar issue when trying to setup the newest

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

2015-06-12 Thread Nicola Soranzo
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

2015-06-12 Thread Nicola Soranzo
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] BioBlend Dependency Issues

2015-06-11 Thread Nicola Soranzo
Hi, I'd suggest you to try to run Galaxy in a virtualenv: $ cd galaxy/ $ virtualenv .venv $ ./run.sh Cheers, Nicola Il 11.06.2015 19:51 Medini Annavajhala ha scritto: Hi All, Trying to install Galaxy via instructions online and having issues with fetching the eggs. Very similar issue to

Re: [galaxy-dev] LSF cluster wierd behaviours!

2015-08-04 Thread Nicola Soranzo
Il 04.08.2015 07:57 Hakeem Almabrazi ha scritto: Hello everyone, I was able to setup galaxy to work with our HPC cluster using the LSF scheduler. So far so good except with few exceptions: ... 3. Finally, how do I control the resources (i.e cores for a job ) given to a submitted job on

Re: [galaxy-dev] LSF cluster wierd behaviours!

2015-08-04 Thread Nicola Soranzo
? Thank you, -Original Message- From: Nicola Soranzo [mailto:nsora...@tiscali.it [1]] Sent: Tuesday, August 04, 2015 2:23 PM To: Hakeem Almabrazi Cc: galaxy-dev@lists.galaxyproject.org [2]Subject: Re: [galaxy-dev] LSF cluster wierd behaviours! Il 04.08.2015 07:57 Hakeem Almabrazi ha

Re: [galaxy-dev] LSF cluster wierd behaviours!

2015-08-04 Thread Nicola Soranzo
=nativeSpecification-n 32 -R span[hosts=1]/param /destination /destinations /job_conf Regards, Hak FROM: Nicola Soranzo [mailto:nsora...@tiscali.it] SENT: Tuesday, August 04, 2015 2:37 PM TO: Hakeem Almabrazi CC: galaxy-dev@lists.galaxyproject.org SUBJECT: RE: [galaxy-dev] LSF cluster

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

2015-10-29 Thread Nicola Soranzo
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

2015-10-28 Thread Nicola Soranzo
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

2015-10-28 Thread Nicola Soranzo
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

2015-11-04 Thread Nicola Soranzo
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

2015-11-03 Thread Nicola Soranzo
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

Re: [galaxy-dev] FASTQ Groomer tool

2015-11-05 Thread Nicola Soranzo
Hi Edgar, you can try to restart Galaxy (both web and handler processes) and re-run the tool. Cheers, Nicola On 05/11/15 19:18, Fernandez Edgar wrote: Hello again, I installed today the tool : fastq_all_to_sanger I get the same SQL error with that one too. Any ideas guys? Thank you!!!

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

2015-11-05 Thread Nicola Soranzo
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

2015-10-08 Thread Nicola Soranzo
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

2015-10-13 Thread Nicola Soranzo
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

2015-10-13 Thread Nicola Soranzo
> > 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"

2015-09-02 Thread Nicola Soranzo
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"

2015-09-03 Thread Nicola Soranzo
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

2015-09-02 Thread Nicola Soranzo
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

2015-09-02 Thread Nicola Soranzo
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"

2015-09-02 Thread Nicola Soranzo
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] not sure what I can do about this...

2015-09-29 Thread Nicola Soranzo
On 29/09/15 15:24, Peter Cock wrote: Nicola - once that's done, can you update the prokka dependency list - or would that fall to your old colleagues at CRS4? https://toolshed.g2.bx.psu.edu/view/crs4/prokka/ Peter I can update prokka, no problem. Just let me know when the new

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

2015-09-24 Thread Nicola Soranzo
. Thanks again ! Carlos From: Nicola Soranzo <nicola.sora...@gmail.com <mailto:nicola.sora...@gmail.com>> on behalf of Nicola Soranzo <nsora...@tiscali.it <mailto:nsora...@tiscali.it>> Date: Tuesday, September 22, 2015 at 6:59 AM To: Carlos Lijeron <clije...@hun

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

2015-09-22 Thread Nicola Soranzo
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 ?

2015-12-09 Thread Nicola Soranzo
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

2015-11-20 Thread Nicola Soranzo
... 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

2015-11-20 Thread Nicola Soranzo
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

2015-11-20 Thread Nicola Soranzo
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

2015-11-19 Thread Nicola Soranzo
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

2016-06-02 Thread Nicola Soranzo
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

2016-06-01 Thread Nicola Soranzo
Hi Marija, LDAP authentication is usually quite site-specific, config/auth_conf.xml.sample contains example and documentation that should help you, but you still need to know the necessary details about how LDAP authentication works on your network, e.g. LDAP type (OpenLDAP or MS Active

Re: [galaxy-dev] LDAP authentification

2016-06-01 Thread Nicola Soranzo
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

2016-06-01 Thread Nicola Soranzo
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] Trimmomatic Tool dependency installation issue

2016-01-28 Thread Nicola Soranzo
Hi Brian, what release of Galaxy are you using? If it's release_15.07 or earlier from Bitbucket, please move to GitHub and update to the latest release_15.07 or (better) to release_15.10 . For more information, read this thread:

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

2016-01-28 Thread Nicola Soranzo
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] Picard tools don't include CreateSequenceDictionary?

2016-02-01 Thread Nicola Soranzo
Hi Scott, it seems that devteam's picard repository in the Tool Shed ( https://toolshed.g2.bx.psu.edu/view/devteam/picard/ ) does not have a tool for this, but 4 tools include an automatic conversion of a FASTA dataset using CreateSequenceDictionary: BedToIntervalList, MergeBamAlignment,

Re: [galaxy-dev] cleanup

2016-02-23 Thread Nicola Soranzo
this in the specific container but how exactly? Thanks a lot for your help. Cheers, Philipp ---Philipp on the road--- Am 23.02.2016 um 16:20 schrieb Nicola Soranzo <nsora...@tiscali.it <mailto:nsora...@tiscali.it>>: Hi Philipp, if you are using Galaxy release 16.01, you should lo

Re: [galaxy-dev] cleanup

2016-02-23 Thread Nicola Soranzo
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...

2016-01-25 Thread Nicola Soranzo
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...

2016-01-25 Thread Nicola Soranzo
-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

2016-03-29 Thread Nicola Soranzo
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

2016-04-07 Thread Nicola Soranzo
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

2016-03-23 Thread Nicola Soranzo
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

2016-03-21 Thread Nicola Soranzo
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

2016-03-01 Thread Nicola Soranzo
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

2016-04-01 Thread Nicola Soranzo
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

2016-04-13 Thread Nicola Soranzo
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] wheels.galaxyproject.org

2016-05-24 Thread Nicola Soranzo
It's a general problem: https://github.com/galaxyproject/galaxy/issues/2399 Cheers, Nicola On 24/05/16 16:10, Patrice Dehais wrote: Hello Since yesterday I've the following warning at Galaxy () start-up : Retrying (Retry(total=4, connect=None, read=None, redirect=None)) after connection

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

2016-05-17 Thread Nicola Soranzo
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] Tool shed tools, manual dep installation

2016-04-14 Thread Nicola Soranzo
ed. > >  > >Thanks again for the pointer to that! > >  > >DT > >  > >-- >David Trudgian Ph.D. >Computational Scientist, BioHPC > >Lyda Hill Department of Bioinformatics >UT Southwestern Medical Center >Dallas, TX 75390-9039 >Tel: (214) 648-4833 > > 

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

2016-04-19 Thread Nicola Soranzo
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?

2016-07-28 Thread Nicola Soranzo
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

2016-08-01 Thread Nicola Soranzo
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?

2016-08-02 Thread Nicola Soranzo
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

2016-07-15 Thread Nicola Soranzo
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] view details not working

2016-08-08 Thread Nicola Soranzo
f28fc1e7442b53f925db Merge: 7c94ac8 5aefe1b Author: Martin Cech <cech.mar...@gmail.com> Date: Wed Apr 20 15:22:20 2016 -0400 Merge pull request #2206 from dannon/master Sanity check of master update. Le 08/08/2016 à 16:14, Nicola Soranzo a écrit : Hi Vincent, what relea

Re: [galaxy-dev] Connecting LDAP with Galaxy

2016-08-08 Thread Nicola Soranzo
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 using and how it is configured. You may need to ask advice to the

Re: [galaxy-dev] Connecting LDAP with Galaxy

2016-08-08 Thread Nicola Soranzo
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

2016-08-08 Thread Nicola Soranzo
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] External user auth and API

2016-08-08 Thread Nicola Soranzo
galaxy-dev-boun...@lists.galaxyproject.org <mailto:galaxy-dev-boun...@lists.galaxyproject.org>> on behalf of Sarah DIEHL <sarah.di...@uni.lu <mailto:sarah.di...@uni.lu>> Date: Monday 1 August 2016 13:06 To: Nicola Soranzo <nsora...@tiscali.it <mailto:nsora...@tiscali.it>>, &qu

Re: [galaxy-dev] view details not working

2016-08-08 Thread Nicola Soranzo
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

2016-08-16 Thread Nicola Soranzo
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

2016-08-16 Thread Nicola Soranzo
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

2016-08-16 Thread Nicola Soranzo
. 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?

2017-01-31 Thread Nicola Soranzo
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] Tools using Galaxy's Python library?

2017-01-31 Thread Nicola Soranzo
es.xml files: I still need to work out how best to make this available under TravisCI, given I am not currently using BioConda for the dependencies. @IUC: Should this also be released on PyPI for easy install via pip? Peter On Tue, Jan 31, 2017 at 11:15 AM, Ni

Re: [galaxy-dev] Resource temporarily unavailable

2017-01-23 Thread Nicola Soranzo
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

2017-02-24 Thread Nicola Soranzo
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

2016-08-31 Thread Nicola Soranzo
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

2016-09-15 Thread Nicola Soranzo
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

2016-10-07 Thread Nicola Soranzo
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

2016-10-07 Thread Nicola Soranzo
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

2016-10-07 Thread Nicola Soranzo
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

2016-08-18 Thread Nicola Soranzo
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?

2016-08-29 Thread Nicola Soranzo
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

2016-10-03 Thread Nicola Soranzo
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

2016-10-03 Thread Nicola Soranzo
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

2016-10-27 Thread Nicola Soranzo
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

2016-10-31 Thread Nicola Soranzo
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

2016-11-04 Thread Nicola Soranzo
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

2016-11-04 Thread Nicola Soranzo
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

2016-12-19 Thread Nicola Soranzo
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

2017-08-10 Thread Nicola Soranzo
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

2017-06-28 Thread Nicola Soranzo
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

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