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Request more details from Nikolaos Tur about pyBamTools & pyBamParser dependency packages message
by Jennifer Hsieh 07 Feb '17

07 Feb '17

Hi, I've installed a local instance of Galaxy (on Ubuntu 16.04, python 2.7.12) and have run in to this exact problem (posted by Nikolaos Tur https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/msg03955.ht… ) while trying to add naive_variant_caller tool. Naive_variant_caller can't install because these two dependency packages can't be installed. I basically get exactly the same error message that ends with "IOError: Could not build the egg." Unfortunately I'm very new to both Galaxy and Python (Taking Coursera Galaxy course at the moment) and I don't really understand the solution Nikolaos described about modifying the setup.py to use "setuptools" instead of "distribute". I don't even know where to find setup.py... Can anyone help me with step-by-step details as to how to solve this dependency problem? Much Thanks! -- Jennifer Hsieh PhD Neuroscience (student) Department of Psychiatry and Mental Health University of Cape Town Tell: +27 21 447 3157 Cell: +27 74 841 4761

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GalaxyAdmins Feb online meetup
by Enis Afgan 06 Feb '17

06 Feb '17

Hello everyone, We are going to have a GalaxyAdmins call this month! This is a wonderful venue to get an update on what's going on in the Galaxy community as mostly relevant to people managing Galaxy instance(s). The talk will be held at the 'standard' GalaxyAdmins time: on Feb 16th at 11AM EST. Here is a short description of the topic that will be presented: CloudLaunch is an application for launching Galaxy on the Cloud instances. In this talk, an all-new version will be presented. The new CloudLaunch ( beta.launch.usegalaxy.org) allows multiple flavors of Galaxy to be deployed, Docker images or applications other than Galaxy. Each application can have its own custom user interface developed to accommodate the specific application needs, which will be demonstrated. The call will be held online, using an online meetup room with Adobe Connect. The online conference room will open 15 minutes before the meetup. The call will use Johns Hopkins' Adobe Connect server, which in turn uses Adobe Flash. You are encouraged to connect a few minutes early to work out any unexpected bumps.

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AD/LDAP Integration
by Yip, Miu ki 06 Feb '17

06 Feb '17

Hi all, After setting up AD/LDAP in Galaxy, we noticed that for some reason, some users are able to log in but others were not. We don’t think that it has anything to do with the set up of LDAP or AD at our institute and we’ve tried to find common threads between the users who can log in but we have not found anything interesting. Could someone explain what exactly Galaxy looks for when signing users in with AD/LDAP? We found the source code here: ./lib/galaxy/auth/providers/ldap_ad.py but all the code seems to be functioning properly. Here is one of the error outputs in the log when somebody tries to log in for the first time, but cannot: galaxy.auth.providers.ldap_ad DEBUG 2017-02-01 17:16:17,954 LDAP authenticate: whoami is u:SCIEDU\chess galaxy.auth.providers.ldap_ad DEBUG 2017-02-01 17:16:17,954 LDAP authentication successful server ip - - [01/Feb/2017:17:16:12 -0400] "POST /galaxy/user/login?use_panels=False HTTP/1.0" 200 - “http:/galaxyurl.edu/galaxy/user/login?use_panels=False<http://galaxy/user/login?use_panels=False>" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.95 Safari/537.36" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 55724) Traceback (most recent call last): File "/localdata1/galaxy/.venv/lib/python2.7/site-packages/paste/httpserver.py", line 1085, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib64/python2.7/SocketServer.py", line 334, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib64/python2.7/SocketServer.py", line 651, in __init__ self.finish() File "/usr/lib64/python2.7/SocketServer.py", line 710, in finish self.wfile.close() File "/usr/lib64/python2.7/socket.py", line 279, in close self.flush() File "/usr/lib64/python2.7/socket.py", line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe Any insight would be appreciated. Thanks!

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Question about Data Managers
by Carlos Lijeron 03 Feb '17

03 Feb '17

Everyone, I’m trying to setup various data managers to automatically download and index reference indices. However, I can’t figure out where to change the default location where these are saved. As you can see in the attached image, the default location for the indexes is the … /tool-data/dbkey/index_name However, I would like to save them in /projects/reference_datasets which is a shared location that has a lot of space available. Please advise. Thank you all ! Carlos. [cid:image001.png@01D25B9D.4F483110]

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Ampliocn Sequencing
by Abebe Fola 03 Feb '17

03 Feb '17

Dear Galaxy Community, I am a Ph.D. student working on Plasmodium Genome. My project mainly focuses on short Amplicon sequence using Miseq platform and I have a total of 200 primers designed for targeted 200 loci on 14 chromosomes. I would like to ask you which pipeline would be better to do demultiplex 200 primers/ sample for 96 samples (output from MiSeq), quality filter, mapping reads and variant calling simultaneously. Since the majority of current pipelines (GATK and others) are designed for large reads and diploid organism like human. Any suggestion or comment highly appreciated for my data (short millions of multiplexed reads for a haploid organism)... With Regards, Abe

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How to include local tools with Docker image of Galaxy ?
by Md. Rezaul Karim 02 Feb '17

02 Feb '17

Dear All, I'm a new user of Galaxy. I have been exploring the things and trying to use the Docker image of Galaxy. Eventually, I am planning to run the docker container on our local Cluster. I was wondering if there's any way to include local tools with the Dockerfile. For example using the Docker image of Galaxy at https://github.com/bgruening/docker-galaxy-stable it shows how to include the tools to the Docker image of Galaxy from the Galaxy tool shed as follows: RUN install-repository \ "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_numpy_1_7" \ "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name package_perl_pdf_api2_2_023" \ This command will pull the tools from the Galaxy tool shed and install inside the docker container. But, is there's any similar way to include my own local tools? Regards, _________________________________ *Md. Rezaul Karim*, BSc, MSc PhD Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html <http://139.59.184.114/index.html>

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Peter Cock <p.j.a.cock@googlemail.com>
by Eduardo de Paiva Alves 01 Feb '17

01 Feb '17

Hi Peter, I am wrapping https://rostlab.org/owiki/index.php/Tmseg which takes a PSSM matrix as one of the inputs so I will add the psiblast locally and test and let yo know how it goes. Thank you Eduardo On 01/02/2017 10:10, "Peter Cock" <p.j.a.cock(a)googlemail.com> wrote: Hi Eduardo, Certainly when Luobin Yang submitted the early work on the PSI BLAST wrapper we need the PSSM datatype to be defined, but as you note, that has been done: https://github.com/peterjc/galaxy_blast/commit/65252ee61fdd98e52454ff045fa0… According to the minimal notes I made on the issue for finishing the PSI BLAST wrapper, it is just help text and unit tests needed (which would include active user testing): https://github.com/peterjc/galaxy_blast/issues/19 If you are a PSI BLAST user, it would be very helpful to have your input here. Right now the wrapper is on the TravisCI blacklist because it would fail testing. Likewise it is not included in the Tool Shed. Peter On Wed, Feb 1, 2017 at 9:47 AM, De paiva Alves, Eduardo <eduardoalves(a)abdn.ac.uk> wrote: Peter I noticed there is now a PSSM datatype which is used by NCBI BLAST+ makeprofiledb. Does that allow you to remove psiblast from blacklist in your repository? https://github.com/peterjc/galaxy_blast/blob/13d5b6deca0663d7f1301428574720 b19aea1380/.tt_blacklist Thank you Eduardo On Tue, Feb 5, 2013 at 4:28 PM, Peter Cock <[hidden email]> wrote: Thanks Luobin, I've checked that into my development repository (on my tools branch): https://bitbucket.org/peterjc/galaxy-central/commits/f8f43f8494abdd228998d4 e9fe67b0f2378494e0 That will allow me to track changes etc as we work on the datatypes. Note I am not yet including ncbi_psiblast_wrapper.xml on the Galaxy Tool Shed. Regards, Peter The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683

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psiblast
by De paiva Alves, Eduardo 01 Feb '17

01 Feb '17

Peter I noticed there is now a PSSM datatype which is used by NCBI BLAST+ makeprofiledb. Does that allow you to remove psiblast from blacklist in your repository? https://github.com/peterjc/galaxy_blast/blob/13d5b6deca0663d7f1301428574720 b19aea1380/.tt_blacklist Thank you Eduardo On Tue, Feb 5, 2013 at 4:28 PM, Peter Cock <[hidden email]> wrote: Thanks Luobin, I've checked that into my development repository (on my tools branch): https://bitbucket.org/peterjc/galaxy-central/commits/f8f43f8494abdd228998d4 e9fe67b0f2378494e0 That will allow me to track changes etc as we work on the datatypes. Note I am not yet including ncbi_psiblast_wrapper.xml on the Galaxy Tool Shed. Regards, Peter The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.

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Check running jobs
by Katherine Beaulieu 30 Jan '17

30 Jan '17

Hi there, We are trying to build our own Galaxy cluster and I was wondering if there was a way to check if there are any running Galaxy jobs on a specific server? This would be to determine whether or not to remove the server from the cluster. Thanks! Katherine

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Problem with 'galaxy_packages' dependency resolver in versionless mode
by Peter Briggs 26 Jan '17

26 Jan '17

Dear developers I'm having problems trying to use the 'galaxy_packages' dependency resolver in versionless mode, as described in the docs at: https://docs.galaxyproject.org/en/latest/admin/dependency_resolvers.html#ga… As I understand this: if I manually create a directory structure of the form e.g. /path/to/local_tool_dependencies/my_package/default/ which contains an env.sh file, and if my dependency_resolvers_conf.xml file includes the line: <galaxy_packages base_path="/path/to/local_tool_dependencies" versionless="true" /> then at run time Galaxy should be able to resolve the following requirement in a tool XML file: <requirement type="package">my_package</requirement> Unfortunately although the "versioned" galaxy_packages resolver works as expected (when placed ahead of the "versionless" resolver), I don't seem able to get this working with Galaxy v16.10. Can anyone point out what I'm doing wrong? Thanks! Best wishes Peter -- 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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