June 2012 - galaxy-dev - lists.galaxyproject.org

Job splitters + SQLIte = OperationalError?
by Peter Cock 14 Jun '12

14 Jun '12

Hi all, We are using PostreSQL for our production Galaxy server, but for development I am using SQLite. Typically it is just me is using the development server, so database contention has not generally been a problem. However, while testing job splitting for breaking up tasks for the cluster, I have noticed today multiple problems with the database when queuing or running the sub-jobs: OperationalError: (OperationalError) database is locked My hunch is that all the child-jobs are created and added to the queue and some of this is happening in parallel leading to contention over the SQLite database. Does this sound likely? Is this something that could be more robust in Galaxy, or should I simply switch to a real database (SQLite or PostreSQL) for these tests? Thanks, Peter

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How to retrieve the current history ID
by Jean-Francois Payotte 14 Jun '12

14 Jun '12

Hi, I already asked a similar question to the Galaxy mailing list toward this topic, but it didn't quite solve my problem. I was seeking help on a way to create a tool which would be able to retrieve all the details (the information you get when clicking on the "eye" icon in a job in the history) for all jobs from an history. This tool would simply create sort of a log file which would contains all the parameters used for each job in the history. I am not interested by retrieving the actual datasets, but only by the "details" information related to the jobs. As I have access to the database, I could create a tool which would access the right tables and retrieve all this information. Although to achieve that, I think I would need to retrieve the history ID first (to be able to retrieve the information related to that particular history from the database). My question is then: Is it possible, from a tool, to retrieve the history ID of the current history? If not, would it be possible to make some changes in galaxy's files, that would make the history ID appear somewhere on the galaxy page, so the user could manually enter the history ID as a tool parameter? Thank you all for your help. This is greatly appreciated!! Thanks, Jean-François

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about apache2 proxy installation and integration with galaxy
by Sabbir Joy 14 Jun '12

14 Jun '12

Dear... can i get one simple apache2 proxy installation process for galaxy.. i tried to follow the instruction in http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy is little bit tricky for me,cause i am new in galaxy as well as ubuntu. but i want it to install in ubuntu. hope i will get one step by step suggestion regards sabbir joy

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Error in db upgrade when updating to May11 distribution
by Liisa Koski 13 Jun '12

13 Jun '12

Hello, I get an error when trying to upgrade my mysql db with sh manage_db.sh upgrade from version 94->95 (see below). Will cause problems with my installation? sh manage_db.sh upgrade 93 -> 94... Migration script to create "handler" column in job table. done 94 -> 95... Migration script to create table for tracking history_dataset_association subsets. (OperationalError) (1059, "Identifier name 'ix_history_dataset_association_subset_history_dataset_association_id' is too long") u'CREATE INDEX ix_history_dataset_association_subset_history_dataset_association_id ON history_dataset_association_subset (history_dataset_association_id)' () done 95 -> 96... Migration script to add column to openid table for provider. Remove any OpenID entries with nonunique GenomeSpace Identifier done 96 -> 97... Migration script to add the ctx_rev column to the tool_shed_repository table. done Thanks in advance, Liisa

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File Type Validators
by Venkat Malladi 13 Jun '12

13 Jun '12

Hi, I am data curator on the ENCODE project. I was looking at the file formats that you support: http://galaxy.genenetwork.org:8080/static/formatHelp.html <http://galaxy.genenetwork.org:8080/static/formatHelp.html%29> and was wondering if you had any file validation software you were using? Thanks, Venkat S. Malladi Data Wrangler ENCODE Project

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How to upload local files in Galaxy
by Mehmet Belgin 13 Jun '12

13 Jun '12

Hi Everyone, I am helping a research group to use Galaxy on our clusters. Unfortunately I have no previous experience with Galaxy, but learning along the way. We are almost there, but cannot figure out one particular issue. This is about configuration of Galaxy, so I thought developers list is a better place to submit than the user list. The galaxy web interface allows for either copy/paste of text, or a URL. Unfortunately we cannot setup a FTP server as instructed due to restrictions on the cluster. The files we are trying to upload are large; around 2GB in size. It does not make sense to upload these files to a remote location (which we can provide an URL for) and download them back, since the data and galaxy are on the same system. However, I could not find a way to open these files locally. I did some reading, and hoped that "library_import_dir" in "universe_wsgi.ini" would do the trick, but it didn't. Therefore, I will really appreciate any suggestions. Thanks a lot in advance! -Mehmet

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Re: [galaxy-dev] Dynamic job runner configuration followup
by Matloob Khushi 12 Jun '12

12 Jun '12

Dear John This sounds interesting, however, I've been struggling for quite a sometimes on limiting the number of options a user could see when it loads the tool wrapper. I have a separate database that records the results obtained from the execution of my developed tool along with the $__user_email__. This way my database table has the results for all galaxy users. My tool also let the users to perform further downstream analysis on the previous run. Therefore, I am using dynamic_options in wrapper xml to populate a dropdown with the results/datasets for the previous run of the tool to choose from. The problem is I have to show the datasets/results for all users, ideally I would like to limit the options in the dropdown to the results belonged to the logged-in user by writing a query something similar to select id, option from myTable where useremail=$__user_email__. However, I have no idea how to grab the $__user_email__ at time of execution of the function assigned via dynamic_options="load_dynamic_values()" in xml wrapper. Would you have any idea how this could be achieved. Thanks. Regards, Matloob

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Configuring Galaxy for FTP upload
by Ciara Ledero 12 Jun '12

12 Jun '12

Hi all, According to Galaxy, uploading files larger than 2GB will surely fail. For this reason, uploading via FTP is recommended. Unfortunately, I cannot download/install an FTP server for Galaxy since I am working on a remote server. I only have access to it via Xming. Is there anyway to allow FTP upload, without using ProFTPd? Can I use Mozilla's fireFTP or Linux's own FTP? (Actually, I tried to connect to Galaxy, but I was denied access.). Thank you in advance for any help. CL

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About the Galaxy Data Library
by Ciara Ledero 12 Jun '12

12 Jun '12

Hi all, I was checking out how to upload large files into Galaxy and I stumbled upon using Data Libraries. In the tutorial, I saw that the 'Create new data library sets' link has a dropdown next to it. When I ran our Galaxy instance, I found out that ours has none. Is that feature available only in the updated version of Galaxy, or could it be activated by changing something in the universe_wsgi.ini? Thanks in advance for any help, CL

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Instructions for migrating users, configuration and data to other Galaxy machine
by Joachim Jacob 12 Jun '12

12 Jun '12

Hi all, I am looking for instructions to migrate users, configuration and data to other Galaxy machine. I have a production Galaxy, with users, histories, pages, data libraries, configured tool panel, running on a postgresdb. I want to move this information to a fresh Galaxy install (same version as production) on another machine. Is this feasible to do without much hassle? I am thinking about a merge/sync of configuration files and dumping and creating the postgresdb,... Has anyone experience with this and a check list for this? The idea is that the user should have no clue that Galaxy is on a new machine: all data, tools, histories, etc... are there. Thanks for your consideration. Kind regards, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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