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

Trouble maintaining Galaxy config on cloud instance
by David Kovalic 01 Apr '15

01 Apr '15

Hi, I am trying to change the ftp dir (and some other modifications) vs. the standard Galaxy Cloudman config. When I modify the appropriate line in /mnt/galaxy/galaxy-app/universe_wsgi.ini on my running cloud instance: my changes disappear when I terminate/restart the cluster. When I modify universe_wsgi.ini.cloud and upload to the S3 bucket the file gets overwritten by the default when I restart the cluster... I can't find anywhere on the net which file I need to modify in order to have config changes persist. Any help would be greatly appreciated. Thanks, David

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storing "set max value" in trackster for wig file display
by Hans-Rudolf Hotz 01 Apr '15

01 Apr '15

Hi We have been using trackster much more in recent times - It really has improved a lot (especially its stability) over the last few years - thank you very much. We are running into a little annoying issue: when we display wiggle files, bedgraph files, bam files in coverage mode, etc, the max value gets somehow calculated. Very often, we want to change that, ie in order to see the full heights of the peaks instead of the capped peaks. This can be easily done by changing the "set max value" at the right hand side of the track. Unfortunately, the new value does not get stored. No matter, whether we click on safe or not. So next time we wanna a look at the same visualization again, we have to set the 'max value' again. Is this a known missing feature (bug) ? I just wanna check before I create a Trello card - so far, I couldn't find in in Trello. Thanks for your help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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strange issue on TEST toolshed
by Lukasse, Pieter 31 Mar '15

31 Mar '15

Hi, We have a strange issue on the test tool shed. Some repositories do not install anymore. For example: https://kuyt002@testtoolshed.g2.bx.psu.edu/repos/kuyt002/vennerable_r Also when just trying to clone this repository we get the error: [cid:image001.png@01D06B9A.58228FA0] Is this a known issue? What is going on with tool shed? I also reported some problems in my previous emails for which I got no response. Should I be reporting this somewhere else? Please let me know! Thanks, Pieter Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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problem with uploading SRA file to our custom galaxy
by Nikhil Joshi 31 Mar '15

31 Mar '15

Hi all, So it is time again for our next bioinformatics course using galaxy and I am trying to add some new tools to our custom galaxy running in the Amazon Cloud. I've installed the ncbi sra toolkit interface from the toolshed and the sra toolkit is installed on our AMI. However, when I upload an SRA file into our galaxy, the file is empty and I get this error: The uploaded binary file contains inappropriate content I am able to extract the fastq from the archive just fine on the command line, so I know it's not a problem with the file itself. Is there a solution to this? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)

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GalaxyAdmins Online Meetup on 19 February
by Dave Clements 31 Mar '15

31 Mar '15

Hello all, The first GalaxyAdmins <https://wiki.galaxyproject.org/Community/GalaxyAdmins> meetup of 2015 <https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2015_02_19> will happen online on Thursday, 19 February <http://bit.ly/1yZJSkN>. GalaxyAdmins <https://wiki.galaxyproject.org/Community/GalaxyAdmins> is a special interest group for Galaxy community members who are responsible for Galaxy installations. A summary of both the user and admin/developer 2014 Galaxy Community Questionnaires <https://wiki.galaxyproject.org/News/2014Questionnaire> will be presented by Dave Clements <https://wiki.galaxyproject.org/DaveClements>, a *Galaxy Project Update* will be offered by a Galaxy Team member <https://wiki.galaxyproject.org/GalaxyTeam>, and Hans-Rudolf Hotz <https://wiki.galaxyproject.org/HansrudolfHotz> will lead a short discussion on *GalaxyAdmins direction*. Thanks to everyone for letting us know what dates and times worked best for you. This time and day of the week worked for a remarkable 91% of respondents. We are looking forward to starting this group up again, Hans-Rudolf Hotz and Dave Clements -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Trouble maintaining Galaxy config on cloud
by David Kovalic 30 Mar '15

30 Mar '15

Hi, I am trying to change the ftp dir (and some other modifications) to the standard Galaxy Cloudman config. When I modify the appropriate line in /mnt/galaxy/galaxy-app/universe_wsgi.ini on my ru8nning cloud instance: my changes disappear when I terminate/restart the cluster. When I modify universe_wsgi.ini.cloud and upload to the S3 bucket the file gets overwritten by the default when I restart the cluster... I cant find anywhere on the net which file I need to modify in order to have config changes persist. Any help would be greatly appreciated. Thanks, David

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Re: [galaxy-dev] data collections - workflow - bug?
by John Chilton 30 Mar '15

30 Mar '15

Sorry again about this mixup (bringing conversation back on channel). Does this happen everytime you run a workflow with collections? Do you know how many job handlers Galaxy is configured with? -John On Mon, Jan 26, 2015 at 11:24 AM, John Chilton <jmchilton(a)gmail.com> wrote: > Ugh.... misread sqlalchemy as sqlite. I will work on this. > > -John > > On Mon, Jan 26, 2015 at 11:16 AM, Torsten Houwaart > <houwaart(a)informatik.uni-freiburg.de> wrote: >> Hi John, >> >> i ran this on the Galaxy server in Freiburg: galaxy.uni-freiburg.de >> Björn (who sits immediately opposite of my desk :) ) told me it's a Postres >> database and that shouldn't be the problem. >> >> Best, >> Torsten >> >> >> On 26.01.2015 16:48, John Chilton wrote: >>> >>> Hey, >>> >>> Really intensive database operations including datasest collections >>> but other things too like multi-running tools or workflows over many >>> individual datasets for instance - can very easily overwhelm the >>> default sqlite database. This is frustrating and shouldn't happen - >>> but it does unfortunately. I would recommend using a postgres database >>> when testing out dataset collections. The good news is that it is >>> easier than ever to get a fully fledged production-quality server >>> thanks to Bjoern's docker server >>> (https://github.com/bgruening/docker-galaxy-stable) - it comes bundled >>> with Postgres and Slurm so it should be able to handle the collection >>> operations. If you need to run Galaxy on a non-containerized server >>> (for instance because that is where the software is) more information >>> on setting up Galaxy can be found here >>> https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer. >>> >>> Here is a Trello card to track progress on the database optimization >>> efforts if you are interested https://trello.com/c/UPLsMKQI. >>> >>> Very sorry. >>> >>> -John >>> >>> >>> >>> -John >>> >>> On Mon, Jan 26, 2015 at 9:35 AM, Torsten Houwaart >>> <houwaart(a)informatik.uni-freiburg.de> wrote: >>>> >>>> Hello Galaxy Devs, >>>> >>>> I was using data collections (for the first time) for a new workflow of >>>> ours >>>> and I ran into this problem. There was no complaint by the >>>> workflow-editor >>>> and I could start the workflow but then <see below> happened. >>>> If you need more information about the workflow or otherwise let me know. >>>> >>>> Best, >>>> Torsten H. >>>> >>>> >>>> job traceback: >>>> Traceback (most recent call last): >>>> File >>>> "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", >>>> line 565, in finish_job >>>> job_state.job_wrapper.finish( stdout, stderr, exit_code ) >>>> File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line >>>> 1250, in finish >>>> self.sa_session.flush() >>>> File >>>> >>>> "/usr/local/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/scoping.py", >>>> line 114, in do >>>> return getattr(self.registry(), name)(*args, **kwargs) >>>> File >>>> >>>> "/usr/local/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/session.py", >>>> line 1718, in flush >>>> self._flush(objects) >>>> File >>>> >>>> "/usr/local/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/session.py", >>>> line 1789, in _flush >>>> flush_context.execute() >>>> File >>>> >>>> "/usr/local/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/unitofwork.py", >>>> line 331, in execute >>>> rec.execute(self) >>>> File >>>> >>>> "/usr/local/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/unitofwork.py", >>>> line 475, in execute >>>> uow >>>> File >>>> >>>> "/usr/local/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/persistence.py", >>>> line 59, in save_obj >>>> mapper, table, update) >>>> File >>>> >>>> "/usr/local/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/persistence.py", >>>> line 485, in _emit_update_statements >>>> execute(statement, params) >>>> File >>>> >>>> "/usr/local/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py", >>>> line 1449, in execute >>>> params) >>>> File >>>> >>>> "/usr/local/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py", >>>> line 1584, in _execute_clauseelement >>>> compiled_sql, distilled_params >>>> File >>>> >>>> "/usr/local/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py", >>>> line 1698, in _execute_context >>>> context) >>>> File >>>> >>>> "/usr/local/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/base.py", >>>> line 1691, in _execute_context >>>> context) >>>> File >>>> >>>> "/usr/local/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/engine/default.py", >>>> line 331, in do_execute >>>> cursor.execute(statement, parameters) >>>> DBAPIError: (TransactionRollbackError) deadlock detected >>>> DETAIL: Process 3144 waits for ShareLock on transaction 2517124; blocked >>>> by >>>> process 3143. >>>> Process 3143 waits for ShareLock on transaction 2517123; blocked by >>>> process >>>> 3144. >>>> HINT: See server log for query details. >>>> 'UPDATE workflow_invocation SET update_time=%(update_time)s WHERE >>>> workflow_invocation.id = %(workflow_invocation_id)s' {'update_time': >>>> datetime.datetime(2015, 1, 26, 14, 20, 4, 155440), >>>> 'workflow_invocation_id': >>>> 5454} >>>> >>>> >>>> ___________________________________________________________ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> https://lists.galaxyproject.org/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >> >>

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Safe / possible to sync toolshed tools and deps from another machine?
by David Trudgian 30 Mar '15

30 Mar '15

Hi, I was wondering whether it might be possible/safe to install tools and deps from the toolshed on a VM galaxy installation, and then rsync the shed_tools and tool dependencies directories to a production galaxy server? Unfortunately, our institution has web access only through a proxy and blocks 'personal web browsing' from servers. This works on a white list - so everything is blocked unless there was considered to be a valid need when the list was originally setup, or an exception request is made and approved. We have an exception in place for the main toolshed, but various dependency downloads will fail, blocked by the proxy. Getting exceptions for each URL we find not to work is painful and slow. The suggestion I've been given is to download things on a workstation (not subject to the blocking) and transfer them manually to the server, hence the question about whether tool directories (and XML conf files) can be synced between installs? Is there anything in the SQL DB that would prevent this working, or being safe? Otherwise I'm installing a lot of deps manually :( Thanks, Dave Trudgian ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Multiple-select checkbox parameters not using default values
by Peter Cock 27 Mar '15

27 Mar '15

Hi all, Unfortunately it appears that the new-look check box controls are wrongly defaulting to ticking the first item rather than following the defaults given. This is a recent regression which I noticed on updating our production Galaxy to the 15.03 release which included a number of visual style updates to the parameter widgets: https://trello.com/c/8alIlOUN/2590-param-type-select-display-checkboxes-mul… e.g. this example from the BLAST+ wrappers should default to all the checkboxes being checked (ticked): <param name="std_cols" type="select" multiple="true" display="checkboxes" label="Standard columns"> <option selected="true" value="qseqid">qseqid = Query Seq-id (ID of your sequence)</option> <option selected="true" value="sseqid">sseqid = Subject Seq-id (ID of the database hit)</option> <option selected="true" value="pident">pident = Percentage of identical matches</option> <option selected="true" value="length">length = Alignment length</option> <option selected="true" value="mismatch">mismatch = Number of mismatches</option> <option selected="true" value="gapopen">gapopen = Number of gap openings</option> <option selected="true" value="qstart">qstart = Start of alignment in query</option> <option selected="true" value="qend">qend = End of alignment in query</option> <option selected="true" value="sstart">sstart = Start of alignment in subject (database hit)</option> <option selected="true" value="send">send = End of alignment in subject (database hit)</option> <option selected="true" value="evalue">evalue = Expectation value (E-value)</option> <option selected="true" value="bitscore">bitscore = Bit score</option> </param> Thus far I've only noticed this where multiple="true" since for single select parameters I've normally opted for the radio-select button instead. Does anyone use multiple="false" (default) with display="checkboxes"? Peter

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simple way to refer to the repository install directory from a tool
by Langhorst, Brad 26 Mar '15

26 Mar '15

I’m working on a very simple tool. <tool id="gc_stat" name="GC Stat" version="0.1.0"> <requirements> <requirement type="binary">Rscript</requirement> <requirement type="package" version="1.1">samtools</requirement> <requirement type="package" version="3.0.3">R</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command><![CDATA[ samtools view $bam | Rscript simple_script.R > $output ]]></command> <inputs> <param name='bam' type='data' format='bam' label='Mapped reads' help='BAM files'/> </inputs> <outputs> <data format='tabular' name='output' label='GC Statistic on ${on_string}'/> </outputs> <help><![CDATA[ Calculates a GC statistic for the specified BAM file. ]]></help> </tool> this won’t work because Rscript is not running in the tool install directory and can’t find simple_script.R… I’ve just been reading https://trello.com/c/9lQ7Sr8I/636-galaxy-tool-enhancement-to-accommodate-re… and it seems that I have to add another file… <?xml version="1.0"?> <tool_dependency> <set_environment version="1.0"> <environment_variable name="TOOL_INSTALL_DIR" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> </tool_dependency> and add a set_enviornment dependency to bring it in. <requirements> ... <requirement type="set_environment">TOOL_INSTALL_DIR</requirement> </requirements> <command><![CDATA[ samtools view $bam | Rscript $TOOL_INSTALL_DIR/simple_script.R > $output ]]></command> I did that but the tool still won’t execute, in fact the . Maybe because I have to put this into a toolshed - or maybe I’ve done something wrong? I think this complexity could be avoided by setting an TOOL_INSTALL_DIR environment var as a tool is executed (though John doesn’t seem to like that idea due to a responsibility mixing issue) I think it’s a worthy goal to make tool development as frictionless as possible. Is there a simpler way to do this? Brad

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