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

mpileup -> ImportError: cannot import name stylesheet_link_tag
by Adhemar 07 Feb '14

07 Feb '14

Hi! I was running mpileup and it's showing the error bellow. The strange thing is that 'galaxy/web/framework/helpers/__init__.py' is trying to import 'stylesheet_link_tag' and it's not available in the webhelpers I've installed for both python versions 2.6.6 or 2.7.3 Could you help me with this? Thanx, Adhemar Traceback (most recent call last): File "./scripts/set_metadata.py", line 29, in <module> import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File "/opt/bioinformatics/share/galaxy20130410/lib/galaxy/model/__init__.py", line 23, in <module> import galaxy.datatypes.registry File "/opt/bioinformatics/share/galaxy20130410/lib/galaxy/datatypes/registry.py", line 5, in <module> import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex, graph File "/opt/bioinformatics/share/galaxy20130410/lib/galaxy/datatypes/data.py", line 2, in <module> import metadata File "/opt/bioinformatics/share/galaxy20130410/lib/galaxy/datatypes/metadata.py", line 24, in <module> from galaxy.web import form_builder File "/opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/__init__.py", line 4, in <module> from framework import expose File "/opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/__init__.py", line 28, in <module> import helpers File "/opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/helpers/__init__.py", line 4, in <module> from webhelpers import date, stylesheet_link_tag, javascript_include_tag, url_for ImportError: cannot import name stylesheet_link_tag

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sysadmin help
by Shrum, Donald C 06 Feb '14

06 Feb '14

I have a galaxy server set up, running off of our HPC cluster file system. I'd like to submit a simple job to test my settings with our moab scheduler. Could someone point me to the easiest possible example of uploading and running a job... possible an example a sysadmin with limited knowledge could follow ;) Thanks, Don FSU RCC

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Galaxy in there server
by Bishwo Adhikari 06 Feb '14

06 Feb '14

Hi Galaxy Team, I want to install a local instance of Galaxy on our lab server. It is a Unix server with pretty good RAM and storage. Is there any wiki page or instruction for installation. Thanks, Bishwo

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Put Galaxy behind an index.php page
by Jingchao Zhang 06 Feb '14

06 Feb '14

Hi Galaxy support, Currently we are using Apache proxy to Galaxy and followed the instructions on this webpage: <https://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy> https://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy. Now I am trying to put Galaxy behind a index.php webpage. The scenario would be: 1. user input the Galaxy URL; 2.directed to the php page and then verify their identity; 3. if approved, redirect to Galaxy. Does anyone knows how to configure this in Apache? The reason I am doing this is because the index.php page contains our two-factor authentication API. Any help is appreciated. Thanks. -Jing

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SIFT error on local server
by Alan WiIliams 06 Feb '14

06 Feb '14

Hi, I am trying to get SIFT to run on my local server. I downloaded the sqlite files, and changed the sift_db.loc file to point to the directory I downloaded them to. The weird thing is that the output is green, as in completed successfully, but there is no output and the stdout is: "failed: SIFT_exome_nssnvs.pl -i "/home/alan/galaxy-dist/database/job_working_directory/000/101/sift_input.txt" -d "/home/alan/galaxy-dist/data/hg19/seq" -o "/home/alan/galaxy-dist/database/job_working_directory/000/101" -B 1 -J 1 -K 1 -L 1" Any help would be appreciated. Thanks, -- Alan Williams Life is short, art long, opportunity fleeting, experience deceptive, judgement difficult.

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Launching External functional tests fails with: local variable 'galaxy_test_proxy_port' referenced before assignment
by Renato Alves 06 Feb '14

06 Feb '14

I'm trying to run functional tests on the stable branch of galaxy using: GALAXY_TEST_EXTERNAL=1 GALAXY_TEST_HOST=galaxy GALAXY_TEST_PORT=80 ./run_functional_tests.sh But I'm getting the error: Traceback (most recent call last): File "./scripts/functional_tests.py", line 457, in <module> sys.exit( main() ) File "./scripts/functional_tests.py", line 362, in main if galaxy_test_proxy_port: UnboundLocalError: local variable 'galaxy_test_proxy_port' referenced before assignment 'run_functional_tests.sh help' for help Am I doing something wrong? I'm following the instructions at https://wiki.galaxyproject.org/Admin/Running Tests Renato

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Suitability of Galaxy Instance for Project
by Alecia Korkowski 05 Feb '14

05 Feb '14

HI there, I work for Dr. Sonia Anand in the Medicine department of McMaster University in Hamilton, Ontario, Canada. The project we are working on requires the set up of queriable/searchable database(s) that can handle a large volume of clinical, diet, microbiome, methylation, genotype and expression data. We have 4 cohorts worth of data that we want to store and access from one platform (even though we will be using multiple database softwares to actually store the data) because we want all data to be able to be linked back to an id number. Ideally we are creating something user-friendly that would allow others to view what data we have collected (hence searchable) while not actually giving the data away (we want to be able to control who has access to the data - i.e. create user accounts for them with their requested data if approved). So far we are thinking of using a software called Opal to store our clinical and dietary data as well as Mica, a web-based software that will act as the platform from which interested parties could view and request data from. However, we still need multiple other software to be able to store the other types of data (methylation, microbiome, genotype and expression data). So where Galaxy comes in (I think) is with regards to our genotype data. From what I've gathered, we would want to create our own Galaxy system as a multi-user production environment. Ideally, we would have this system linked to our Mica web page so that our data is still linked in some way. So on that note, would someone be able to tell me if Galaxy is suitable for this type of project? I have already looked into the installation instructions. What I'm more interested in is the data storage aspect. Can it only store genome data or can it also store say methylation data? We want to use as few software as we need to accommodate our data storage issue. Sorry for the long email. I hope I explained everything well enough. We have a large task on our hands so any input at all is greatly appreciated! Alecia Korkowski Data Management Assistant McMaster University 1280 Main St. West, MDCL Rm. 3200Hamilton, ON L8S 4L8

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html output with javascript
by Laure QUINTRIC 05 Feb '14

05 Feb '14

Hello galaxy users, one of my tools returns an html output in which I have links to images and javascripts. Images and Javascripts of the dataset_XXX.dat file are located in a dataset_XXX_files directory. Images are well displayed in galaxy output but javascripts aren't executed. Even an alert('foo') cannot be retrieved. Has somebody already experiment this ? In other related posts, it's said to look at rgenetics fastqc wrapper but no javascript fonctions are called in the fastqc_report.html. Thanks, Laure

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Tool dependencies - how to reinstall manually via command line
by Renato Alves 05 Feb '14

05 Feb '14

Hi everyone, I've just recently decided to try out the automatic installation of dependencies but ran into a few problems. The first is that the machine that currently runs the web component lacks most libraries which would be required for compilation. I realize that this will make it hard/impossible to install anything using this approach. The current setup uses Torque to dispatch to workers behind the scenes. What I would like to know is how to trigger installation (and re-installation in case of errors) of dependencies on the workers. I'm ok with doing this manually directly in the shell of the workers, but would also like to know if the compilation can be setup to happen as job via Torque, therefore compiling in the computing nodes. Furthermore, I'm having some problems with a few dependencies that failed to compile but are still reported as "Installed". One of such tools is: package_r_2_11_0 Which failed to compile with the errors: (from INSTALLATION.log) STDERR configure: WARNING: you cannot build DVI versions of the R manuals configure: WARNING: you cannot build DVI versions of all the help pages configure: WARNING: you cannot build PDF versions of the R manuals configure: WARNING: you cannot build PDF versions of all the help pages configure: error: No F77 compiler found ############################################# but still reports: Name Version Type Installation status R 2.11.0 package Installed Thanks, Renato

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IGV display_application configuration failed with require_login=TRUE
by navratil 05 Feb '14

05 Feb '14

Dear galaxy-dev team, We have configured a galaxy-dist server (stable release) behind an Apache2 proxy (with mod_xsendfile) by following the galaxy wiki. We would like to use the galaxy embeded user authentification with require_login=True option instead of a remote_user configuration on the proxy side. With require_login = False it works but with require_login=True configuration we fail to load .bam files into IGV (local) : The IGV (Version 2.3.18) send this error: */INFO [2014-02-04 16:05:56,660] [MessageUtils.java:60] [Thread-9] Error loading http://XXXXXX/display_application/03501d7626bd192f/igv_bam/local_default/84…: An error occurred while accessing: http://XXXXXX/display_application/03501d7626bd192f/igv_bam/local_default/84…<br>Invalid GZIP/**/header/**/ /* and the galaxy-server send this error_log: */----------------------------------------/**/ /**/XXXXXX - - [04/Feb/2014:16:05:40 +0200] "HEAD /display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam HTTP/1.1" 302 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"/**/ /**/XXXXXX - - [04/Feb/2014:16:05:40 +0200] "HEAD /root HTTP/1.1" 200 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"/**/ /**/----------------------------------------/**/ /**/Exception happened during processing of request from ('127.0.0.1', 46142)/**/ /**/Traceback (most recent call last):/**/ /**/ File "/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread/**/ /**/ self.finish_request(request, client_address)/**/ /**/ File "/usr/lib/python2.7/SocketServer.py", line 334, in finish_request/**/ /**/ self.RequestHandlerClass(request, client_address, self)/**/ /**/ File "/usr/lib/python2.7/SocketServer.py", line 651, in __init__/**/ /**/ self.finish()/**/ /**/ File "/usr/lib/python2.7/SocketServer.py", line 710, in finish/**/ /**/ self.wfile.close()/**/ /**/ File "/usr/lib/python2.7/socket.py", line 279, in close/**/ /**/ self.flush()/**/ /**/ File "/usr/lib/python2.7/socket.py", line 303, in flush/**/ /**/self._sock.sendall(view[write_offset:write_offset+buffer_size])/**/ /**/error: [Errno 32] Broken pipe/**/ /**/----------------------------------------/**/ /**/XXXXXX - - [04/Feb/2014:16:05:40 +0200] "GET /display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam HTTP/1.1" 302 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"/**/ /**/XXXXXX - - [04/Feb/2014:16:05:40 +0200] "GET /root HTTP/1.1" 200 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM/* Any idea ? Vincent -- Vincent Navratil, PhD IR UCBL - PRABI http://www.prabi.fr Bâtiment Gregor Mendel Université Claude Bernard -- Lyon 1 16, rue Raphaël Dubois 69622 VILLEURBANNE CEDEX Tel: +33 472432826 My 'ome' page http://vinavratil.free.fr

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