July 2015 - galaxy-dev - lists.galaxyproject.org

Bug on current history when using prefix in galaxy input file
by Ata Roudgar 30 Jul '15

30 Jul '15

Hi, I am using the most recent version of Galaxy. There seems to be a bug in viewing the current (active) history when I use prefix in galaxy input file. Here is the detail: When I do not use prefix, e.g., in /config/galaxy.in : prefix = / cookie_path = / and run galaxy server, I can upload a file and I can see my uploaded file in the current history even after I refresh the web browser (e.g., close and reopen the web browser) which seems to be working fine. However when I use prefix, e.g. in /config/galaxy.in : prefix = /galaxy-1/ cookie_path = /galaxy-1/ then after I upload a file and refresh the browser I do not see the uploaded file in the current (or active) history. It always shows me a new (clean history). This is a problem because I get a error which seems to be related to the history when I attempt to run any workflow. Any idea where the problem should be? Please note that I use external authentication but it shouldn't be matter because it is working when the prefix is "/". Thanks a lot, Cheers, Ata ---- Ata Roudgar Research Computing WestGrid Site IT Services Simon Fraser University Burnaby, British Columbia Canada V5A 1S6 phone: 778 782-8860 fax: 778 782-4242

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Problems installing pbs_python from scramble.
by Zuzanna K. Filutowska 30 Jul '15

30 Jul '15

Hello All, I am trying to setup job submission to pbs server running on our cluster. I have python 2.7 installed in /usr/local along with easy_install. But when trying to compile pbs_python I am getting following error: [galaxy@galaxy galaxy-dist]$ LIBTORQUE_DIR=/usr/lib python scripts/scramble.py -e pbs_python fetch_one(): Trying to fetch: http://eggs.galaxyproject.org/pbs_python/pbs_python-4.3.5.tar.gz fetch_one(): Fetched to: /home/galaxy/galaxy-dist/scripts/scramble/archives/pbs_python-4.3.5.tar.gz unpack_source(): Unpacked to: /home/galaxy/galaxy-dist/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python copy_build_script(): Using build script /home/galaxy/galaxy-dist/scripts/scramble/scripts/pbs_python.py run_scramble_script(): Beginning build run_scramble_script(): Executing in /home/galaxy/galaxy-dist/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python: /home/galaxy/galaxy-python/python scramble.py Traceback (most recent call last): File "scramble.py", line 14, in <module> from scramble_lib import * File "../../../lib/scramble_lib.py", line 146, in <module> from setuptools import * File "build/bdist.linux-x86_64/egg/setuptools/__init__.py", line 11, in <module> File "build/bdist.linux-x86_64/egg/setuptools/extension.py", line 8, in <module> File "build/bdist.linux-x86_64/egg/setuptools/dist.py", line 21, in <module> AttributeError: 'module' object has no attribute 'packaging' Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 210, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for pbs_python 4.3.5 I also tried setuptools-18.0.1 installed in user's local path but I am still getting the same error. It is Centos 6.6 OS. Any help would be appreciated. -- Regards, -- Zuzanna K. Filutowska, HPC Systems Administrator Poznan Supercomputing and Networking Center Institute of Bioorganic Chemistry Polish Academy of Sciences Seize the day boys! Make your lifes extraordinary! --John Keating

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Setting up Galaxy without e-mail
by Raymond Wan 29 Jul '15

29 Jul '15

Dear all, I just started setting up a galaxy instance and I'm a bit stuck with user account activation without e-mail. Is it possible to run Galaxy without an SMTP server set? For example, for the administrator user, I set: admin_users = <my e-mail> in galaxy.ini . I'd also like to require login (i.e., require_login = True) but it seems that I can't do that from the outset. That has to be False and allow_user_creation has to be True. Then I can create a user with the same account as above, who will then become an administrator. But, the account has to be validated some how and I can't seem to figure out how to do that without enabling an SMTP server. Am I doing something that wasn't intended? Perhaps I must have an SMTP server set? Or are there other steps I should do to activate the administrator? The web page https://wiki.galaxyproject.org/Admin/GetGalaxy makes it look easy...so I am concerned I'm doing it all wrong... Also, if this instance will be a production system some day, should I start using a database (Postgres or MySQL) right away and not bother with the default SQLite? Otherwise, I will have to port the data over, which the documentation implies is not an easy thing to do... Thank you! Ray

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tool with multiple undefined output datasets
by Sabrina Legoueix Rodriguez 29 Jul '15

29 Jul '15

Hi, I am trying to develop a tool to untar, unzip... an archive file in order to obtain each file contained in the archive as a dataset in the current history. My problem is about the unknown various number of files contained within the archive file. I was thinking about having an output variable in my .xml that would be fed by my wrapper and returned in order to filter the number of outputs in my .xml ; but the <output> section in the .xml can only get "files" not numbers, right? In my tool, I ask the user to fill the number of files he wants from the archive ; in .xml I have put 10 outputs for files contained in the archive (out1, out2...) precised in my command and in the output section (for now I can retrieve maximum 10 outputs from my archive). In the output section, I would like to use <filter> tag in order to select only the output number inferior than the number specified by the user: <outputs> <data name="output_uncomp1" format="${uncompressed_files_format}" label="${input_compressed.name}_1"/> <data name="output_uncomp2" format="${uncompressed_files_format}" label="${input_compressed.name}_2"> <filter>num_uncompressed_files >= "2"</filter> </data> <data name="output_uncomp3" format="${uncompressed_files_format}" label="${input_compressed.name}_3"> <filter>num_decompressed_files>= "3"</filter> </data> It does not seem to work well. Could you please tell me if it is possible to use the filter tag as such? If so, how? Would you have a better idea to implement that tool? Thanks in advance, best regards, -- Signature e-mail TWB Sabrina *Attention changement de coordonnées à partir du 15 Juin 2015:* **Sabrina LEGOUEIX RODRIGUEZ** Responsable Plateau Bioinformatique Tél. : +33 (0) 5 61 28 57 92 sabrina.legoueix(a)toulouse.inra.fr <mailto:[MAIL]> www.toulouse-white-biotechnology.com <http://www.toulouse-white-biotechnology.com/> LinkedIn <https://www.linkedin.com/company/2757525h> Twitter <https://twitter.com/TWB_Biotech> TWB - Parc technologique du canal • Bâtiment NAPA CENTER B • 3, rue Ariane • 31520 Ramonville Saint-Agne Ce message et ses pièces jointes sont strictement personnels. Ils peuvent contenir des informations confidentielles. Si vous avez reçu ce message par erreur, merci d'en avertir l'expéditeur et de détruire le message et les documents joints. Toute utilisation des informations reçues par erreur est interdite. This message and the attachments are strictly personal. They may contain confidential information. If you have received this message in error, please notify the sender and delete the message and the attachments. Any use of this communication received in error is prohibited.

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Galaxy Torque
by Benjamin Datko 29 Jul '15

29 Jul '15

Hello all, I am trying to config a cluster galaxy server using PBS torque. I have gone through the documentation but it is not clear to me how the job_conf.xml should be set up. Are there detailed documents on how galaxy works with the resource manger and how galaxy submits jobs? My current problem jobs can be created and submitted but within the history tab I have "this job is waiting to run". The job never gets submitted to PBS torque queue and cannot be seen using qstat. My job_conf.xml is shown below. If anyone can give a sample to a working configuration file for job_conf.xml using PBS torque that will be most appreciated. Ben <?xml version="1.0"?>  <job_conf> <plugins> <plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner"/> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="Core2"> <destination id="Core2" runner="pbs"> <param id="Resource_List">-l walltime=24:00:00,nodes=1:ppn=2</param> </destination> </destinations> </job_conf>

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I need some advice on what type of Galaxy server to implement
by Shane Kelly 29 Jul '15

29 Jul '15

Hi I have been tasked with getting a Galaxy server up and running for a group at work. 1. No-one can tell me how many users (concurrent or otherwise) there will be 2. Most of the analyses will be NGS. 3. Tools will be developed in-house but we will use public domain tools also. 4. There will be a guy running the server/developing tools pretty much full time. I have two favoured solutions at the moment: 1. A pipeline processor ( 64 Core, 512G Ram, with DAS of about 150TB ), and a Web server to act as frontend and database server, and another, smaller box for a total install of galaxy, but doing only the development work. 2. An all-in-one server with 128 Cores, 1TB ram, DAS storage of 150TB, and development work done on a VM. Any input would be hepfull. Thanks Shane

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Cannot import or download workflow
by Jeltje van Baren 28 Jul '15

28 Jul '15

Hi, I'm running the bgruening/galaxy-stable docker image. After making some changes to the tools, I can no longer upload workflows. How do I debug? What I get from the server is Internal Server Error Galaxy was unable to successfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. *The error has been logged to our team.* Since I am 'our team', I'd like to find out how to see the log! None of the logs under /home/galaxy indicate a problem (that I notice), but uwsgi.log does list a GET command for the workflow: [28/Jul/2015:16:31:50 +0000] "GET /api/datatypes?extension_only=False& HTTP/1.1" 200 - "http://128.114.61.147:8080/workflow/import_workflow" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:39.0) Gecko/20100101 Firefox/39.0" I figured it was an issue with the workflow, so I created a simple workflow on the same galaxy instance. When I tried to download the workflow file, I got the exact same error. Restarting the instance (several times) didn't help. How do I get more info on these errors? Thanks, -Jeltje

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Re: [galaxy-dev] problems installing htseq in local Galaxy
by Lance Parsons 28 Jul '15

28 Jul '15

Hi Ramon, I'm sorry your' having problems with the htseq-count tool. Could you elaborate a bit on an error messages you see for the missing tool dependencies? You should be able to click on those repositories that show missing dependencies and see which ones are not properly installed and then clicking on those get to an error message. I know there has been an issue with the freetype_2_4 package, at least for me, I am unable to download the file from sourceforge at the moment. Also, there has been a bug that can cause some fairly tough to trace errors during installation that was recently patched: https://github.com/galaxyproject/galaxy/pull/403. I've also copied this message to the galaxy-dev mailing list in case anyone there has additional insight. - Lance > Garcia Escudero, Ramon <mailto:ramon.garcia@ciemat.es> > July 28, 2015 at 7:17 AM > Dear Lance, > > I'm having problems installing "htseq-count wrapper for Galaxy" in my > local galaxy from the Galaxy Toolshed at > https://toolshed.g2.bx.psu.edu/repository?repository_id=2df7e24ce6c1f224 > > Main problems include missing tool dependencies for > > htseq > package freetype > package imaging > package matplotlib > > I'm runing ubuntu 14.04 LTS > > Coul you help me with this problem? > > Many thanks > > Ramon > ---------------------------- > Confidencialidad: > Este mensaje y sus ficheros adjuntos se dirige exclusivamente a su > destinatario y puede contener informaci?n privilegiada o confidencial. > Si no es vd. el destinatario indicado, queda notificado de que la > utilizaci?n, divulgaci?n y/o copia sin autorizaci?n est? prohibida en > virtud de la legislaci?n vigente. Si ha recibido este mensaje por > error, le rogamos que nos lo comunique inmediatamente respondiendo al > mensaje y proceda a su destrucci?n. > > Disclaimer: > This message and its attached files is intended exclusively for its > recipients and may contain confidential information. If you received > this e-mail in error you are hereby notified that any dissemination, > copy or disclosure of this communication is strictly prohibited and > may be unlawful. In this case, please notify us by a reply and delete > this email and its contents immediately. > ---------------------------- > -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Reasons to choose psql over mysql or not
by Eric Kuyt 28 Jul '15

28 Jul '15

Hi All, We are thinking of putting our galaxy instance in a new more powerful environment. Galaxy is now on a single server containing a psql database which is migrated from mysql a few years ago. The new environment already houses a really nice backupped highly available mysql server. as galaxy admin I am quite reluctant of migrating back to mysql, the system admin is quite reluctant of installing this psql database with the same grade of backup and availability just for galaxy. I could only come up with the line "*PostgreSQL is much preferred since we've found it works better with our DB abstraction layer, SQLAlchemy <http://www.sqlalchemy.org/>.*" from the galaxy wiki, which is a rather slim argument. My question now is. Is Postgres still the preferred database or is Mysql now also a safe bet. For mysql we would have to migrate back, system management would have a lot of experience tuning databases and a high quality instance is already running. For Psql a new database instance would have to be installed, less knowledge of the database system is available but it is the preferred database. Could someone point out some more pros and cons in this question? Thanks, Eric -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt(a)wur.nl Web: http://www.cvi.wur.nl

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bwa mem index builder error
by Stef van Lieshout 27 Jul '15

27 Jul '15

Hi all, Maybe someone can help with a question I posted at biostars about a week ago but have no solution yet.. https://biostar.usegalaxy.org/p/13206/ Its about a bwa mem index builder error. If anyone could help me out on this...! Stef

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