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 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
Re: [galaxy-user] Peep view for history elements broken on IE?
Weird.. the proxy shouldn't be relevant. Could you open the javascript error console and see what the error is? On Thu, Jan 27, 2011 at 8:57 AM, Peter wrote: > On Wed, Jan 26, 2011 at 7:49 PM, Kanwei Li wrote: >> 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 > > Hi Kanwei, > > I just tried the public Galaxy at http://usegalaxy.org aka > http://main.g2.bx.psu.edu/ and also ttp://test.g2.bx.psu.edu/ which > says it tracks the galaxy-central repo, and for both the history peep > links don't work. This is using Internet Explorer version 7.0.5730.13, > which I believe is the current release (from back in 2007), from two > different Windows XP machines at our institute (which are accessing > the internet via a proxy - perhaps relevant?). > > Peter > ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
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 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] does Galaxy record tool versions?
Hmm, actually the version is the version of the tool wrapper. Unless the wrapper version reflects the actual tool version, we're not keeping track of the tool version as we're simply running the command. Perhaps history annotation is the solution here. -Kanwei On Thu, Jan 27, 2011 at 6:17 PM, Kanwei Li wrote: > 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 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] [galaxy-dev] Peep view for history elements broken on IE?
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 wrote: > On Mon, Jan 31, 2011 at 5:54 PM, Leandro Hermida > 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] [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 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 wrote: > >> On Mon, Jan 31, 2011 at 5:54 PM, Leandro Hermida >> 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] galaxy
Hello Musa, I am forwarding this question to the mailing list so that someone better qualified can help you. -K On Mon, Feb 21, 2011 at 12:18 PM, Musa A. Hassan wrote: > I am trying to use galaxy for the first time and am running into some early > problems. While trying to upload my file which is basically a fq containing > illumina short reads, the file won't upload. When I try the fastq extension > of the same file, it does but then the file isn't recognized by the groomer > hence it's like I have no file uploaded. Do you know how I can circumvent > this problem. > > > Musa Hassan, PhD > Wellcome Trust-MIT Fellow > Massachusetts Institute of Technology > Department of Biology, 68 > 77 Massachusetts Avenue, > Cambridge, MA 02139 > USA ___ 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] 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 wrote: > 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?
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 wrote:
> > On Fri, Feb 18, 2011 at 3:13 PM, Kanwei Li 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 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] Only first 5000 reads are displayed in this tile
Hi Jeremy, The limit means that for the span where the red line is, only the first 5000 features sorted by start position, starting from the tile with the red line, is shown. That usually means it will cut off at some point midway through the tile.. it doesn't indicate that the blank part of the tile has no data. We're working on making this better so that you can at least see some data where the blank space is. Thanks, Kanwei On Sat, Apr 30, 2011 at 5:28 PM, Jeremy Chien wrote: > Hi > > During the visualization of my mRNAseq data, some area have red line > indicating that only the first 5000 reads are displayed. Within this > region, some area have many reads. Some area, where exons exist, I > don't see any reads. How do I interpret the data? If there are no > reads shown in the visualization, although there is a read line saying > only the first 5000 reads are displayed, does the absence of reads > corresponding to a particular exon means it is not expressed? > > Thanks, > Jeremy > > > > ___ > 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] bed to bigbed conversion
Hi Gijs, We only have one node on our main instasnce to do these bigBed and bigWig conversions since they take so much memory, so it may be queued for a while. Thanks, K On Sun, Jun 19, 2011 at 3:38 AM, Gijs Santen wrote: > Dear users, > > I am only recently beginning to discover Galaxy, so please bear with me... > > I am trying to convert a bed to bigbed file, but the job remains > 'grey', it does not start. I repeated the same conversion with the > UCSC sample file > (http://genome.ucsc.edu/goldenPath/help/examples/bedExample.txt) , but > it still does not work. I simply uploaded the file directly from the > link and then used the bed-to-bigbed conversion tool. > > So either I am doing something wrong or could there be an issue with > this conversion on the server? > > Thanks for your insights, > > Gijs > ___ > 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 wrote:
> 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
> 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/
>
___
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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
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use the Galaxy Development list:
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To manage your subscriptions to this and other Galaxy lists,
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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 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] exporting HTML with associated files
Hi Joern, I believe this is caused by the bug of extra_files of shared items having the wrong path. It would be fixed in the upcoming week. Thanks, K On Tue, Jul 12, 2011 at 5:38 AM, Joern Toedling wrote: > Hello, > > I have a question regarding exporting data from Galaxy. I have written a > tool which creates an HTML page and an associated directory containing > pictures and text files. However, if I want to export or share the result > files, only the resulting HTML is shared/exported and not the associated > folder, meaning other people can see the HTML but without the images or > included/linked text files. > > Is there are a way around this? Do I need to export the data in another > format or change the output format of the tool? > > Any suggestions would be appreciated. > > Thanks, > Joern > > -- > Joern Toedling, PhD > Core Facility Bioinformatics > Institute of Molecular Biology gGmbH (IMB) > http://www.imb-mainz.de > Tel.: +49 6131 39 21511 > > ___ > 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 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] 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 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/
