February 2014 - galaxy-dev - lists.galaxyproject.org

Question on storage configuration for Galaxy datasets
by Lukasse, Pieter 28 Feb '14

28 Feb '14

Hi , We would the location of the datasets our Galaxy stores to be determined dynamically based on a set of rules. For example: for a specific role we would like a datasets to be stored in a folder /storage/no_backup and for another role this should be /storage/with_backup Is there currently a configuration file in Galaxy to set this up? Or perhaps any alternative solutions? Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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universe_wsgi.ini question for Cistrome
by ruiwang.sz 28 Feb '14

28 Feb '14

Hi Guys, Are there anyone who is using Cistrome? I tried to merge Cistrome's setting into our own galaxy instance. A new entry is # Path to the static library files for assembly, ceaslib, chromLen, conservation, liftOver and MAT-lib # Then in other tool configuration xml file, we can use 'from galaxy import config' then '$config.Configuration().cistrome_static_library_path' # default would be in tool-data/ folder cistrome_static_library_path = /home/bioinfoadmin/app/cistrome-apps/cistrome_library However, I got error when I tried CEAS: Enrichment on chromosome and annotation: ***************************************************************************** Dataset 23: CEAS: Enrichment on chromosome and annotation on data 16 and data 13 The Galaxy framework encountered the following error while attempting to run the tool: Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 121, in prepare_job job_wrapper.prepare() File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/jobs/__init__.py", line 707, in prepare config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 2609, in build_config_files f.write( fill_template( template_text, context=param_dict ) ) File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/bioinfoadmin/app/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1391037616_15_43258.py", line 274, in respond NotFound: cannot find 'cistrome_static_library_path' while searching for '__app__.config.cistrome_static_library_path' Tool execution generated the following error message: failure preparing job ******************************************************************************** I'm quite confused since '__app__.config.cistrome_static_library_path' should be defined? or right now __app__ is dropped as Galaxy evolves? Besides, what does the comment mean by # Then in other tool configuration xml file, we can use 'from galaxy import config' then '$config.Configuration().cistrome_static_library_path' Does that mean that we should not be using __app__.config...but how to use this? I tried to insert 'from galaxy import config' into the xml file but only got error... I'll appreciate any input. Thanks, Rui

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Mercurial wants to overwrite my job_conf.xml
by Ganote, Carrie L 27 Feb '14

27 Feb '14

Hi Galaxy devs, I had an issue recently where I must have messed up my .hgignore file or done something terrible to my repository. I created a bitbucket and pushed my instance to it. I then pulled that onto my laptop and hooked it all up with Eclipse. After I was happy with my code, I pushed to bb and tried to pull to my instance, but the job_conf.xml file was overwritten. I had all of my tools set up there for the instance; on my laptop I had removed all that because it didn't apply. Would it have messed up if I deleted the file on my laptop and replaced it with a copy of job_conf.xml.simple? I took the .simple out of course and altered it to just what I needed. This is cross-posted with Stack Overflow: http://stackoverflow.com/questions/22055348/mercurial-update-seems-to-overw… Here is my repo: https://bitbucket.org/cganote/iu-ncgas-galaxy Any help would be greatly appreciated. -Carrie

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Apache problem
by Kucukural, Alper 27 Feb '14

27 Feb '14

Hi, I need to solve a problem in Apache and could not find a solution. So, we are using remote authentication for galaxy.myserver.edu. It is like a basic authentication in apache. AuthType Basic So I want to allow machine1 to access galaxy.myserver.edu/display_application without password. On machine1 we have ucsc genome browser mirror and it needs to access to these files like below; When I try with wget on machine1 wget http://galaxy.myserver.edu/display_application/38ac7832780d5a98/ucsc_bam/ma… But it is not working, I always get this error Resolving galaxy.myserver.edu... Connecting to galaxy.myserver.edu ||:80... connected. HTTP request sent, awaiting response... 401 Authorization Required Authorization failed. I allow those sites like below in httpd.conf but it is not working. <Location "/display_application"> Satisfy Any Order deny,allow Deny from all Allow from machine1.myserver.edu Allow from machine2.myserver.edu </Location> Another thing; galaxy is working with proxy, since it is installed port 8080. I directed galaxy.myserver.edu to here. I defined it like below; <Proxy http://localhost:8080> Order deny,allow Allow from all </Proxy> So, everything is working good but ucsc mirror need to access these files served by galaxy without password. http://galaxy.meyserver.edu/display_application/38ac7832780d5a98/ucsc_bam/m… when I write like below; wget http://myuser:mypass@galaxy.myserver.edu/display_application/38ac7832780d5a… It is working. Thanks, Alper Kucukural, PhD Bioinformatics Core, University of Massachusetts Medical School 368 Plantation St.Room AS4.2067 Worcester, MA 01605-2324 Phone: 774-312-4493 E-mail: Alper.Kucukural(a)umassmed.edu

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documentation
by Shrum, Donald C 27 Feb '14

27 Feb '14

I'm new to galaxy and I discovered during the install process... That I needed a folder named ../shed_tools that is writable by galaxy. migrated_tools_conf.xml:<toolbox tool_path="../shed_tools"> shed_tool_conf.xml:<toolbox tool_path="../shed_tools"> I spend a good chuck of time as a new user figuring this out so it's probably worth adding to the docs if it's not there already. Donny FSU Research Computing Center

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Re: [galaxy-dev] [galaxy-user] Galaxy + user program unable to locate files
by Peter Cock 27 Feb '14

27 Feb '14

On Thu, Feb 27, 2014 at 9:32 AM, do kadya <dokadya(a)gmail.com> wrote: > Hi, > Thank You for your kind reply. > > I am having problem in running command in Galaxy. > my current command: > > <tool_name> <file_having_multiple_file_name_tab_delimited.txt or .tab> > <file1.bam> <file2.bam> > > /usr/bin/x_tool fileList.tab file1.bam file2.bam > > I have created xml file so that i can run this command through Galaxy. Its > showing error: > Can't call method "print" on an undefined value at > /usr/local/share/perl/5.14.2/GTF/tool_x/Calc.pm line 110. > > When I am running same command from terminal, its working. > > From these I have hypothesize: > - Galaxy is having different path to run its script, and different file > name. > - FileList.tab contains list of other files which present in same folder. > - As tool is not able to search those files, may be galaxy is having > different path where it run the command. > ------- > While uploading file, I am using user defined path so that galaxy will not > create replica of it, > hence when I see error file of Galaxy output (by clicking on (i) symbol ) > its showing the same path where all my files are located. Normally tool development questions are on the galaxy-dev list (CC'd). It sounds like your problem is inside your own Perl script? Perhaps within Galaxy there is a problem with the Perl environment variables defining where to find Perl libraries... Peter

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UCSC Display option
by Alper Kucukural 27 Feb '14

27 Feb '14

Hi, When I map the reads with bowtie2 to hg19. I got the output like below and there are four display options. When I map the reads to mm10. I got only display in “IGB Local Web option". So, how can I fix this for mm10 or others and show all options? 101: Bowtie2 on data 4: aligned reads 91.6 KB format: bam, database: hg18 [bam_header_read] EOF marker is absent. The input is probably truncated. [samopen] SAM header is present: 45 sequences. 2500 reads; of these: 2500 (100.00%) were unpaired; of these: 1829 (73.16%) aligned 0 times 279 (11.16%) aligned exactly 1 display at UCSC main test display at Ensembl May 2009 display with IGV web current local display in IGB Local Web Best, Alper Kucukural, PhD Bioinformatics Core, University of Massachusetts Medical School 368 Plantation St.Room AS4.2067 Worcester, MA 01605-2324 Phone: 774-312-4493 E-mail: alper(a)kucukural.com

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bioblend run_tool function used with a tool containing repeats for inputs in its XML
by Olivia Doppelt-Azeroual 27 Feb '14

27 Feb '14

Dear Developpers, I'm still trying to use the bioblend function run_tool and now that I've uptdated my version of galaxy, the problem comes from the input_dict used to define the inputs. The command line generated is right except for the inputs information, it is either None are sometimes, nothing is just written there. I'm starting to think that it is due to the fact that in my xml tool, there is a way to add as many inputs as needed using the repeats tag. This maybe confuses the link between bioblend and galaxy as the variables are named differently in the cheetah command line. Is there an example of a run_tool utilisation ? somewhere ? Thanks in advance for your help. Have a nice day, -- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur

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Difficulty dispatching toolshed tool jobs via job_conf.xml
by Guest, Simon 27 Feb '14

27 Feb '14

I am having trouble getting a toolshed tool to be dispatched to the destination I list in the job_conf.xml file. My job_conf.xml file looks like this: <?xml version="1.0"?> <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="20"/> <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="condor"> <destination id="local" runner="local"/> <destination id="condor" runner="condor">  </destination> </destinations> <tools> <tool id="upload1" destination="local"/>  <tool id="ucsc_table_direct1" destination="local"/>  ... stuff omitted ... <tool id="toolshed-dev.agresearch.co.nz/toolshed/repos/guestsi/emboss_5_native/EMBOSS: infoseq46/5.0.0" destination="local"/> </tools> </job_conf> So, you can see I have a default destination of condor, but I'm trying to run my toolshed EMBOSS infoseq tool on local. However, it is stubbornly running on condor. In lib/galaxy/tools/__init__.py:1132, I see this comment which got me wondering: # In the toolshed context, there is no job config. Is it possible to define tool destinations for toolshed tools? Are there some gotchas that I should know about? Any other ideas why my job is ignoring the config in job_conf.xml? (By the way, I can change say the upload1 tool to run on Condor by setting its destination in that file, so it is doing something.) The other thing I saw in the source code is stuff about old_id and toolshed guids. Do I need to understand this stuff? The paster.log contains the following when I submit the infoseq job: 147.158.130.216 - - [11/Sep/2013:13:53:34 +1300] "GET /tool_runner?tool_id=toolshed-dev.agresearch.co.nz/toolshed/repos/guestsi/emboss_5_native/EMBOSS%3A%20infoseq46/5.0.0 HTTP/1.1" 200 - "http://galaxy-dev.agresearch.co.nz/" "Mozilla/5.0 (X11; Linux x86_64; rv:23.0) Gecko/20100101 Firefox/23.0" 147.158.130.216 - - [11/Sep/2013:13:53:40 +1300] "POST /tool_runner/index HTTP/1.1" 200 - "http://galaxy-dev.agresearch.co.nz/tool_runner?tool_id=toolshed-dev.agresea…" "Mozilla/5.0 (X11; Linux x86_64; rv:23.0) Gecko/20100101 Firefox/23.0" galaxy.jobs DEBUG 2013-09-11 13:53:40,886 (92) Working directory for job is: /home/galaxy-dev/galaxy/database/job_working_directory/000/92 galaxy.tools DEBUG 2013-09-11 13:53:40,886 Tool::get_job_destination: {'runner': 'condor', 'legacy': False, 'params': {}, 'tags': None, 'url': None, 'converted': False, 'id': 'condor'}. galaxy.jobs.handler DEBUG 2013-09-11 13:53:40,894 (92) Dispatching to condor runner (I added the debug output for Tool::get_job_destination to see what was going on.) Any ideas? cheers, Simon ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

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GATK2 is unable to find reference genomes
by Fenglou Mao 26 Feb '14

26 Feb '14

Dear All, I installed gatk2 from tool_shed, and see below for my gatk2_picard_index.loc Anyone can tell me what the mistake is? Old gatk can use this file to find all reference genomes, but gatk2 cannot. Fenglou

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