Hi,I am looking how to improve the import of BAM files into galaxy.I often use the Upload tool in the Data Libraries to upload a number of BAM files into galaxy (after recombining several readgroups into a BAM file for the library, which I unfortunately have to do OUTSIDE of galaxy since it cannot
,SamOn Wed, Aug 21, 2013 at 4:11 PM, Anthonius deBoer <thondeb...@me.com> wrote:Hi,I am using the latest version of galaxy at my local installation and I try to use trackster to display a simple BED file, but it invariably complains about not having a converter for this datatype and it tells
Hi,I am using the latest version of galaxy at my local installation and I try to use trackster to display a simple BED file, but it invariably complains about not having a converter for this datatype and it tells me to check my datatypes_conf.xml which I did (not sure what I should be looking for,
Hi,I was very excited to see the re-run option and associate with paused jobs option working very well..I was hoping to be able to re-run a job like this from the API, but cannot seem to find any API calls that corresponds to this here:http://galaxy-dist.readthedocs.org/en/latest/lib/galaxy.webapps
I don't think it's a memory issue (but what made you say that?) since each process is hardly using any memory, although VIRT memory in top is showing 2.7GB per python process, RES is only ever going to 250MB and I have a 16GB machine (although SWAP is only 4GB but not using any of the swap either,
Hi,I am getting the error "FATAL: sorry, too many clients already" in in my local Galaxy instance in the POSTGRES database log.I have set max_connections = 1000 in already in "postgresql.conf" and STILL get this error...I was running a Flowcell with about 96 samples and a workflow with about 50 st
u On Wed, Jun 5, 2013 at 5:15 PM, Anthonius deBoer <thondeb...@me.com> wrote: > Hi, > > I am trying desperately to setup my GALAXY system so that if you enter the > website, you need to authenticate yourself using the proxy setup... > I also would like to be able to BYPASS th
Hi,I am trying desperately to setup my GALAXY system so that if you enter the website, you need to authenticate yourself using the proxy setup...I also would like to be able to BYPASS the proxy server when an API call is made...In the example proxy setting I have setup in the following way:ReWriteR
Hi,I am trying to use the API to upload a file and since the upload can take a long time (see my previous post) I need to check if the upload has completed so I know I can start a workflow (or can I start a workflow even when the file is still in the "queued" state?)...I have successfully used the
Hi,I am uploading a lot of data to our galaxy system, and it seems that the index creation is always happening on the server instance of the galaxy server and NOT on the cluster.This seems to be particularly true for BAM files, where the index creation is being done on the galaxy server and it is d
I have not seen any reply to this question from last year, so I wanted to re-up it again...I also run into this issue quite often and with the recent introduction of the (half completed?) feature of the notion of Paused-Jobs it seems we are getting very close to this working...I know I can re-run a
d, Apr 3, 2013 at 9:44 PM, Anthonius deBoer <thondeb...@me.com> wrote:Hi,There seem to be some undocumented changes to the way multiple datasets are provided to workflows.There seems to be some loss of functionality, since I cannot figure out how to select ALL files in the window...I can selec
Hi,There seem to be some undocumented changes to the way multiple datasets are provided to workflows.There seems to be some loss of functionality, since I cannot figure out how to select ALL files in the window...I can select individual files, but not all files that I can see..It used to be possibl
Hi,I would like to allow interactive use of the Galaxy UI to be run in a different "destination" from a tool that is run from a workflow...I am looking into setting up the dynamic running method in jobs_conf.xml and a special dynamic function I am defining, but not too sure how I can determine (if
It seems that the examples in the jobs_conf.xml file incorrectly defines the DRMAA runner asgalaxy.jobs.runners.drmaa:DRMAARunnerwhich should begalaxy.jobs.runners.drmaa:DRMAAJobRunnerIt's really unhelpful if a major change to the way things are run contains these kinds of issues/bugs in the exampl
Hi,I have some problems with the cleanup scripts...I seem to have a dataset_instance that is "None" and if it tries to delete that you obviously get an error. (See below..>I added the print statement, but the line is the same)...I wonder how I could get a dataset with a None definition and how can
Ah...Found what root squashing is and yes, that is turned on our isilon system...So out of luck I take it? We need to chown? we cannot fake the submission name in another way ;)ThanksThonOn Feb 20, 2013, at 10:32 AM, Anthonius deBoer wrote:I cannot run chown even as a sudo command...Same error
I cannot run chown even as a sudo command...Same error...What is root squashing? I am reading on the internet that it is very common not to allow users to change the ownership of files...ThonOn Feb 20, 2013, at 05:52 AM, Nate Coraor wrote:On Feb 19, 2013, at 11:02 PM, Thon de Boer wrote: > Hi, >
sis/svcgalaxy/galaxy-dist/static/favicon.ico [L]RewriteRule ^/robots.txt /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/robots.txt [L]RewriteRule ^/admin/jobs(.*) http://localhost:8079/admin/jobs$1 [P]RewriteRule ^(.*) http://localhost:8080$1 [P]On Feb 14, 2013, at 02:41 PM, Anthonius deBoer
Hi,I have been struggling with setting up my galaxy system to allow it to use the LDAP authentication for users that come in through the frontend, while not wanting to have to use authentication when user want to access through the APII found some solution and I thought I'd share it with the wo
Hi,I have noticed that in the latest version of galaxy-dist, my history does not automatically update anymore.I have to press the refresh circle to have it update...I did change my proxy setup a little, so it would no longer require API calls to be authenticated, while access through the frontend w
Hi,One very cool feature was to be able to search quickly for datasets using the search feature.You could continue to add terms until your search results in the correct set...It was basically doing an AND search for the terms you entered.This feature has seem to have disappeared?Now a search te
this list?Are there any groups that routinely do 100-200 pairs of FASTQ files from within galaxy?I would like to hear their experience...ThanksThonOn Feb 13, 2013, at 01:44 PM, Nate Coraor wrote:On Feb 13, 2013, at 4:12 PM, Anthonius deBoer wrote: > Would this problem go away if I only used
Hi,I see this in the log file...this really "suc"ks :)ThonException in thread Thread-1:Traceback (most recent call last): File "/usr/lib64/python2.6/threading.py", line 532, in __bootstrap_inner self.run() File "/usr/lib64/python2.6/threading.py", line 484, in run self.__target(*self.__args
100's of BAM files can take hours just to get started...ANy change we can run multiple managers?ThanksOn Feb 13, 2013, at 07:59 AM, Nate Coraor wrote:On Feb 7, 2013, at 2:43 PM, Anthonius deBoer wrote: > That's very unfortunate... > I have a ton of tools and I guess now I have to
defined On Feb 13, 2013, at 06:00 AM, Jeremy Goecks wrote:I will try to reproduce. In the meantime, can you please check the _javascript_ console and forward along any errors that you see? Thanks, J. On Feb 12, 2013, at 11:15 PM, Anthonius deBoer wrote: > Hi, > > I had created a tr
Hi,I am continue to struggle with the proccess of killing jobs that run on the SGE cluster when deleting histories.I would assume that jobs get removed from the queue when a history they are part of is deleted but in most cases, the jobs stay on the cluster and are not killedI also never have b
I think the hg clone link on the news brief is incorrect:it states: hg clone https://bitbucket.org/galaxy-dist#stableProbably should be hg clone https://bitbucket.org/galaxy/galaxy-dist#stableThon
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Hi,I had created a trackster vizualization that had not finished indexing yet, and I decided to change it into a circster visualization.I then added a few more BAM files and tried to save the visualization and now it just hangs there...no errors in the logs so far, but no saving of the visualizatio
te rolling restart of your web processes to avoid service disruption while still loading the tool updates. -Dannon On Feb 6, 2013, at 8:40 PM, Anthonius deBoer <thondeb...@me.com> wrote: > I am indeed using multiple web processes and I guess I am talking about the "old" admine to
esses, and are you referring to the old admin tool reloader or the toolshed reloading interface? -Dannon On Feb 5, 2013, at 9:13 PM, Anthonius deBoer <thondeb...@me.com> wrote: > Hi, > > I find that reloading a tool's configuration file does not really work. > First, yo
Hi,I find that reloading a tool's configuration file does not really work.First, you have to click the reload buttow twice to actually have it update the VERSION number (so it does read something)...But when I try to run my tool, the old bug is still there...I am using proxy server so something may
Nope...Still only through the API can you access multiple, related files in a workflow...There is some ugly hack where you have to select the related files, and you need to hack some of the code, but if you are willing to do some editing of the source code, I believe there is something in this mail
Hi,I am trying to build some workflows for people that are part of a group and I want to share that workflow with them, so that they can run the workflow without having to make a local copy for them self.It seems I can only share a workflow in that manner with an individual, and not with a group...
nctions, like I did here for getThonOn Jan 31, 2013, at 11:44 AM, Carl Eberhard wrote:Hello Anthonius,Can you elaborate on how you're invoking the API? How are you calling it?Thanks,CarlOn Wed, Jan 30, 2013 at 6:30 PM, Anthonius deBoer <thondeb...@me.com> wrote:Hi,I am trying to use
Hi,I am trying to use the API with my galaxy server running behind a proxy server.How do I pass username/password information to the API so it can actually run?If I use the regular API calls I get a access denied...ThanksThon
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Hi,I continue to see this error in the logs, every time a jobs finishes:galaxy.objectstore CRITICAL 2013-01-30 11:42:14,161 /mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/327 deleteerror [Errno 39] Directory not empty: '/mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/327'When
e where the chrom column is "1" rather than "chr1"? Column auto-detection for interval files looks for a name like chr, contig, scaffold, ...--James Taylor, Assistant Professor, Biology/CS, Emory UniversityOn Tue, Jan 22, 2013 at 4:35 PM, Anthonius deBoer <thondeb...@me.com> wr
n is "1" rather than "chr1"? Column auto-detection for interval files looks for a name like chr, contig, scaffold, ...--James Taylor, Assistant Professor, Biology/CS, Emory UniversityOn Tue, Jan 22, 2013 at 4:35 PM, Anthonius deBoer <thondeb...@me.com> wrote:Hi,I have
I also second this request to get it addressed (Where can we vote on bug fixes ?! :) ...It is very weird that samtools is run on the local machine and it even does the indexing sequentially...ThonOn Jan 23, 2013, at 03:28 PM, Kyle Ellrott wrote:I'm currently in the process of loading (path paste)
Hi,I have noticed for a while now that BED files are not recognized correctly or at least not parsed out correctly.I notice that invariably, the (9 column) BED file comments state there is 1 region and X comments, where X + 1 is the actual number of regions in the file..Here's a few lines from the
I have seen this same issue exactly. Python just dies without any errors in the
log. Using the latest galaxy-dist
Sent from my iPhone
On Jan 20, 2013, at 8:35 PM, Derrick Lin wrote:
> Update to the 11 Jan 2013 dist does not help with this issue. :(
>
> I checked the database and have the look
Hi,I am seeing this in the log files when I start up...It seems to identify a name error in the file update_manager.pyI am not sure if it is related, but some of my manager processes are just dying without any errors in the log...The processes are just killed (The PID is just gone, so run.sh --sto
an me just waiting for bug reports before getting it)?Thanks,A very grateful Thon...On Jan 17, 2013, at 05:23 AM, Jeremy Goecks wrote:This has been fixed in -central and will be available in the next Galaxy distribution.Thanks,J.On Jan 16, 2013, at 10:02 PM, Anthonius deBoer wrote:Hi,Tried to rem
Hi,Tried to remove a trackster visualization in the latest galaxy-dist and got this error:Error Traceback:View as: Interactive | Text | XML (full)⇝ NameError: global name 'util' is not definedURL: http://srv151/visualization/list?f-sharing=All&sort=-update_time&f-tags=All&operation=Delete&f-t
Never mind...I was pointing to some older galaxy-central scripts in my proxy setup...It's all good now :)ThonOn Jan 14, 2013, at 08:03 PM, Anthonius deBoer wrote:Hi,I just updated to the latest galaxy-dist, but now my history pane is not showing the options and no reload etc.Attached a pi
Hi,I just updated to the latest galaxy-dist, but now my history pane is not showing the options and no reload etc.Attached a picture, not sure it will come through...Any ideas? Now my galaxy is totally broken...I was hoping not to have to worry about it as much by switching to the galaxy-dist,from
You could rename the file from "GenomeAnalysisTKLite.jar" to "GenomeAnalysisTK.jar" in the directory where you placed GATK...Something like/home/svcgalaxy/g/tool-data/shared/jars/gatkand it should work...ThonOn Jan 03, 2013, at 02:54 PM, mark.r...@syngenta.com wrote:Hello Is it possible to redirect
(UCSC; chr[0-9XYM]*) (hg19)On Jan 03, 2013, at 04:48 PM, Anthonius deBoer wrote:Got this when trying CIRCSTER on latest galaxy-dist.Does this mean my system does not know about certain genomes?aTrackster works fine...ThonError Traceback:View as: Interactive | Text | XML (full)⇝ TypeError
Got this when trying CIRCSTER on latest galaxy-dist.Does this mean my system does not know about certain genomes?Trackster works fine...ThonError Traceback:View as: Interactive | Text | XML (full)⇝ TypeError: argument of type 'NoneType' is not iterableURL: http://srv151/visualization/circster
Hi,I installed PICARD from the main tool shed in the latest update from galaxy-dist and when I clicked on the picard installed dependency link in the admin tool, I got this...Error Traceback:View as: Interactive | Text | XML (full)⇝ TypeError: 'NoneType' object is not iterableURL: http://srv1
Hi Greg,Indeed you need to install many many tools to make galaxy run.You may be better off getting the cloud version, which has many tools already installed.Getting GALAXY to run with all the tools that are provided is not a trivial task...It gets MUCH better with the TOOLSHED option, since this c
I have a similar problem in the latest galaxy-dist version from Dec 3rd.When I run BWA or BOWTIE2 (but it probably is not limited to those) the resulting SAM/BAM file is shown to be empty and none of the metadata has been updated.When I do a manual "Auto-detect" in the "Edit Attributes" section of
Great solution...Glad I could help!On Dec 05, 2012, at 02:56 PM, Nate Coraor wrote:On Dec 5, 2012, at 5:10 PM, Anthonius deBoer wrote: > I confirmed that you have to include the version numbers for these toolshed tools: > > This works: > toolshed.g2.bx.psu.edu/repos/devteam/
smp 4/ThonOn Dec 05, 2012, at 02:00 PM, Anthonius deBoer wrote:Hi Ross,I was indeed expecting something like that and when I tried what you suggestyed, it worked :)you need to use the complete path to the tool (including version number??!?!) in the tool-runner definition to make it be able to be set
s tool names to keep versions under control. Fixing this might be a little tricky since one goal is to keep multiple tool versions separate - but we will all want all versions of bwa_wrapper to use the same runner flags?On Thu, Dec 6, 2012 at 8:40 AM, Anthonius deBoer <thondeb...@me.com> wrote:H
Hi,In my fresh copy of galaxy-dist I am having a problem with tools being run only with the default tool runner and not with the assigned tool runner I created in the [galaxy:tool_runners] section...This is the setting for bwa_wrapper in my universe_wsgi.ini:bwa_wrapper = drmaa://-V -q long.q -pe s
Hi,I installed a fresh copy of galaxy-dist on my VM machines and I am seeing this as the first line of the log files./mnt/ngs/analysis/svcgalaxy/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indic
alaxy-dist in your local Galaxy instance to use the main Galaxy tool shed.Greg Von KusterOn Dec 4, 2012, at 7:06 PM, Anthonius deBoer wrote:Got this when trying to install GMAP from the tool shed...Any ideas?Error Traceback:View as: Interactive | Text | XML (full)⇝ Key
Got this when trying to install GMAP from the tool shed...Any ideas?Error Traceback:View as: Interactive | Text | XML (full)⇝ KeyError: 'includes_repository_dependencies'URL: http://srv151/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=4131098be
Hi,I am trying to figure out how to run galaxy distributed over several physical servers, with different IP addresses...The wiki on scaling and load balancing only speaks of balancing on the same physical server, but does not address how to put a handful of managers on a different physical server..
e doable now in Galaxy (since pull request 75). All
> you need to do is comment out line 40 of templates/workflow/run.mako
> and then you should be good to go.
>
> -John
>
> On Sat, Nov 10, 2012 at 4:04 PM, Anthonius deBoer wrote:
>> Very likely you have to use the API
Very likely you have to use the API for these kinds of workflows.
The UI for Galaxy is very limited in workflows that deviate from the One Input
paradigm.
Even for the most common workflow (paired end DNA sequencing of multiple
samples ) you have to resort to using the API...Puzzling...
Regards
Hi,I always see this error pop up in the logs when one of the steps failed...It seems to have a problem deleting the working directory since it claims they are not empty.Ofcourse when I check, the directory is empty, but I am left with a gazilion empty working directories, alhtough no problems with
I am running under virtualenv and running python 2.6 but I am suspecting that it is not passed on to my cluster that I am running under 2.6But thanks for pointing me in this direction...On Nov 07, 2012, at 01:08 AM, Geert Vandeweyer wrote:We recently ran into that issue as well. It seems that
Got this in the latest pull of galaxy central...Ideas?Traceback (most recent call last):
File "./scripts/set_metadata.py", line 24, in ?
import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers
File "/mnt/ngs/analysis/svcgalaxy/
Hi Geert,I did something similar but two things I got stumped on and maybe you found a way to do this through the API.1) I would like to put some of my results into a datalibrary. But i can't find the API call for that. Do you know if this is possible? I asked repeatedly here on the dev list but n
So I take it this is currently not possible with the API?I know I could dump the files to the filesystem and re-load it with the load into library from disk step in the API, but it seems slightly wasteful :)ThanksThonOn Oct 22, 2012, at 06:29 PM, Anthonius deBoer wrote:Hi,I am trying to
and if you use something like;label="#echo os.path.splitext ( str ( $input.name ) ) [ 0 ] #-BWA.bam"You can change "SomeFile.fastq" into "SomeFile-BWA.bam".This allows you to remove the extension (.fastq in this case), insert some extra text after the original name and set the right extension (Not
d to running.
>
>
> For our server, switching from "set_metadata_externally = False" to
> "set_metadata_externally = True" did not speed up anything.
>
> Regards, Hans-Rudolf
>
>
> On 09/19/2012 04:27 PM, Nate Coraor wrote:
>> On Sep 18, 2012, at 6
Hi,
I am trying to automatically move certain outputs from my workflow into a
particular folder of a particular library THROUGH THE API.
I can find how to do the reverse, but can't find an example of how to do this...
Is there an equivalent of passing the history ID, like you can pass the Librar
The API allows you to do some of that...
If you pass it the ID of the object (input.id) you can do all kinds of requests
with the API.
Look in the scripts/api folder of your local Galaxy instance...
NOTE: The API seems to be a bit of a stepchild, since there is no good
documentation and it seem
Thanks, but that's too free form. Leaving it up to the user to define the keys.
I would like to add defined keys that users can fill in in some form.
Regards,
Thon
===
Thon Deboer | Bioinformatics Guru
thondeb...@me.com | 650-799-6839
On Oct 12, 2012, at 12:49 PM, Jere
Hi,Is there an easy way to add meta data to a dataset without having to resort to coding it into the dataset definition?I am looking for things beyond tags and just a simple key value pair association would be enough...I cannot see anything that is obvious, but I feel something must be there...Than
I gave up on figuring out why jobs don't get started for 15 minutes and started a new instance of galaxy, but when I tried to create a new data library, I got this error...Error attempting to display contents of library (TEST DATA): No module named controllers.library_common.Any ideas?Thon
Hi,Jobs that I start on my in-house Galaxy instance now take up to 3-4 min to go from queued to Running, even though there is nothing much going on on the galaxy server...I have been running this instance since June and use a relatively new version of Galaxy-central (Last update, 22-Aug changeset:
Hi,I am running into some out-of-disk space errors with some of my jobs and this was because the /tmp space is running out of space.I want to use a different temporary directory but I can't get GALAXY to pick up my settings...I use this in the .ini file# Temporary files are stored in this directory
, you may have caused problems with your environment that could render it un-useable.On Jul 11, 2012, at 6:46 PM, Anthonius deBoer wrote:Hi,I had some more bad luck trying to install the GMAP stuff from the TOOLSHEd but revision 10 is broken since it does not allow you to select a section and just
Hi,I had some more bad luck trying to install the GMAP stuff from the TOOLSHEd but revision 10 is broken since it does not allow you to select a section and just stores the programs in the main tree...But when I tried to remove the tool I got the following error for every run, since the sniffers wh
track down the problem in your environment. Thanks! Greg Von Kuster On Jul 11, 2012, at 2:46 PM, Anthonius deBoer wrote: > I'm getting this error when I try to run the tool migration: > > sh ./scripts/migrate_tools/0003_tools.sh install_dependencies > No handlers could be
the problem in your environment. Thanks! Greg Von Kuster On Jul 11, 2012, at 2:46 PM, Anthonius deBoer wrote: > I'm getting this error when I try to run the tool migration: > > sh ./scripts/migrate_tools/0003_tools.sh install_dependencies > No handlers could be found for
I'm getting this error when I try to run the tool migration:sh ./scripts/migrate_tools/0003_tools.sh install_dependenciesNo handlers could be found for logger "docutils"Repositories will be installed into configured tool_path location ../shed_toolsAdding new row (or updating an existing row) for r
I am running galaxy on a system that normally runs all jobs on the cluster, but some jobs need to be run locally...But when I restart galaxy when these jobs are running, those jobs fail (and I am fine with that)...But then when I check the logs, I see a lot of this kind of errors and the word CRITI
OK...I tried this and it no longer removes the entries from the history...Thanks!I do see that each of the new histories I create still have a reference to some of the other files I pick up from the library (such as dbSNP) but those entries in the history have the number "None" in stead of the usua
Hi,I am about to embark of embedding PINDEL into GALAXY since it is not available in the TOOLSHED.Before I do, I thought I check if someone has already done this and could send me their XML so I don't have to start from scratch...Thanks!Thon
_
WOW...I guess I know how you guys that designed the API think :)Small other question...Is it possible (yet) to pass a parameter to the API yet, that is NOT an input step?Things that get defined in the workflow step such as {Analysis_Run} that get filled in at runtime?Now it reverts to "X__oc__Analy
Hi,I am still having serious issues with running galaxy workflows from the API on my installation...I am getting random files on which the workflows are run, rather than the files I select in my script.I am suspecting that my database may be corrupt...Is there any test script that can test my theor
The cluster was busy I think, so you just have to wait for the queue to clear...On Jun 25, 2012, at 02:25 PM, Kristen Roop wrote:Hello,I am having an issue on the Galaxy Main server.I had reached my maximum disk space this morning. So I cleaned out some items until my space was down to 61%. I the
Hi,I have a very bizarre problem with Galaxy.I have to run a workflow through the API, since Galaxy cannot deal with many pair-end FASTQ files...In the past I had no issues with this and it always run as expected.But in the last few days when I select 2 FASTQ files to be run in with the API, invari
f you chose to try this out, good luck and let me know what goes wrong. -John John Chilton Senior Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 On Fri, Jun 1, 2012 at 1:32 PM, Anthonius d
On Fri, Jun 1, 2012 at 1:02 PM, Anthonius deBoer <thondeb...@me.com> wrote: > Could you give me a pointer where in the codebase I should start looking to > implement this, please? > I'd be happy to share this with the community if it is useful for others > > Thon > &
extend the Galaxy codebase to implement this behavior.Best,J.On Jun 1, 2012, at 1:50 PM, Anthonius deBoer wrote:Hi Jeremy,Thanks for the info...But it's not clear from your message if I could use this Key/Value approach at the moment to distinguish if a job should be run in the fast or in the slo
Hi Jeremy,Thanks for the info...But it's not clear from your message if I could use this Key/Value approach at the moment to distinguish if a job should be run in the fast or in the slow queue.I would like to add a parameter to every tool that would have it determine if it should be in the fast que
Hi,I often find my self having to battle with other users of the cluster, even for the one-off jobs that someone runs interactively...We have setup Fast/short queues and Long queues...Is there a way for a tool to sometimes be placed in the fast queue and sometimes in the long queue?I know I can set
Hi,I am trying to run MEME and I got this error below when running it.Is this an error complaining about the non-ASCII nature of the OUTPUT or of the program (or input?). ThanksThonError Traceback:View as: Interactive | Text | XML (full)⇝ UnicodeDecodeError: 'ascii' codec can't decode byte 0x
012, at 6:49 PM, Anthonius deBoer wrote: > Interestingly when I open the Developer Tools in Chrome, my VCF file is actually loading...As soon as I close the developer tool, it stops loading the the page again (and it resumes loading when I re-open the Developer tools...) > > Really funky... >
share a VCF file with me that doesn't display properly? -Dannon On May 29, 2012, at 5:50 PM, Anthonius deBoer wrote: > Hi, > > Is there a way to turn of the special pretty print version for VCF files since it is not working correctly? > > I now have to download every VCF fi
Hi,Is there a way to turn of the special pretty print version for VCF files since it is not working correctly?I now have to download every VCF file I want to look at rather than being able to see the first MB of the text file it is...Where is this pretty printer and how do I turn it off?ThanksThon
Never mind :)...I found my bug...I had inadvertently removed the comment line before some line that contains the 4 dashes :)problem solved...ThonOn May 29, 2012, at 09:52 AM, Anthonius deBoer wrote:Hi,All of a sudden I am getting these errors when I submit a job in my Galaxy system.I can't r
Unfortunately this is one of the most glaring problems with the UI based workflow engine that is Galaxy (That, and no modular workflows)...You cannot easily pair up more than one set of paired end reads from the UI, you need to use the API to run pairs of FASTQ files like that...I have written a sc
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