January 2015 - galaxy-dev - lists.galaxyproject.org

NFS configuration questions + NFS /etc/fstab configuration issue with AMI issue
by Scott Jeschonek 25 Jan '15

25 Jan '15

Hi, I’m setting up a ‘local’ Galaxy server in AWS and had a few questions that I can’t seem to answer. 1. Directory configuration in universe_wsgi.ini — I want to use an NFS from another server. The purpose would be to deposit results there. I may also want to point to another NFS server as a centralized reference / index file system. I tried changing the path for the Indices setting and restarted Galaxy, but CloudMan is showing the file system as “error”. Basically I am trying to wrap my head around the steps to re-pointing to NFS mounts (is it just change the paths in universe_wsgi.ini then restart everything?) 2. CloudMan AMI and fstab — I’m using the latest AMI Cloudman instance and it seems to have an issue with NFS configurations in the fstab. I am not quite sure what is going on, the entry is correct. I’m able to manually mount the filesystems as well so the paths are correct. Is there something specific I need to change on that image? Thanks in advance for any assistance! Scott Jeschonek Avere Systems

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History not updated after upload from custom data source
by Jonathan Laperle 25 Jan '15

25 Jan '15

Hi, I am trying to add a custom data source to my local galaxy following approximatly the methodology described here: https://wiki.galaxyproject.org/Admin/Internals/DataSources?action=show&redi… <https://wiki.galaxyproject.org/Admin/Internals/DataSources?action=show&redi…> The way I went about it is : 1. Galaxy displays my website in the middle frame with a GET containing an URL and a tool_id. 2. The user selects parameters and presses a button which sends a POST request at the URL obtained at point 1. This request contains the URL to download the file and the tool_id 3. Galaxy does a GET request to the given URL and downloads the file. For the xml file it is mostly copy-paste from the UCSC main tool except that it ends with a get rather than a post. The communication seems to work, in fact I can see that the data is properly written to a dataset_XXX.dat file at database/files/000/ just like UCSC. Unfortunately, despite not detecting any error there seems to be an issue as the history is never updated to reflect the fact that a file was added. By comparing the terminal output of UCSC main and my custom data source tool I noticed that the difference was the following line which is not present when I run my tool: 127.0.0.1 - - [24/Jan/2015:19:17:30 -0400] "GET /api/histories/24d84bcf64116fe7/contents HTTP/1.1" 200 - "http://127.0.0.1:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_1) AppleWebKit/600.2.5 (KHTML, like Gecko) Version/8.0.2 Safari/600.2.5” This occurs right after: galaxy.jobs.handler DEBUG 2015-01-24 19:17:30,330 (110) Dispatching to local runner The request to the history API seems to never occur with my custom tool but I cannot figure out why. Thank you for your help.

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Adding a new web-service or perhaps a "webapp" to Galaxy
by Lukasse, Pieter 23 Jan '15

23 Jan '15

Hi, In one of my tools I generate a HTML report which I would like to enhance with some ajax functionality. I would like the possibility to do some backend computations based on the ajax requests. My question is: is there an easy way to add a new web-service to my Galaxy server? The web-service implementation would be in python. Ideally I would like to be able to ship this python file together with my tool via tool shed (and when installing from toolshed, the necessary configurations are applied to the server to enable this python code as a local web-service on the respective Galaxy server). Thanks! Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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show stopper for my galaxy installation
by Fernandez Edgar 23 Jan '15

23 Jan '15

Hello gents, I started this new thread because I have a showstopper for my installation of galaxy. Here's my situation: 1. I have a galaxy server that has internet access. 2. My galaxy server is also my torque server and my only torque submit node. 3. I have three torque compute nodes that DOESN'T have internet access. Now, I've tried uploading a file (larger than 2Gb) via and URL and it fails. However, I've added my galaxy server as a compute node and re-tried to upload the same file and I made sure the job will run on that machine and it works. Now, my compute nodes are in a network that is completely protected from the outside world. So no internet access. What are my option in this case? Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218

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Manually installing rsem_datatypes package from toolshed
by Ryan G 22 Jan '15

22 Jan '15

I'm trying to manually install rsem_datatypes package into my local Galaxy install. I can't use the Toolshed for various reasons. Anyway, I downloaded the package using hg clone https://toolshed.g2.bx.psu.edu/repos/jjohnson/rsem_datatypes I see two files: 1) datatypes_conf.xml, and 2) rsem.py I copied the <datatype extension ...> lines into my config/datatypes_conf.xml file. I also copied rsem.py to lib/galaxy/datatypes/. When I restart Galaxy, it doesn't seem that Galaxy knows how to handle rsem datatypes, as I get this error: galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,519 Error importing datatype module galaxy.datatypes.rsem: 'module' object has no attribute 'rsem' Traceback (most recent call last): File "/data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 210, in load_datatypes module = getattr( module, mod ) AttributeError: 'module' object has no attribute 'rsem' galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,519 Error importing datatype module galaxy.datatypes.rsem: 'module' object has no attribute 'rsem' Traceback (most recent call last): File "/data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 210, in load_datatypes module = getattr( module, mod ) AttributeError: 'module' object has no attribute 'rsem' galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,520 Error importing datatype module galaxy.datatypes.rsem: 'module' object has no attribute 'rsem' Traceback (most recent call last): File "/data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 210, in load_datatypes module = getattr( module, mod ) AttributeError: 'module' object has no attribute 'rsem' I'm obviously missing something but not sure what. I suspect maybe the rsem.py file is not in the right place? Ryan

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Local Galaxy + Google Drive ?
by Nicholas Kline 22 Jan '15

22 Jan '15

Hello and Happy New Year, Back in September 2014, Google announced unlimited storage for users of Google Drive for Education: "Unlimited storage: No more worrying about how much space you have left or about which user needs more gigabytes. Drive for Education supports individual files up to 5TB in size and will be available in coming weeks." source: http://googleforeducation.blogspot.com/2014/09/announcing-drive-for-educati… Pardon me if I missed a discussion about this, but I was wondering if there are any plans to include a feature in Galaxy that would allow it to use Google Drive for storage instead of the local disk? Thanks :)

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galaxy and torque - resource allocation
by Fernandez Edgar 22 Jan '15

22 Jan '15

Hello gents, Hope everyone had a great holiday break! Wish you guys all the best for 2015! I have a couple of questions about how resources (CPU and memory) is allocated when you have a galaxy and torque installation. So I've setup torque with some default and maximum amount of CPU and memory allocations. However, I have some worries when it comes to application (like tophat for example). By default, it takes half the CPU of a server unless specified otherwise. How is the CPU allocation is specified to application like tophat through galaxy? Also, how does galaxy react if a job needs more memory than the limit set by torque? Any information would help me a lot! My sincere salutations to you all!!! Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218

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GALAXY_DATA_INDEX_DIR problem
by Lukasse, Pieter 22 Jan '15

22 Jan '15

Hi, In the documentation page https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax it mentions that "the reserved parameter name GALAXY_DATA_INDEX_DIR - it points to the ~/tool-data<https://bitbucket.org/galaxy/galaxy-central/src/tip/tool-data> directory." However, when we use this in a tool that is installed via toolshed we get a different interpretation of the variable: it seems to point to something like this at runtime: ./database/tmp/tmp-toolshed-gmfcrIr59Sq Ideas? Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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dataset collections
by Jorrit Boekel 22 Jan '15

22 Jan '15

Hi all, I’m toying around a little in galaxy-dist with the dataset collections feature. Since I know this is work in progress, I was wondering about some things I haven’t really found online. It seems to work really well to run a tool on a list of datasets, and a new job is run for each list item. But when I want to reduce to a smaller amount of list items, I understand I need to write some sort of merge tool myself, dependent on the data (all proteomics data here currently). This works well for reducing a dataset to a single file, but I am not sure about how to reduce to a new smaller collection. In the tool I’m writing, I let the user choose the size of the collection. Is there some way to tell galaxy dynamically how many outputs to expect AND put them in a collection? Something like: <outputs> <output type=“data_collection” amount_of_files=“3”/> </outputs> Where 3 is set by the user in a param also. Also, when running with two or more lists as input, is there some sort of correlation between the lists? It seems like it takes the files in dataset no order, so just checking. By the way, thanks very much John and everyone else involved in collections for doing and pushing this stuff. If there are smaller issues I can help with, I’d be thrilled. Can’t stress enough how much this feature means for galaxy adoption in our lab and possibly field. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

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Setting a file download link in Galaxy help
by XiaoTao Jiang 22 Jan '15

22 Jan '15

Dear all I have installed Galaxy in local and I want to set a file download link in galaxy help. I want the user to download a small data-set from the help with a link. However, the general HTML download syntax does not take effect, look the figure I set. Anyone knows how to set the download link? [image: 内嵌图片 1] Thanks for all your attention. Regards Jimmy -- Department of Engineering The University of HongKong

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