January 2016 - galaxy-dev - lists.galaxyproject.org

Sample tracking / external services - still supported?
by Matthias De Smet 20 Jan '16

20 Jan '16

Hi all, Is there still any support out there for sample tracking / data transfers from sequencer / external services? Or is this part of Galaxy completely abandoned/deprecated? All the info in the wiki or other sources is at least 5 years old or refers to files and code that isn’t there anymore. Any help? Thanks! Matthias

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Re: [galaxy-dev] CEAS error - solved
by Philipp Rathert 19 Jan '16

19 Jan '16

Dear Peter, Thanks for your answer. I checke all the above tings and repairing the repository had the effect that the above mentioned error randomly appeared at different dependencies of CEAS (I tried it different times and every time another one or two showed this error). I finally was able to fix the issue earlier this morning by installing mysqldb and mysql-server directly in the docker container. After a restart it worked. Sorry that I didn't write before but there are additional tools that kept me busy. Cheers, Philipp -----Original Message----- From: Peter Briggs [mailto:peter.briggs@manchester.ac.uk] Sent: Dienstag, 19. Januar 2016 13:29 To: Rathert, Philipp, Dr. <philipp.rathert(a)ibc.uni-stuttgart.de>; Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org> Subject: Re: [galaxy-dev] CEAS error Hello Philipp I'm assuming this is the 'ceas' tool from the toolshed which is owned by 'pjbriggs' (that is me)? If it is then from what you describe I'm not sure whether this is a problem with the specific tool or a more general issue with Galaxy's tool installation. My own experiences of trying to debug tool dependency installation issues have been quite haphazard, and although I've seen this particular error (i.e the "database had no record") a few times with various tools, I've never been able to understand what has caused it. First it may be worth trying the "Repair repository" option from the "Repository Actions" menu. If that doesn't help then I've also had some success in the past using the "Manage tool dependencies" option (which allows individual dependencies to be uninstalled and then re-installed). This might work if just one dependency is giving an error. Beyond that I've found it necessary to start drilling into the Galaxy log files. Aside from the log of the actual Galaxy process (verbose but sometimes useful, I don't know how easy this is to find on your Docker instance - I don't have any experience of working with them), often the tool dependencies also create their own INSTALLATION.log files which are worth looking for/at. The following recipe should allow you to access these from within Galaxy (this is for v15.10): - Go to "Admin" -> "Manage installed tools" - Click on the name of the tool of interest (e.g. 'ceas') - Click on the name of an errored dependency under the "Missing tool dependencies" section - In the list of dependencies, click on the name of the errored dependency again This should take you to a page which includes a "folder browser" underneath the heading "Contents", where you can browse the contents of the installed tool dependency folder. Hopefully this will include a file called INSTALLATION.log, and if you click on it then the contents should be displayed and you can look to see if there are any error messages to indicate what went wrong. Sometimes there is no INSTALLATION.log file however, in which case the main log file of the Galaxy process is probably the next place to look (if possible). Sorry I don't have any more definitive answers - please let me know if any of the above helps. Best wishes Peter On 17/01/16 18:36, Rathert, Philipp, Dr. wrote: > Dear All, > > > We are running a local docker-galaxy-stable instance on a Mac OS X > system. and observe a strange error: > > > CEAS > Description: > Revision:f411ce97a351 > > is not installing correctly. > > After installing mysql-python in the container directly basically > every package is installed: > > Installed tool dependencies/ - click the name to browse the dependency > installation directory/ > Name Version Type Installation status > R > <http://129.69.102.42/admin_toolshed/browse_tool_dependency?id=52d6bdfafedbb…> > 3.1.2 package Installed > ucsc_fetchChromSizes > <http://129.69.102.42/admin_toolshed/browse_tool_dependency?id=ae9879a80bd0a…> > 1.0 package Installed > python_mysqldb > <http://129.69.102.42/admin_toolshed/browse_tool_dependency?id=03552bdee8c81…> > 1.2.5 package Installed > bx_python > <http://129.69.102.42/admin_toolshed/browse_tool_dependency?id=f6509e5875624…> > 0.7.1 package Installed > > > Missing tool dependencies/ - click the name to install the missing > dependency/ > Name Version Type Installation status > cistrome_ceas > <http://129.69.102.42/admin_toolshed/manage_repository_tool_dependencies?too…> > 1.0.2.d8c0751 package Error > > > > cistrome_ceas > <http://129.69.102.42/admin_toolshed/manage_repository_tool_dependencies?rep…> > 1.0.2.d8c0751 package Error > The installation directory for this tool dependency had contents but the database had no record. The installation log may show this tool dependency to be correctly installed, but due to the missing database record it is now being set to Error. > > > > A reinstall results in the same error on different dependencies and > it looks like a random event. > > > Does anybody have an idea what could solve the issue? > > > I hope I provided enough information. In your answer please keep in > mind I am a newcomer to all this and a wet lab scientist. > > > Thank you for your help. > > > Cheers, > > > philipp > > > > ___________________________________________________________ > 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/ > -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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tool development
by Matthias De Smet 19 Jan '16

19 Jan '16

Hi All, I would like to create a tool to import data from a sequencer on a networked share to a users history. The ideal setup would be that a query can be submitted to a database which contains all metadata from the sequencer + the path of the sequencer output. The tool should then show the available datasets found in the database and provide checkboxes to select which data should be imported. My question is: how do you guys propose I get started on this? Do I use the API? Is it even possible to get a tool to return some output without submitting it as a job, e.g. using it interactively? Thanks for the help! PS: I know the basics of tool development, but I haven’t got much experience, so all comments are welcome! Matthias

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python_mysqldb caused zip_safe flag not set
by Mic 19 Jan '16

19 Jan '16

Hello, I tried to install CEAS from testtoolshed, but I have recieved the below error from python_mysqldb (tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f) The installation directory for this tool dependency had contents but the database had no record. The installation log may show this tool dependency to be correctly installed, but due to the missing database record it is now being set to Error. I installed MariaDB 10.1 on Ubuntu 14.04 in the following way: apt-key adv --recv-keys --keyserver hkp://keyserver.ubuntu.com:80 0xcbcb082a1bb943db add-apt-repository 'deb [arch=amd64,i386] http://mirror.aarnet.edu.au/pub/MariaDB/repo/10.1/ubuntu trusty main' apt-get update apt-get install mariadb-server libmariadbclient-dev The INSTALLATION.log shows the following information: ... byte-compiling build/bdist.linux-x86_64/egg/MySQLdb/cursors.py to cursors.pyc creating stub loader for _mysql.so byte-compiling build/bdist.linux-x86_64/egg/_mysql.py to _mysql.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying MySQL_python.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying MySQL_python.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying MySQL_python.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt creating dist removing 'build/bdist.linux-x86_64/egg' (and everything under it) Creating /home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python/site.py Processing MySQL_python-1.2.5-py2.7-linux-x86_64.egg Copying MySQL_python-1.2.5-py2.7-linux-x86_64.egg to /home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python Adding MySQL-python 1.2.5 to easy-install.pth file Installed /home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python/MySQL_python-1.2.5-py2.7-linux-x86_64.egg Processing dependencies for MySQL-python==1.2.5 Finished processing dependencies for MySQL-python==1.2.5 ############################################# ############################################# export PYTHONPATH=$PYTHONPATH:/home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python && python setup.py install --install-lib /home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/lib/python --install-scripts /home/lorencm/galaxy/tool_dependency/python_mysqldb/1.2.5/pjbriggs/ceas/82df5af2995f/bin STDERR zip_safe flag not set; analyzing archive contents... What did I miss? Thank you in advance. Mic

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CEAS error
by Rathert, Philipp, Dr. 19 Jan '16

19 Jan '16

Dear All, We are running a local docker-galaxy-stable instance on a Mac OS X system. and observe a strange error: CEAS Description: Revision:f411ce97a351 is not installing correctly. After installing mysql-python in the container directly basically every package is installed: Installed tool dependencies - click the name to browse the dependency installation directory Name Version Type Installation status R <http://129.69.102.42/admin_toolshed/browse_tool_dependency?id=52d6bdfafedbb…> 3.1.2 package Installed ucsc_fetchChromSizes <http://129.69.102.42/admin_toolshed/browse_tool_dependency?id=ae9879a80bd0a…> 1.0 package Installed python_mysqldb <http://129.69.102.42/admin_toolshed/browse_tool_dependency?id=03552bdee8c81…> 1.2.5 package Installed bx_python <http://129.69.102.42/admin_toolshed/browse_tool_dependency?id=f6509e5875624…> 0.7.1 package Installed Missing tool dependencies - click the name to install the missing dependency Name Version Type Installation status cistrome_ceas <http://129.69.102.42/admin_toolshed/manage_repository_tool_dependencies?too…> 1.0.2.d8c0751 package Error cistrome_ceas <http://129.69.102.42/admin_toolshed/manage_repository_tool_dependencies?rep…> 1.0.2.d8c0751 package Error The installation directory for this tool dependency had contents but the database had no record. The installation log may show this tool dependency to be correctly installed, but due to the missing database record it is now being set to Error. A reinstall results in the same error on different dependencies and it looks like a random event. Does anybody have an idea what could solve the issue? I hope I provided enough information. In your answer please keep in mind I am a newcomer to all this and a wet lab scientist. Thank you for your help. Cheers, philipp

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Error in matplotlib
by Shane Kelly 19 Jan '16

19 Jan '16

Could anyone shed some light on this error please? (Information from the Galaxy operator here who is having trouble posting) The error is for the dependency “package_matplotlib1_2” The full error information is Name: matplotlib Version: 1.2.1 Type: Package Status: Error Error: File "/home/little_galaxy/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 128, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( install_environment, tool_dependency, actions_dict ) File "/home/little_galaxy/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 86, in install_and_build_package initial_download=True ) File "/home/little_galaxy/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step initial_download=initial_download ) File "/home/little_galaxy/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 694, in execute_step dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums ) File "/home/little_galaxy/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 187, in url_download raise Exception( err_msg ) Error downloading from URL https://github.com/matplotlib/matplotlib/archive/v1.2.1.tar.gz#md5#47ee56f5…: HTTP Error 400: Bad Request

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package dependencies
by Langhorst, Brad 16 Jan '16

16 Jan '16

Hi: I just tried to install khmer from the toolshed. I don’t think it’s installing correctly - but I don’t know if it’s a tool problem or something with my setup. the tool-dep directory has khmer/2.0/crusoe/package_khmer_2_0/c7702a7d26e8/ but it’s empty. This tool has a package dependency like this: <?xml version="1.0"?> <tool_dependency> <package name="khmer" version="2.0"> <install version="1.0"> <actions> <action type="setup_python_environment"> <repository changeset_revision="5caf592bb259" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="python" version="2.7" /> </repository> <package>https://pypi.python.org/packages/source/k/khmer/khmer-2.0.tar.gz#md5=1f610a…</package> </action> </actions> </install> </package> </tool_dependency> what does that fragment tag mean? How does this work. Do I have to set up something to deal with making a python environment? It also uses this @BINARY@ variable that I have not seen before. galaxy search for ‘@BINARY@‘ turns up nothing. Can anybody point me in the right direction here? Thanks! Brad — Brad Langhorst, Ph.D. Development Scientist New England Biolabs

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Re: [galaxy-dev] Bowtie2
by Laforest, Martin 13 Jan '16

13 Jan '16

Seems to work after server reboot... Thanks Martin De : Laforest, Martin Envoyé : 13 janvier 2016 10:00 À : 'galaxy-dev(a)lists.galaxyproject.org' Objet : RE: Bowtie2 Oups I made a mistake.... I have problems with the tophat wrapper, not bowtie. Bowtie runs fine... Tophat - fast splice junction mapper for RNA-Seq reads 4eb3c3beb9c7 Devteam Packages package_bowtie_2_2_5 and package_2_0_14 are installed... Thanks Martin De : Laforest, Martin Envoyé : 13 janvier 2016 09:43 À : 'galaxy-dev(a)lists.galaxyproject.org' Objet : Bowtie2 Hello, Please excuse my simple question since I'm a newbie... I've searched the mailing list but did not find the appropriate answer... I have a new Galaxy installation. I installed the tool "Bowtie2: Fast and sensitive read alignment" (Revision 019c2a81547a, Owner: devteam). The tool apparently runs fine and I can download the BAM file at the end and see its content (with IGV for example). The problem is that my dataset is red and when I check the error, I get "OSError: [Errno 2] No such file or directory"... Maybe it is when Galaxy tries to set the data type, I don't know. Many thanks for your help. Martin

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Graceful restart with uWSGI/Supervisor
by Anthony Bretaudeau 13 Jan '16

13 Jan '16

Hi, To manage our galaxy server startup, I am trying to switch from an old init.d script to uWSGI and supervisor. I followed the help in https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling, and I am now able to start, and even to stop galaxy (5 processes) and its 2 handlers. I am quite proud of myself \o/ BUT there is one thing that is missing from my good old init.d script: I use to be able to do a graceful restart (i.e. no downtime for users) with something like: GALAXY_RUN_ALL=1 ${GALAXY_DIST_HOME}/run.sh restart --wait Has anyone ever found a way to do it with uwsgi? I find very few helpful information about that on google... I suppose what I need is "chain reloading", but am not sure how to implement it correctly. Anthony

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Re: [galaxy-dev] Bowtie2
by Laforest, Martin 13 Jan '16

13 Jan '16

Oups I made a mistake.... I have problems with the tophat wrapper, not bowtie. Bowtie runs fine... Tophat - fast splice junction mapper for RNA-Seq reads 4eb3c3beb9c7 Devteam Packages package_bowtie_2_2_5 and package_2_0_14 are installed... Thanks Martin De : Laforest, Martin Envoyé : 13 janvier 2016 09:43 À : 'galaxy-dev(a)lists.galaxyproject.org' Objet : Bowtie2 Hello, Please excuse my simple question since I'm a newbie... I've searched the mailing list but did not find the appropriate answer... I have a new Galaxy installation. I installed the tool "Bowtie2: Fast and sensitive read alignment" (Revision 019c2a81547a, Owner: devteam). The tool apparently runs fine and I can download the BAM file at the end and see its content (with IGV for example). The problem is that my dataset is red and when I check the error, I get "OSError: [Errno 2] No such file or directory"... Maybe it is when Galaxy tries to set the data type, I don't know. Many thanks for your help. Martin

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