Re: [galaxy-user] blastn Q.
Hi Todd, Are you using the blastn wrapper from the galaxy-central repository? Thanks, K On Tue, Jul 26, 2011 at 12:40 PM, Todd Yilk ty...@lanl.gov wrote: Hello all, I'm using the blastn tool and Galaxy is generating this command (pasting from the log file): command is: perl /opt/galaxy/dev/galaxy_dist_dev_umma/tools/blast/psub -l galaxy_normal.c --fasta /opt/galaxy/dev/galaxy_dist_dev_umma/database/files/001/dataset_1377.dat --cat /opt/galaxy/dev/galaxy_dist_dev_umma/database/files/001/dataset_1378.dat blastn -query /opt/galaxy/dev/galaxy_dist_dev_umma/database/files/001/dataset_1377.dat -db /house/blast_db/ncbi/nt/2011-01-11/nt -task blastn -evalue 0.001 -out /opt/galaxy/dev/galaxy_dist_dev_umma/database/files/001/dataset_1378.dat -outfmt 6 It's failing in Galaxy and I get a script psub: No such file kind of error running it at the command line ... I'm assuming psub here isn't the Unix command. According to find, my Galaxy installation doesn't have a galaxy_normal.c file either. Is there something I didn't install? Thanks, - Todd Yilk Software Developer Los Alamos National Laboratory ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] problem in saving visualizations in trackster
Hi Suman, We have fixed this bug but it has not been pushed to our main instance yet. Sorry for the inconvenience! -K On Wed, Jul 13, 2011 at 2:39 AM, suman pal jiga...@yahoo.com wrote: Hello, I am registered as jiga...@yahoo.com in Galaxy main. recently I am trying to save visualizations in Trackster and repeatedly getting a message unable to save visualization. Is this something related to my PC memory ? This is in reference to RNAseq track visualization while adding tracksGalaxy tutorial): a) accepted hits track bam file b) splice junction bed file c) and the table browser chr19 ref seq track Kindly see where the problem is? sincerely Suman ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] samtools output
As an alternative, you can easily install Galaxy on your own computer to negate the upload time.. it's very easy if you have a *nix system: https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy -K On Thu, Jul 7, 2011 at 11:12 PM, Alison Gardner alison.gard...@adelaide.edu.au wrote: Hello, I am having trouble replicating the great output you get after running samtools Filter pileup on coverage snps with ten columns (with consensus) when I try to run samtools locally on my computer. Unfortunately we are unable to use Galaxy with our new data as our files are too large to upload to the website. Do you use some other scripts in the back ground to get such an informative output? When I run the samtools commands samtools pileup -i -vcf RefSeq.fa aln_sorted.bam aln_ivcf.pileup and then samtools.pl varFilter aln_ivcf.pileup | awk '($3==* $6=20 $7=20 $8=10)' final_aln_ivcf.pileup I do not get useful information in the output that tells me how many reads are calling the alternative allele, what the alternative allele is. Any help would be gratefully received. Thank you Alison Gardner ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] blastn: NameError: name 'cmd' is not defined
Hi Sergei, This is a bug in the script, I will ask Peter, the author, to look into it. Thanks! K On Thu, Jun 30, 2011 at 12:44 PM, Sergei Ryazansky s.ryazan...@gmail.comwrote: Hello all, First of all I would like to thank you guys for developing and mainting this so useful tool as Galaxy! I have our own installation fo Galaxy (galaxy-dist version) with ncbi-blast-plus. Calling blastn results to the following error message: An error occurred running this job:*Traceback (most recent call last): File /home/galaxy/galaxy-dist/tools/ncbi_blast_plus/hide_stderr.py, line 29, in module sys.stderr.write(Error invoking command:\n%s\n\n%s\n % (cmd, err)) NameError: name 'cmd' is not defined* * * Could you please explain, what this error can mean? The link to the shared history is* * http://dmbcserv.dyndns.org:8080/u/hogart/h/test-of-blast* * * * Thank you in advance! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] [galaxy-dev] Peep view for history elements broken on IE?
Hi Peter,
The error when clicking tool menu links is now fixed on galaxy-central tip.
Thanks for reporting!
On Mon, Feb 21, 2011 at 4:48 AM, Peter pe...@maubp.freeserve.co.uk wrote:
On Fri, Feb 18, 2011 at 3:13 PM, Kanwei Li kan...@gmail.com wrote:
All:
I retested under IE7 and found the bugs you were mentioning. This has
all
been fixed on trunk by using a newer local storage library. The only IE7
issue that I am now aware of is when the tool pane is empty when using
workflows. Please let me know if you see any other issues.
Thanks,
K
On Fri, Feb 18, 2011 at 10:50 PM, Kanwei Li kan...@gmail.com wrote:
The empty tool pane issue for IE is now fixed on tip as well.
Thanks,
-K
Hi Kanwei,
I presume this was the fix for the peep view not working on IE7,
https://bitbucket.org/galaxy/galaxy-central/changeset/1dfad17e81a8
That doesn't seem to have been included in the latest galaxy-dist
release.
I've tried both main.g2.bx.psu.edu and test.g2.bx.psu.edu with
IE7 and the peep view is still unchanged. Should the test machine
be working? Perhaps there is a caching problem...
Also, when using either main.g2.bx.psu.edu or test.g2.bx.psu.edu
with IE7 I am now getting a JavaScript error when I click on any tool:
Line: 52
Error: Object doesn't support this property or method
Offending line:
var section_title =
$(this).parents(div.toolSectionWrapper).find(div.toolSectionTitle).text().trim();
Context:
// Log clicks on tools.
$(div.toolTitle a).click( function()
{
var tool_title = $(this).attr('id').split(-)[1];
var section_title =
$(this).parents(div.toolSectionWrapper).find(div.toolSectionTitle).text().trim();
var search_active =
$(this).parents(div.toolTitle).hasClass(search_match);
// Log action.
galaxy_async.log_user_action(tool_menu_click. + tool_title,
section_title,
JSON.stringify({search_active : search_active}));
});
This may be unrelated, but you said you'd been working on the tool
pane too, so I'm mentioning it here rather than starting a new thread
or filing a bug..
Peter
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Re: [galaxy-user] Installing Galaxy locally
Hi David, Yes, it is free and easy to set up, and we have instructions here: https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy Thanks! Kanwei On Mon, Feb 21, 2011 at 5:42 PM, David Matthews d.a.matth...@bristol.ac.ukwrote: Hi, I am not a computer person and very much like using Galaxy because its nice and easy for non-bioinformaticians. Tomorrow I am going to have a meeting with the computer science department here at Bristol and I am hoping to persuade them to install Galaxy within the High Performance Computing Centre for University of Bristol users. As I understand it this is relatively straight forward - that is to say the project was designed for them to install the whole thing locally and reproduce the set up here so I and others can use it here instead of clogging up your machines with our data and requests (!). Is this right? There are no fees or anything and this is something most computer centres should be able to do? I know this may seem a silly question but it seems prudent to ask! Cheers David ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] [galaxy-dev] Peep view for history elements broken on IE?
Hi Peter, The changes are on tip, which aren't in galaxy-dist or on main yet. I will look into the other issues when I get access to my IE7 VM tomorrow. Thanks! K ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] [galaxy-dev] Peep view for history elements broken on IE?
The empty tool pane issue for IE is now fixed on tip as well. Thanks, -K On Fri, Feb 18, 2011 at 3:13 PM, Kanwei Li kan...@gmail.com wrote: All: I retested under IE7 and found the bugs you were mentioning. This has all been fixed on trunk by using a newer local storage library. The only IE7 issue that I am now aware of is when the tool pane is empty when using workflows. Please let me know if you see any other issues. Thanks, K On Mon, Jan 31, 2011 at 1:06 PM, Peter pe...@maubp.freeserve.co.ukwrote: On Mon, Jan 31, 2011 at 5:54 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi, In IE go to Tools - Internet Options - Advanced Tab, then under Browsing section: Uncheck Disable Script debugging (Internet Explorer) Uncheck Disable Script debugging (Other) Check Display a notification about every script error Then you will see the Javascript error when you try to reload the Galaxy page and then try to expand a history item. I would help debug the Galaxy IE issues but I am at work and cannot change these settings on my work computer (the are grey out :( ) -Leandro I had done Disable Script debugging (Internet Explorer) and Display a notification about every script error, but not Disable Script debugging (Other). However I still don't see any javascript error when using Galaxy. Peter ___ galaxy-dev mailing list galaxy-...@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] does Galaxy record tool versions?
Hi Yury, Yes, the jobs table keeps track of the tool version run. I am implementing a new view details feature (already on trunk) and I will add the tool version to the information displayed. Thanks, Kanwei On Thu, Jan 27, 2011 at 5:57 PM, Yury Bukhman ybukh...@glbrc.wisc.edu wrote: Hi, in order to reproduce an analysis, it's good to know not only what tools were used, but also their versions. Is there a way to figure that out from a Galaxy history? I would like to be able to answer questions like what version of bowtie have I run in an analysis performed 6 months ago? Thanks. Yury -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukh...@glbrc.wisc.edu ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Re: [galaxy-user] Peep view for history elements broken on IE?
Hi Peter, Is this still an issue? The error you describe sounds like a jStore problem but I tested it in IE7 and it works. Thanks, Kanwei On Fri, Dec 17, 2010 at 6:34 AM, Peter pe...@maubp.freeserve.co.uk wrote: Hi all, I've recently been testing Galaxy on Microsoft Internet Explorer, IE6 and now IE7. It seems that the peep view for history entries isn't supported. The history elements' names are not links, so clicking on them does not make them expand to show the info (e.g. number of sequences of file size, and the start of the data). This happens both on the public Galaxy instance at Penn State (http://usegalaxy.org) and our local Galaxy instance. Is this a known issue? Peter ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
