[galaxy-dev] From NCBI SRA to UCSC viewer pipeline.

Hi all, i am trying to use a local instance of my galaxy to pre-format data stored at sra-ncbi. Does anyone has a working pipeline that (s)he could share. Here is the pipeline I am using, with some questions. 1/ download sra files to my server. 2/ transform them in fastq using the sra toolbox. 3/

Re: [galaxy-dev] suggestions for the SAM-to-BAM tool

Hello - We haven't forgotten about these suggestions and still plan on working a least a few of them (Kelly would know more). I decided to put them into a bitbucket ticket for easier tracking: http://bitbucket.org/galaxy/galaxy-central/issue/601 Many thanks, as always, for the feedback! Bes

Re: [galaxy-dev] rgWebLogo3 with Probabilities instead of Entropy

FYI: I patched the wrapper to offer all the weblogo Y axis scale options and an additional test to central #5766 and some additional dependency error reporting in #5772 - latest wrapper version is 0.4 On Fri, Jul 1, 2011 at 8:28 AM, Ross wrote: > Thanks - code to accompany good suggestions is

[galaxy-dev] Error in running

Hello, My name is Dayananda Sagar Gangadharaiah and I am a computational biology research associate at the University of Nebraska, Lincoln. We have been trying to install Galaxy for running a software tool called KIRMES. We are encountering the following errors when we run Galaxy using sh .

Re: [galaxy-dev] Several errors from run.sh

> Hi all, > > I am upgrading to the most recent galaxy-dist > 720455407d1c > . > First time run.sh shows following errors as in attachment. > It seems when I use 'manage_db.sh upgrade' it doesn't create necessary > tables for these t

Re: [galaxy-dev] [galaxy-user] Fwd: deleting datasets from history

Thanks for reply! set_dataset_sizes.py works fine for me. By the way, what is difference between file_size and total_size fields? It seems that their values are equal. Although 'allow_user_dataset_purge' setting seems to be very usefull, but it is absent in my universe_wsgi.ini file (galaxy_dis

Re: [galaxy-dev] [galaxy-user] Fwd: deleting datasets from history

Hello Assaf, thank you for the exellent explanation, the situation is become more clearly for me. 06.07.2011 21:19, Assaf Gordon пишет: Hello Sergei, I'm experimenting with the clean-up scripts myself, so perhaps I can offer some information (the galaxy team is welcomed to correct me and/or

Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy

Hi Nate, No, our Galaxy server is not behind Apache. Our Galaxy is configured as it is can be used only by registered users, not anonymous. If I disable require_login in universe_wsgi.ini file then displaying of tracks in our UCSC mirror work fine. But enabling this setting results to the men

[galaxy-dev] bug or feature :)

In our local instance (central version) up to changeset (June 28th) I noticed in the admin panel to manage jobs some odd behaviour; When I set the update Jobs cutoff on 10 seconds and press refresh the item below (administrative Job Lock) is also activated and new jobs are locked. Is that a p

[galaxy-dev] Hidden history item

Hi all, by default I let my tools produce ("the old way") a logfile of the console and additional running statistics. This is convenient at tool setup and ocassionally for troubleshooting. Anyway I would like to make the corresponding history item hidden. I tried including hidden="true" in the

Re: [galaxy-dev] [galaxy-user] double login / deleting users

> 2, > switched from SQLlite to postgres and have this strange double login issue. > Included image - need to login twice and logout twice. Double tab - By any chance, are you using require_login = True in the config? Which logout link are you clicking to get to that page? -- 1, yes, it i

Re: [galaxy-dev] [galaxy-user] double login / deleting users

Joseph Hargitai wrote: > > > 2, > > switched from SQLlite to postgres and have this strange double login issue. > > Included image - need to login twice and logout twice. Double tab - > > By any chance, are you using require_login = True in the config? Which > logout link are you clicking to ge

Re: [galaxy-dev] [galaxy-user] problem with displaying tracks from Galaxy

Sergei Ryazansky wrote: > Hello all, > > we have the UCSC genome browser mirror as well as Galaxy mirror. The > Galaxy has a feature enabling a user to display the data at UCSC genome > browser as custom tracks. I have configured the galaxy to display the data > to our UCSC browser mirror but it d

Re: [galaxy-dev] [galaxy-user] Fwd: deleting datasets from history

Assaf Gordon wrote: > Hello Sergei, > > I'm experimenting with the clean-up scripts myself, so perhaps I can offer > some information (the galaxy team is welcomed to correct me and/or explain > better). > > > 1. If you look at the output of your query, you'll notice that the "purged" > field

[galaxy-dev] BAM display at Trackster

Hi Galaxy team, I am experiencing a problem with visualizing my BAM files through Trackster at my Galaxy instance. Please find the attached image along with this mail. >From the log file I am not seeing any clues about the error message which is displayed on my browser page (A dependency (bai) wa

Re: [galaxy-dev] [galaxy-user] double login / deleting users

Joseph Hargitai wrote: > > Hi, > > 1, > referencing old thread: > http://gmod.827538.n3.nabble.com/Deleting-accounts-td867222.html > > is the delete functionality still status-quo? i.e - there is no delete other > than the workaround? Hi Joe, Since this is regarding a local installation, I've

Re: [galaxy-dev] [galaxy-user] Fwd: deleting datasets from history

Hello Sergei, I'm experimenting with the clean-up scripts myself, so perhaps I can offer some information (the galaxy team is welcomed to correct me and/or explain better). 1. If you look at the output of your query, you'll notice that the "purged" field is 0 for all datasets (I assume 0 is "f

[galaxy-dev] adding qseq2fastq tool to the main instance

Hi, Is it possible to add the qseq2fastq tool developed by vipints (found under repositories) to the Galaxy web portal (the central server, not my own instance of Galaxy)? I believe this would be a popular tool used by many Illumina users? Best Regards, Mete Civelek ___

Re: [galaxy-dev] [galaxy-user] Fwd: deleting datasets from history

Hi, thank you for answer. I have tried to use the mentioned scripts but it seems that the order of their using at first time was incorrect.. As a result, the metadata in database tables are modified but the datasets files corresponded to deleted datasets in history remains unremoved. So, the follow

Re: [galaxy-dev] Bam to fastq

Hi Aaron, On 07/06/2011 04:45 PM, Zschunke, Aaron M. wrote: > Is there any way to convert a certain section of a bam file to fastq > using the galaxy tools? I just want to convert a certain part of the > genome. Thanks. there is the bam_to_fastq tool on the toolshed (http://toolshed.g2.bx.psu.e

[galaxy-dev] Bam to fastq

Hi, Is there any way to convert a certain section of a bam file to fastq using the galaxy tools? I just want to convert a certain part of the genome. Thanks. Aaron ___ Please keep all replies on the list by using "reply all" in your mail cli

Re: [galaxy-dev] [galaxy-user] Fwd: deleting datasets from history

Hi Sergei This is a question better asked on 'galaxy-...@bx.psu.edu' since you refer to your local Galaxy installation. In order to remove the data from your file system, you need to run the 'cleanup scripts', as described on this wiki page: https://bitbucket.org/galaxy/galaxy-central/wik

Re: [galaxy-dev] Cleanup scripts - question or bug ?

Hello Assaf, Thanks very much for your patch - I've applied it in change set 5770:a5e0a5d3c0a1. Greg Von Kuster On Jul 1, 2011, at 5:35 PM, Assaf Gordon wrote: > Hi, > > I'm trying to use the built-in cleanup scripts (instead of my own), came > across a possible bug: > > 1. When running "de

Re: [galaxy-dev] New Tool Shed: Inconsistent field names

On Tue, Jul 5, 2011 at 7:24 PM, Greg Von Kuster wrote: >> >> I have previously commented on the problem with showing the >> "description" on its own without the context of the tool name as >> displayed in Galaxy: >> >> http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-June/005640.html >> >> and: >

[galaxy-dev] Saved Histories - default view on deleted histories (bug)

hi all, in galaxy-central: 1. default view in "Saved Histories" section is set on deleted items ( Jeremy, I did double check this morning on fresh instance :)) 2. in advanced search option: one of the filter switch is deleted and does the same job as active switch 3. Sugestion: Saved Histo