- galaxy-dev - lists.galaxyproject.org

workflow delete cancelled but workflows are still deleted
by Evan Bollig 20 May '14

20 May '14

I am working in the galaxy-dist stable branch. I select a workflow and select "Delete". An alert pops up asking if I'm sure I want to do that. I press "Cancel" and the alert disappears, along with the workflow. This shouldn't happen. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

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How to save job details outside of Galaxy
by Guillaume Penderia 20 May '14

20 May '14

Hi, I am currently working on some user-service functionalities on a local version of galaxy (cistrome actually) and I am looking for a way to save some job details outside of Galaxy. This would allow the users to consult those even after the datasets are deleted from Galaxy (in order to free some memory on disks). It would be great to get the same presentation as in the job details (with a column "input parameter", "value", etc), and I have found out that it has something to do with a "show params" function in the Galaxy code, but I can't figure out how to use it. I would like it to be called in the command line when we use a tool (I'll just have to put it in the xml file), is that even possible ? Oh and by the way, losing the stderr and stdout links is not a problem as long as it doesn't screw the whole file. Thank you for your help Guillaume

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error: flexbar dependency is not installed by the toolshed
by ruiwang.sz 20 May '14

20 May '14

Hi Guys, I tried to install flexbar from toolshed, but upon running, error said it could not find it. I checked and found <id>toolshed.g2.bx.psu.edu/repos/jtilman/flexbar/flexbar/2.4</id> in the config file, but this path does not exist. Is it that I need to install the dependency on my own? I had the impression that toolshed will do it for me. Please correct me if I'm wrong. Thanks, Rui

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Redirecting page after tool completes
by Neil.Burdett＠csiro.au 20 May '14

20 May '14

Hi, I have a tool that generates some png files. These are viewed when you click on the "eye" symbol. I was wondering if there is a way to automatically redirect to this html page once the job completes without the user needing to click on the "eye" symbol? (as this could be a small part in a larger workflow) Thanks Neil

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The main Tool Shed is now tracking the next-stable branch in preparation for the upcoming Galaxy release
by Greg Von Kuster 20 May '14

20 May '14

Hello all, The upcoming Galaxy release is currently scheduled for Monday, June 2. In preparation for this release, the main Galaxy Tool Shed is now tracking the next-stable branch and is currently running changeset 13542:11403745e7ce. The main Tool Shed will be regularly updated with any additions made to the next-stable branch between now and the upcoming Galaxy release. Please let us know if you encounter any issues. Thanks very much, Greg Von Kuster

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GCC2014 Early Registration closes this Friday, May 23
by Dave Clements 20 May '14

20 May '14

Hello all, This just a reminder that early registration<https://wiki.galaxyproject.org/Events/GCC2014/Register> for the 2014 Galaxy Community Conference (GCC2014)<https://wiki.galaxyproject.org/Events/GCC2014> *closes this Friday, May 23* Register early and *avoid paying 70% more for regular registration costs.* Early registration is downright affordable, with combined registration (Training Day<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> + main meeting) starting at $140 for post-docs and students. Registering early assures you a place at the conference and also a spot in the Training Day workshops<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay>you want to attend. And ... - The program <https://wiki.galaxyproject.org/Events/GCC2014/Program> , and abstracts <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts> for all accepted talks are now available. - Registration for the GCC2014 hackathon<https://wiki.galaxyproject.org/Events/GCC2014/Hackathon> is also open (and also has limited capacity - register for that now too<https://wiki.galaxyproject.org/Events/GCC2014/Hackathon> ) - We are pleased to have Penguin Computing<http://www.penguincomputing.com/>as a Silver Sponsor for GCC2014 You are strongly encouraged to register this week. Registration is capped this year at 250 participants, *and we expect to hit that limit*. Thanks a bunch, and hope to see you in Baltimore! Dave C -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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InvalidVersionError: 103 is not 105
by Evan Bollig 19 May '14

19 May '14

I have an empty posgresql database: psql -c "create database galaxy;" I'm trying to launch run.sh from the latest version of galaxy-dist. Migration proceeds normally up to this point: ######### galaxy.model.migrate.check INFO 2014-05-16 19:11:17,121 galaxy.model.migrate.check INFO 2014-05-16 19:11:17,121 Migration script to add the cleanup_event* tables. galaxy.model.migrate.check INFO 2014-05-16 19:11:17,121 galaxy.model.migrate.check INFO 2014-05-16 19:11:17,121 galaxy.model.migrate.check INFO 2014-05-16 19:11:17,121 Migrating 105 -> 106... galaxy.model.migrate.check INFO 2014-05-16 19:11:17,121 Traceback (most recent call last): File "/opt/galaxy/web/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/opt/galaxy/web/lib/galaxy/app.py", line 45, in __init__ self._configure_models( check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file ) File "/opt/galaxy/web/lib/galaxy/config.py", line 629, in _configure_models create_or_verify_database( db_url, config_file, self.config.database_engine_options, app=self ) File "/opt/galaxy/web/lib/galaxy/model/migrate/check.py", line 73, in create_or_verify_database migrate() File "/opt/galaxy/web/lib/galaxy/model/migrate/check.py", line 57, in migrate migrate_to_current_version( engine, db_schema ) File "/opt/galaxy/web/lib/galaxy/model/migrate/check.py", line 131, in migrate_to_current_version schema.runchange( ver, change, changeset.step ) File "/opt/galaxy/web/eggs/sqlalchemy_migrate-0.7.2-py2.7.egg/migrate/versioning/schema.py", line 89, in runchange (self.version, startver)) InvalidVersionError: 103 is not 105 ######### I re-run run.sh and get: ######### migrate.versioning.repository DEBUG 2014-05-16 19:12:22,132 Repository lib/galaxy/model/migrate loaded successfully migrate.versioning.repository DEBUG 2014-05-16 19:12:22,132 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) galaxy.model.migrate.check DEBUG 2014-05-16 19:12:22,136 psycopg2 egg successfully loaded for postgres dialect /opt/galaxy/web/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/url.py:105: SADeprecationWarning: The SQLAlchemy PostgreSQL dialect has been renamed from 'postgres' to 'postgresql'. The new URL format is postgresql[+driver]://<user>:<pass>@<host>/<dbname> Traceback (most recent call last): File "/opt/galaxy/web/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/opt/galaxy/web/lib/galaxy/app.py", line 45, in __init__ self._configure_models( check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file ) File "/opt/galaxy/web/lib/galaxy/config.py", line 629, in _configure_models create_or_verify_database( db_url, config_file, self.config.database_engine_options, app=self ) File "/opt/galaxy/web/lib/galaxy/model/migrate/check.py", line 111, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) Exception: Your database has version '103' but this code expects version '120'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'. ######### I manually run manage_db.sh upgrade. This step passes, and then I run run.sh a third time and galaxy finally starts properly. My question is: why can't the manage_db.sh upgrade step be included automatically when the initial DB build fails? This is the first time a DB is being built, so it should be dead simple.... Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

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user specific access/options
by Jennifer Jackson 19 May '14

19 May '14

Hi Petr, I am going to forward your email to the galaxy-dev list so that the development community can offer comments/suggestions. Best, Jen Galaxy team On 8/30/11 2:27 AM, Petr Novak wrote: > Hi everybody, > I am developing the application on Galaxy server. One of the requirement > is to create user specific list of options. Is it possible to access > somehow $__user_email__ in <options> tag or in <conditional> ?. I did > not found documentation how to used cheetah in galaxy tool xml files but > from files provided with galaxy, cheetah is used only in <command> and > <config> tag. Is that rigth? If it can be used in any part of xml > definition file it would make much easier to generate xml dynamicaly > based on the $__user_email__ > Does anybody have an idea how to manage this problem? > Petr Novak > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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Get the user credentials from the tool.
by Dmitry 19 May '14

19 May '14

Hello, Is there any way to provide a protected resource link to the external application? My tool is supposed to call a Web service via SSL which should access to the Galaxy resources. In ideal it would be something like ftp://user:password@mygalaxy.net/fasta.gz The Web service then downloads the resource and do the computation. Since user is already provided the login to galaxy, I do not want to ask the password again on a tool page. Sincerely, Dmitry

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replacing XML fragments in mycustomtool.xml
by Pierre Lindenbaum 19 May '14

19 May '14

This question was cross-posted on https://biostar.usegalaxy.org/p/7619/ "Adding custom tools: resolving (external ) XML entities" I'd like to replace fragments of XML code in my custom tool declaration. My first idea was to use XML entities but it seems that the XML engine doesn't resolve them. (BTW: I know I can replace/declare things in $PATH and tool_dependencies.xml ) Another idea was to use <macros><token...> but I cannot make it work (see https://gist.github.com/lindenb/b2a04e0fefd4d295dba9 ) my macros definition: <?xml version="1.0"?> <macros> <token name="@JAVA_EXE@">/usr/lib/jvm/jre-1.7.0-openjdk.x86_64/bin/java</token> <token name="@JVM_OPTIONS@">-Xmx500m</token> </macros> my tool definition: as a test, I echoed the value of @JAVA_EXE@ in /tmp/galaxy.txt (the macro was *not replaced* ) <?xml version="1.0" encoding="UTF-8"?> <tool id="com_github_lindenb_jvarkit_tools_misc_VcfHead" name="VcfHead" version="e098748b85acd5158a1ce612bd3d46e60948b9db" hidden="false"> <description>Print the first lines of a VCF</description> <macros> <import>jvarkit_macros.xml</import> </macros> <command>echo "@JAVA_EXE@" > /tmp/galaxy.txt && zcat -f ${input} | @JAVA_EXE@ @JVM_OPTIONS@ -cp /commun/data/packages/htsjdk/dist/apache-ant-1.8.2-bzip2.jar:/commun/data/packages/htsjdk/dist/htsjdk-1.112.jar:/commun/data/packages/htsjdk/dist/commons-jexl-2.1.1.jar:/commun/data/packages/htsjdk/dist/commons-logging-1.1.1.jar:/commun/data/packages/jvarkit-git/vcfhead.jar com.github.lindenb.jvarkit.tools.misc.VcfHead -n ${number} 2> /dev/null > ${output}</command> <inputs> <param format="vcf" name="input" type="data" label="Source VCF" optional="false"/> <param name="number" type="integer" value="10" label="Number of rows" optional="true"/> </inputs> <outputs> <data format="input" name="output" metadata_source="input"/> </outputs> <help>see https://github.com/lindenb/jvarkit/wiki/VcfHead</help> </tool> the output of 'hg tip' changeset: 9312:788cd3d06541 tag: tip parent: 9310:19f6e62bd372 parent: 9311:d7f37a2fe690 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Apr 08 12:30:08 2013 -0400 summary: Merged stable. what's wrong in my <macros> definition ? Thanks. Pierre

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