galaxy-dev October 2014

galaxy-dev@lists.galaxyproject.org

64 participants
99 discussions

Re: [galaxy-dev] galaxy-dev Digest, Vol 100, Issue 10
by Iry Witham 17 Oct '14

17 Oct '14

So I have finally determined the cause and found a resolution. The issue was the fact that the version of Java on the Ubuntu linux VM from AWS is 1.6.x. GATK2 requires version 1.7.0 or higher. This is fine, but you will need to manually upgrade the java version. To do so you will need to complete the following: SSH to the VM sudo su - root CD to /mnt/galaxy/ Complete the following steps: 1. sudo apt-get purge openjdk* (This removes java 1.6 completely) 2. Modify this file: vi /etc/apt/sources.list.d/cloudbiolinux.list (Remove the leading section of line 11) 3. sudo add-apt-repository ppa:webupd8team/java 4. sudo apt-get update 5. sudo apt-get install oracle-java7-installer 6. java -version Now if you plan to add nodes via the Cloudman Console you will need to perform these tasks for each node you install. I worked with AWS Support to setup an "Auto Scaling Group" to accommodate this process. This required getting my Master instance upgraded and creating an AMI from it. >From that point you can build the group based on the following: http://docs.aws.amazon.com/AutoScaling/latest/DeveloperGuide/creating-your- auto-scaling-groups.html This was, in theory, a great idea. However, it did not work for me. Each of the node that were generated by this tool had Java version 1.6.x and this caused GATK2 to fail. My recommendation is that if you have time you should paly around with this more, but I did not have that luxury for this project. Iry On 10/11/14 12:00 PM, "galaxy-dev-request(a)lists.bx.psu.edu" <galaxy-dev-request(a)lists.bx.psu.edu> wrote: >Send galaxy-dev mailing list submissions to > galaxy-dev(a)lists.bx.psu.edu > >To subscribe or unsubscribe via the World Wide Web, visit > http://lists.bx.psu.edu/listinfo/galaxy-dev >or, via email, send a message with subject or body 'help' to > galaxy-dev-request(a)lists.bx.psu.edu > >You can reach the person managing the list at > galaxy-dev-owner(a)lists.bx.psu.edu > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of galaxy-dev digest..." > > >HEY! This is important! If you reply to a thread in a digest, please >1. Change the subject of your response from "Galaxy-dev Digest Vol ..." >to the original subject for the thread. >2. Strip out everything else in the digest that is not part of the thread >you are responding to. > >Why? >1. This will keep the subject meaningful. People will have some idea >from the subject line if they should read it or not. >2. Not doing this greatly increases the number of emails that match >search queries, but that aren't actually informative. > >Today's Topics: > > 1. Re: Tool development: Is it possible to pass a user's id in > dynamic_options() parameter? (Dooley, Damion) > 2. Re: Tool development: Is it possible to pass a user's id in > dynamic_options() parameter? (Daniel Blankenberg) > 3. Anyone else having issues with cloudman cloudlaunch? > (Chris Dagdigian) > 4. Re: Anyone else having issues with cloudman cloudlaunch? > (Dannon Baker) > 5. Re: Anyone else having issues with cloudman cloudlaunch? > (Dannon Baker) > 6. Re: Anyone else having issues with cloudman cloudlaunch? > (Chris Dagdigian) > 7. Re: Anyone else having issues with cloudman cloudlaunch? > (Dannon Baker) > 8. Re: Anyone else having issues with cloudman cloudlaunch? > (Chris Dagdigian) > 9. GATK2 java version related issues (Iry Witham) > 10. Why does Galaxy CloudMan 2.3 (ami-a7dbf6ce) run the boinc > client? (Chris Dagdigian) > 11. Re: GATK2 java version related issues (Daniel Blankenberg) > 12. Re: Why does Galaxy CloudMan 2.3 (ami-a7dbf6ce) run the boinc > client? (Dannon Baker) > 13. Re: GATK2 java version related issues (Iry Witham) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Fri, 10 Oct 2014 09:02:50 -0700 >From: "Dooley, Damion" <Damion.Dooley(a)bccdc.ca> >To: Daniel Blankenberg <dan(a)bx.psu.edu> >Cc: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> >Subject: Re: [galaxy-dev] Tool development: Is it possible to pass a > user's id in dynamic_options() parameter? >Message-ID: > <7891813F3C8F424B97D8BF2E5600E51903302322C5B5(a)VEXCCR02.phsabc.ehcnet.ca> > >Content-Type: text/plain; charset="Windows-1252" > >Hi Dan, > >I'd like to get the user's galaxy user name directly - but the <code >file="..."> that drives my dynamic_options select list has no access to >any information in a galaxy's user session, right? (Ultimately I'm >trying to get the dynamic_options code to make galaxy api calls using the >user's api key.) I saw the GenomeSpace tool earlier - but got the >impression that a user was entering their genome login in the tool form. >I was hoping just to get a user's galaxy id without any re-entry of it. > >p.s. Its been really great getting advice from all of you; I hope to >contribute likewise. > >d. > >Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC >Centre for Disease Control >655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada >________________________________________ >From: Daniel Blankenberg [dan(a)bx.psu.edu] >Sent: Friday, October 10, 2014 8:08 AM >To: Dooley, Damion >Cc: galaxy-dev(a)lists.bx.psu.edu >Subject: Re: [galaxy-dev] Tool development: Is it possible to pass a >user's id in dynamic_options() parameter? > >Hi Damion, > >Text fields are not currently able to be populated by dynamic_options, >but in a dynamic_options select list you could access the user?s username >directly. If you want the user to be able to override it, you could have >a conditionally used empty text box that your tool defaults to using when >it is populated. > >An example that you might want to look at could be the GenomeSpace Export >tool (tools/genomespace/genomespace_exporter.*), which queries the >GenomeSpace API to get a list of available folders for export for a >specific user using attributes of the current user?s preferences >(GenomeSpace username and token). It generates a drill_down type select >parameter, but the same can be done for a standard select list. > > >Thanks for using Galaxy, > >Dan > > >------------------------------ > >Message: 2 >Date: Fri, 10 Oct 2014 12:59:06 -0400 >From: Daniel Blankenberg <dan(a)bx.psu.edu> >To: "Dooley, Damion" <Damion.Dooley(a)bccdc.ca> >Cc: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> >Subject: Re: [galaxy-dev] Tool development: Is it possible to pass a > user's id in dynamic_options() parameter? >Message-ID: <1A8CFB92-0432-4FAC-B139-84E05F0EDE57(a)bx.psu.edu> >Content-Type: text/plain; charset="windows-1252" > >Hi Damion, > >In the genomespace exporter case, the call to >?dynamic_options="galaxy_code_get_genomespace_folders( genomespace_site = >'prod', trans=__trans__, value=__value__, input_dataset=input1, >base_url=base_url )?? is passing in trans, which it is using to >determine user and an attribute of the user. You could then check to see >if trans.user is not None, and then get trans.user.username. > >You may be able to access user or username here by the more recently >added ?__user__? or even ?__user_name__? / ?__user_id__? / >?__user_email__" variables directly, but I didn?t test that they were >available in this dynamic_options context example (if they are available, >they would be preferred over accessing trans). > >For accessing a user?s API key, this trello card is of interest: >https://trello.com/c/hL4NYsSp/2108-request-from-jxtx-provide-consistent-in >terface-to-tools-for-communicating-with-the-api. Of course the Key can be >obtained directly from the user object as well. > > >Hope this helps, > >Dan > > >On Oct 10, 2014, at 12:02 PM, Dooley, Damion <Damion.Dooley(a)bccdc.ca> >wrote: > >> Hi Dan, >> >> I'd like to get the user's galaxy user name directly - but the <code >>file="..."> that drives my dynamic_options select list has no access to >>any information in a galaxy's user session, right? (Ultimately I'm >>trying to get the dynamic_options code to make galaxy api calls using >>the user's api key.) I saw the GenomeSpace tool earlier - but got the >>impression that a user was entering their genome login in the tool form. >> I was hoping just to get a user's galaxy id without any re-entry of it. >> >> p.s. Its been really great getting advice from all of you; I hope to >>contribute likewise. >> >> d. >> >> Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC >>Centre for Disease Control >> 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada >> ________________________________________ >> From: Daniel Blankenberg [dan(a)bx.psu.edu] >> Sent: Friday, October 10, 2014 8:08 AM >> To: Dooley, Damion >> Cc: galaxy-dev(a)lists.bx.psu.edu >> Subject: Re: [galaxy-dev] Tool development: Is it possible to pass a >>user's id in dynamic_options() parameter? >> >> Hi Damion, >> >> Text fields are not currently able to be populated by dynamic_options, >>but in a dynamic_options select list you could access the user?s >>username directly. If you want the user to be able to override it, you >>could have a conditionally used empty text box that your tool defaults >>to using when it is populated. >> >> An example that you might want to look at could be the GenomeSpace >>Export tool (tools/genomespace/genomespace_exporter.*), which queries >>the GenomeSpace API to get a list of available folders for export for a >>specific user using attributes of the current user?s preferences >>(GenomeSpace username and token). It generates a drill_down type select >>parameter, but the same can be done for a standard select list. >> >> >> Thanks for using Galaxy, >> >> Dan > >

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CloudMan auto-scaling - Use spot instance for worker node?
by Petit III, Robert A. 16 Oct '14

16 Oct '14

Hi all, I realize when you manually add a node you can request that it be a spot instance. Is it also possible to use spot instances for auto-scaling? Thank you very much, Robert ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Galaxy Training Network
by Dave Clements 16 Oct '14

16 Oct '14

Hello all, We are pleased to announce the *Galaxy Training Network (GTN) <https://wiki.galaxyproject.org/Teach/GTN>*, a network of trainers who teach bioinformatics using Galaxy, or teach about Galaxy itself. The GTN aims to make it easy to find Galaxy trainers <https://wiki.galaxyproject.org/Teach/Trainers>, and to share and discover the wealth of training resources available for Galaxy. This includes training materials <https://wiki.galaxyproject.org/Teach/Resources>, a trainer directory <https://wiki.galaxyproject.org/Teach/Trainers>,best practices <https://wiki.galaxyproject.org/Teach/BestPractices>, and guidance on computing platforms <https://wiki.galaxyproject.org/Teach/ComputingPlatforms> for teaching with Galaxy. The Galaxy Training Network is accessible to the entire community. If you teach with Galaxy, then please consider adding your organization <https://wiki.galaxyproject.org/Teach/Trainers#Add_a_Trainer>, materials <https://wiki.galaxyproject.org/Teach/Resources#Add_a_Training_Resource>, and best practices <https://wiki.galaxyproject.org/Teach/BestPractices>. The Trainer Directory <https://wiki.galaxyproject.org/Teach/Trainers> already includes 16 organizations and there may be one (or 6!) near you <http://bit.ly/gxytrnmap>. Thanks, The Galaxy Training Network (GTN) <https://wiki.galaxyproject.org/Teach/Trainers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Create select list parameter from input
by Nikos Sidiropoulos 16 Oct '14

16 Oct '14

Hi all, Is it possible to read id's from a column of an input dataset and create a checkbox parameter with the unique id's of that column within the same tool? The only remotely similar action that I found is on the sorting tool where it reads the number of the columns of that dataset and creates a dropdown select list. Bests, Nikos

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Help with Galaxy server migration
by Sarah Diehl 16 Oct '14

16 Oct '14

Dear all, I'm trying to migrate our local Galaxy server from a standalone server running on CentOS 5 to a setup that runs Galaxy in a Docker container (bgruening/galaxy-stable). Due to Docker and the setup of the container, almost all data, tools, configs etc. have to move to a different place. Since our old server is pretty cluttered up anyway, I would like to move just user data (logins, histories, datasets ...), but none of the tool installations, tool data or configs. My plan was to start with a fresh and clean new Galaxy installation, transfer the datasets and the database and then reinstall all tools through the toolshed (of course there are many more small odds and ends that need fixing). The problem is that after transfering the database, I always get an error when going to "Manage installed tool shed repositories" (see end of the mail). I tried just overwriting the pg_data directory (PostgreSQL versions are identical) and also exporting to sql (pg_dump) and importing in the new DB. Both times I made sure to run manage_db.sh upgrade afterwards. The error stays the same. I can't make much sense of the error message, my only guess is that it looks for something that's not there. However, I really don't want to transfer the tool directories and tool configurations, because that will get messy and difficult, since many paths need to be adjusted. There's a high chance for error and this way I also carry over the clutter. So is there a way to remove all tool installation information from the database, before I transfer it? Can this even be disentangled from the histories and datasets? Any help or other ideas on how to do this migration are highly appreciated! Thanks, Sarah 10.1.5.190 - - [16/Oct/2014:09:54:35 +0000] "GET /admin_toolshed/browse_repositories HTTP/1.1" 500 - "http://deep2:8080/admin/index" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0" Error - <type 'exceptions.UnicodeDecodeError'>: 'ascii' codec can't decode byte 0xe2 in position 393: ordinal not in range(128) URL: http://deep2:8080/admin_toolshed/browse_repositories File 'lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/galaxy-central/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/galaxy-central/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File 'lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File 'lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File 'lib/galaxy/web/framework/decorators.py', line 87 in decorator return func( self, trans, *args, **kwargs ) File 'lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 167 in browse_repositories return self.installed_repository_grid( trans, **kwd ) File 'lib/galaxy/web/framework/helpers/grids.py', line 306 in __call__ kwargs=kwargs ) File 'lib/galaxy/web/framework/webapp.py', line 771 in fill_template return self.fill_template_mako( filename, **kwargs ) File 'lib/galaxy/web/framework/webapp.py', line 786 in fill_template_mako return template.render( **data ) File '/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/galaxy-central/database/compiled_templates/base.mako.py', line 66 in render_body __M_writer(unicode(next.body())) File '/galaxy-central/database/compiled_templates/grid_base.mako.py', line 91 in render_body __M_writer(unicode(self.load())) File '/galaxy-central/database/compiled_templates/grid_base.mako.py', line 120 in render_load __M_writer(unicode( h.dumps( self.get_grid_config( embedded=embedded, insert=insert ) ) )) File '/galaxy-central/database/compiled_templates/grid_base.mako.py', line 303 in render_get_grid_config value = column.get_value( trans, grid, item ) File 'lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py', line 106 in get_value return suc.get_tool_shed_repository_status_label( trans.app, tool_shed_repository ) File 'lib/tool_shed/util/shed_util_common.py', line 829 in get_tool_shed_repository_status_label elif tool_shed_repository.tool_dependencies_being_installed: File 'lib/galaxy/model/tool_shed_install/__init__.py', line 408 in tool_dependencies_being_installed for tool_dependency in self.tool_dependencies: File '/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py', line 168 in __get__ File '/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py', line 453 in get File '/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py', line 508 in _load_for_state File '/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py', line 574 in _emit_lazyload File '/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2115 in all File '/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2341 in instances File '/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', line 3204 in fetchall File '/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py', line 3171 in _fetchall_impl UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 393: ordinal not in range(128)

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16 Oct '14

Hello galaxians, I'm currently trying to set up a production galaxy and make it available to the public but I face a weird issue, probably because of my nginx proxy configuration. Galaxy is on a kvm virtual machine running on a host using nginx as proxy. to make it a bit clearer: 172.30.24.35 (client) ---> http://172.30.24.63/machine1 (Host & nginx proxy) --- > http://192.168.122.254:8080/ (virtual machine) I can connect to galaxy but when logging in, the virtual machine redirects me on 192.168.122.254:8080, which is unreachable from the 172.30.24.0 network. If I log in from the Host, it's all fine. in the universe_wsgi.ini, i've set: # Define the proxy-prefix filter. [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /machine1 ... # [filter:proxy-prefix] section above. filter-with = proxy-prefix as described in the documentation. My virtual machine nginx conf file: user galaxy; worker_processes 2; #error_log logs/error.log; #error_log logs/error.log notice; #error_log logs/error.log info; #pid logs/nginx.pid; events { worker_connections 1024; } http { include mime.types; default_type application/octet-stream; #log_format main '$remote_addr - $remote_user [$time_local] "$request" ' # '$status $body_bytes_sent "$http_referer" ' # '"$http_user_agent" "$http_x_forwarded_for"'; #access_log logs/access.log main; sendfile on; #tcp_nopush on; #keepalive_timeout 0; keepalive_timeout 65; gzip on; gzip_http_version 1.1; gzip_vary on; gzip_comp_level 4; gzip_proxied any; gzip_types text/plain text/css application/x-javascript text/xml application/xml text/javascript application/json; gzip_buffers 16 8k; gzip_disable "MSIE [1-6].(?!.*SV1)"; upstream galaxy_app{ server localhost:8080; } server { client_max_body_size 10G; listen 80; server_name localhost; #charset koi8-r; #access_log logs/host.access.log main; location /machine1 { proxy_pass http://galaxy_app; proxy_set_header Host $host; proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; } location /machine1/static { alias /home/galaxy/galaxy-dist/static; } location /machine1/static/style { alias /home/galaxy/galaxy-dist/static/june_2007_style/blue; } location /machine1/static/scripts { alias /home/galaxy/galaxy-dist/static/scripts/packed; } location /machine1/favicon.ico { alias /home/galaxy/galaxy-dist/static/favicon.ico; } location /machine1/robots.txt { alias /home/galaxy/galaxy-dist/static/robots.txt; } location /_x_accel_redirect/ { internal; alias /machine1; } #error_page 404 /404.html; #redirect server error pages to the static page /50x.html # error_page 500 502 503 504 /50x.html; location = /50x.html { root html; } } } And my host configuration : server { listen 80 default_server; listen [::]:80 default_server ipv6only=on; root /usr/share/nginx/html; index index.html index.htm; # Make site accessible from http://localhost/ server_name localhost; location / { try_files $uri $uri/ =404; } location /machine1 { proxy_pass http://192.168.122.254:8080; } }

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snpEff and java issue
by Iry Witham 15 Oct '14

15 Oct '14

Hi Team, I had manually installed the latest version of snpEff based on the recommendation of Pablo and after modifying the XML files I had a working version of snpEff that produced a vcf. However, this morning I reran my workflow and it is failing again, but this time I am getting the following error: Fatal error: Exit code 1 (Error) Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpEffect/commandLine/SnpEff : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:643) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:277) at java.net.URLClassLoader.access$000(URLClassLoader.java:73) at java.net.URLClassLoader$1.run(URLClassLoader.java:212) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:323) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:268) Could not find the main class: ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff. Program will exit. Nothing has been changed since I had success. Regards, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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snpeff tool for Galaxy extra_files_path
by Jim Johnson 15 Oct '14

15 Oct '14

Andrew, Thanks for investigating this. I changed the subject and sent to the galaxy dev list. I've had a number of tools quit working recently. Particularly tools that inspect the extra_files_path when setting metadata, Defuse, Rsem, SnpEff. I think there was a change in the galaxy framework: The extra_files_path when referenced from an input or output in the cheetah template sections of the tool config xml will be relative to the job working directly rather than the files location. I've just changed a few of my tools on my server yesterday from: <param_name>.extra_files_path to: <param_name>.dataset.extra_files_path and they now work again. Dan or John, is that the right way to handle this? Thanks, JJ On 10/13/14, 9:29 PM, Andrew Lonie wrote: > Hi Jim. I am probably going about this the wrong way, but I am not > clear on how to report tool errors (if in fact this is a tool error!) > > I've been trialling your snpeff wrapper from the test toolshed and > getting a consistent error with the SnpEff Download and SnpEff sub > tools (the SnpSift dbNSFP works fine). The problem seems to be with an > attribute declaration and manifests during database download as: > > Traceback (most recent call last): > File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/runners/__init__.py", > line 564, in finish_job > job_state.job_wrapper.finish( stdout, stderr, exit_code ) > File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/__init__.py", line > 1107, in finish > dataset.datatype.set_meta( dataset, overwrite=False ) # call > datatype.set_meta directly for the initial set_meta call during > dataset creation > File "/mnt/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/iuc/snpeff/1938721334b3/snpeff/lib/galaxy/datatypes/snpeff.py", > line 21, in set_meta > data_dir = dataset.files_path > AttributeError: 'HistoryDatasetAssociation' object has no attribute 'files_path' > > > We fiddled around with the wrapper, eventually replacing > 'dataset.files_path' with 'dataset.extra_files_path' in snpeff.py, > which fixed the download bug, but then SnpEff subtool itself threw a > similar error when I tried to use that database from the history. > > I chased up a bit more but cannot understand the various posts on > files_path vs extra_files_path > > I've shared a history with both of these errors here: > http://130.56.251.62/galaxy/u/alonie/h/unnamed-history > > Maybe this is a problem with our Galaxy image? > > Any help appreciated! > > Andrew > > > > > A/Prof Andrew Lonie > University of Melbourne -- James E. Johnson Minnesota Supercomputing Institute University of Minnesota

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Set output dbkey from parameter value
by Nikos Sidiropoulos 15 Oct '14

15 Oct '14

Hi all, I'm trying to set the dbkey of an output file from the value (text) of a parameter. The parameter I want to use is genome. <conditional name="bedgraph"> <param name="check" type="select" label="Produce BedGraph output" help="Can be displayed directly on UCSC browser. One file per normalisation method." > <option value="no" selected="True">No</option> <option value="yes">Yes</option> </param> <when value="yes"> <param name="bed_file" type="data" format="bed" label="Transcripts ins BED format" help="12 column BED file containing trancript definitions." /> <param name="genome" type="text" label="Genome Build" help="E.g. hg19" /> <param name="track_name" type="text" label="Track Name" size="20" value="Track Name" /> </when> <when value="no" /> </conditional> and this is how I've set the output: <data format="bedgraph" name="bedgraph_slograt" label="${tool.name} on ${on_string}: Smoot Log2ratio (bedGraph)" from_work_dir="output_dir/slograt.bedgraph"> <filter> bedgraph['check'] == 'yes' and slograt['check'] == 'yes' </filter> <action type="metadata" name="dbkey"> <option type="from_param" name="bedgraph.genome" param_attribute="value" /> </action> </data> When I run the tool the dbkey isn't set to the output file. Does anyone know a workaround? Bests, Nikos

2 4

UCSC Main table browser
by Shrum, Donald C 15 Oct '14

15 Oct '14

When I click get output in the UCSC main table browser in firefox nothing happens. I can fix this by going to about:config in firefox and disabling security.mixed_content.block_active_content I am running galaxy behind an apache proxy using https as we have users authenticate with their hpc accounts. Is there a fix for this aside from making the change to firefox? Thanks, Don FSU Research Computing Center

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