I think this is great. Do we have it clearly explained on the wiki somewhere
about how to turn on mailing list mode within biostar? I didn’t see anything in
a quick search, but it would probably help ease the transition for people that
just love the mailing list approach. I also find it
Actually, if the ones I ordered last year are expiring soon, I'd suggest people
continue to use those before recently ordered kits.
Les
- Original Message -
Send galaxy-user mailing list submissions to
galaxy-user@lists.bx.psu.edu
To subscribe or unsubscribe via the World
Hello Carrie,
Yes. UCSC changed the way that they organized their track groups,
breaking out Variation and Repeats into two distinct categories. When
doing the Table browser query, simply pick Variation (instead of
Variation and Repeats) from the group drop down menu. The dbSNP track
will be
On Thu, Feb 27, 2014 at 9:32 AM, do kadya doka...@gmail.com wrote:
Hi,
Thank You for your kind reply.
I am having problem in running command in Galaxy.
my current command:
tool_name file_having_multiple_file_name_tab_delimited.txt or .tab
file1.bam file2.bam
/usr/bin/x_tool
Respected Sir,
I don't think so that problem is in tool, because when I run same tool of
normal terminal, it generate output.
What I am thinking is:
Consider Galaxy is running from its own directory, my files are in
*/home/user/Documents/*
While uploading file, I am choosing for Link to files
On Thu, Feb 27, 2014 at 4:20 PM, do kadya doka...@gmail.com wrote:
I don't think so that problem is in tool, because when I run same tool of
normal terminal, it generate output.
This is why I was asking about Perl environment variables - they may be
different compared to when you run the tool.
Hello Martina,
how did you try to upload it and on what server? I assume it was
usegalaxy.org but please confirm. DId you use the upload button on the main
page or *Get Data / Upload File* from the tool menu? How big is the file?
thanks
Martin, Galaxy team
On Mon, Feb 17, 2014 at 11:37 AM,
Hi Martina,
this is the actual URL of the file:
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA046/SRA046351/SRX099052/SRR349685.fastq.bz2
The URL that you were using is the link to the folder, not the file (you
can tell e.g. by the suffix of the file - my link has it, yours does not).
Martina:
it seems that the server you are downloading from has troubles
communicating with Galaxy. This is probably FTP issue that we cannot
control. The workaround is to download it yourself to your computer from
the site and then upload it to Galaxy directly.
Let me know how it goes
regards
Hi,
I just notice that NGS FASTQ
Trimmerhttps://usegalaxy.org/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Ffastq_trimmer%2Ffastq_trimmer%2F1.0.0by
column can't detect the fastq file I loaded. Anyone knows why. thanks
a
lot.
On Fri, Jan 24, 2014 at 11:00 AM,
Hi Mo,
Datasets are a bit tricky for the download/import steps on Pages. Do this:
1 - click on the dataset name to expand it
2 - you will see a message This dataset is large and only the first
megabyte is shown below. | Show all.
3 - Click on the Show all. On the resulting view, the import
Dear Graham,
Thanks for the info. However, my problem is that the Tool Version field
is completely empty in my history items (eg. Tophat2, Cuffdiff). I suppose
I can check the dependancies list you described, but it would be important
to know precisely which version was run on any given query.
Thanks for the info. However, my problem is that the Tool Version field is
completely empty in my history items (eg. Tophat2, Cuffdiff). I suppose I
can check the dependancies list you described, but it would be important to
know precisely which version was run on any given query.
If
Hello,
First, I've moved this question from the Galaxy development mailing list to the
Galaxy user mailing list; in the future, please send questions about using
Galaxy to the galaxy-user list.
To answer your question, files larger than 2GB must be uploaded via FTP to
Galaxy. This is
Hi Itys,
The public server has been undergoing upgrades, and this included some
data transfers. This has been going on behind the scenes for several
months - I am sorry that your account was impacted and that we did not
hear about it/solve it when the issue first began! When usegalaxy.org
Hi PT,
What exactly do you mean by Galaxy on the Cloud appears to expect that the
imported and converted fastq files are in the same S3 bucket where the
fastq.gz files were? Once imported from S3, you're correct in that
everything will be on the local EBS volume.
-Dannon
On Sun, Oct 6, 2013
Hello,
New tools go into the Tool Shed, links with instructions are here:
http://usegalaxy.org/toolshed
http://wiki.galaxyproject.org/Tool%20Shed
We tweet new tool additions to let the community know about them, info
and recent tweets are here:
Hello Nathan,
The view history issue has been resolved. However, there were known
failures over the weekend. These jobs should be re-run. The NGS cluster
is down at this moment due to a datacenter problem, but is expected to
be restored shortly. Queued jobs will process when back up as
Hello Ben,
The public Main Galaxy server experienced issues leading to unexpected
downtime over the weekend. These have since been resolved. Please let us
know if problems persist.
Our apologies for the inconvenience,
Jen
Galaxy team
On 9/9/13 6:44 AM, Ben Ben wrote:
Co-ask : When will
Hello Boaz,
The public Main Galaxy server experienced issues leading to unexpected
downtime over the weekend. These have since been resolved. Please let us
know if problems persist.
Our apologies for the inconvenience,
Jen
Galaxy team
On 9/9/13 2:03 AM, Boaz Shaanan wrote:
Hi,
Any idea
Co-ask : When will the Galaxy Server work again?
Thanks for Galaxy Team's work and support!
On Mon, Sep 9, 2013 at 5:03 AM, Boaz Shaanan bshaa...@bgu.ac.il wrote:
Hi,
Any idea when the server is going to be up again?
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion
Hi Scott,
please click on the 'i' info icon in one of your datasets (next to the
download button) you will find many additional information's, including
the wrapper version and the version of the underlying tool.
Cheers,
Bjoern
To Whom it May Concern,
I was trying to find the version
FTP issues are fixed now so things will be functional out of the box
without any of these workarounds.
On Tue, Jul 16, 2013 at 4:04 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hey Mo,
You can use ssh to connect to the Galaxy machine. If you used cloudlaunch
to create your instance, it
Hi Jen,
Maybe I have not explained my question cleared which caused the
confusion: I did not mean the name of dataset. Actually I asked about the
display of the tool in the graphic view from the default value (guess it is
the name attribute in the tool element of the wrapper) to something
Hi Jun,
Thanks for the clarification. Workflow step annotations would best suit
your needs, I think. When you're in the editor, click on any step and on
the right side you'll see a field Annotation / Notes which will be
displayed when the workflow is viewed. This can be used to clear up any
From: galaxy-user-boun...@lists.bx.psu.edu
[galaxy-user-boun...@lists.bx.psu.edu] on behalf of Anto Praveen Rajkumar
Rajamani [a...@hum-gen.au.dk]
Sent: Monday, August 05, 2013 7:53 AM
To: Elizabeth Clare; galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Galaxy
Hello,
Thanks for your response. I can almost never get anything done on the
public instance of Galaxy. It can take an entire day to even load a.bed
file. When I was encountering the error I was on the Broad Instance.
Marco, I tried following the instructions above to ensure that genome was
Toni,
As a quick work-around until set up natively, you may be able to use the
Extract DNA tool with a custom reference genome:
http://wiki.galaxyproject.org/Support#Custom_reference_genome
See the example in: Tools on the Main server, should work on any
Galaxy set up as a production server
Hi Toni,
to convert a bed file to a fasta file you need the genomic sequence. You
can specify a genome-build for every bed file in your history. You
probably don't have a genome build specified or its specified as
sacCer2. sacCer2 is not configured I would guess, so no genome is
available. Try to
Hi Toni,
Bjoern is correct - if you are using a local Galaxy that does not have
this reference genome available, it needs to be added. The Extract DNA
tool requires a .2bit version of the genome available and the
alignseq.loc file configured. More is here, section LASTZ and EXTRACT
Genomic
Hey Mo,
You can use ssh to connect to the Galaxy machine. If you used cloudlaunch to
create your instance, it should display an example connection string that will
work from e.g. a linux/mac shell, something like: 'ssh -i cloudman_keypair.pem
ubuntu@IP', after your instance launched.
Once
Hello Elizabeth,
Are you still having problems today, when using the public Main Galaxy
instance at https://main.g2.bx.psu.edu/ (usegalaxy.org)? The server was
very busy last week and wait times were variable depending on the job
type. Allowing jobs to queue and run is still the best
Hey Nate,
Thanks for the response and instructions.
I understand the last three steps of your protocol, but the first step is
difficult for me to understand. I'm guessing that, 1. Set 'use_pbkdf2 =
False' in universe_wsgi.ini anywhere in the [app:main] section, is telling
me to change a setting
Please unsubscribe
Sent from my iPhone
On Jun 28, 2013, at 12:01 PM, galaxy-user-requ...@lists.bx.psu.edu
galaxy-user-requ...@lists.bx.psu.edu wrote:
Send galaxy-user mailing list submissions to
galaxy-user@lists.bx.psu.edu
To subscribe or unsubscribe via the World Wide Web, visit
Hello Delong ZHOU,
On 6/7/13 8:23 AM, Delong, Zhou wrote:
Hello,
I'm using the main galaxy server to analyse some data and then I got
this messege:
An error occurred while getting updates from the server. Please
contact a Galaxy administrator if the problem persists.
This message indicates
Hi Sarah,
We'd be happy to put this on the Galaxy Event Horizon page on the wiki.
Since the event is over, we would list it in the past events section.
Is there a web page for the workshop or slides that we can link to?
And, for future reference, wiki update requests can be sent directly
to
Hi David
I have not used or tested it myself yet, but: have you looked into
Bio-Linux ?
The latest release (Bio-Linux 7) comes with Galaxy pre-installed, see:
http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info
Regards, Hans-Rudolf
On 04/25/2013 12:52 AM, David Joly wrote:
Thanks
I was pretty much interested in Bio-Linux. However, the version of Galaxy that
comes with it is already outdated and there is no easy way to update it. It is
possible to delete it and re-install a newer version, this would be another
possibility...
Le 2013-04-25 à 05:50, Hans-Rudolf Hotz a
Hi David,
Using Galaxy to teach undergraduates is a long term interest of mine.
Which, unfortunately, does not mean I have yet put a lot of thought into
it. However, lack of thought hasn't stopped me yet.
First, this topic was discussed in a breakout at last year's GCC:
Thanks Dave!
The focus is clearly more like your second description. The course is not
intended to show them how to use command lines, or how to navigate in a
UNIX environment and how to program. In fact, I think some would call what
I have in mind more of a computational biology course than a
Hi David,
Galaxy does sound like a great match for this course. It could also play a
(smaller) part in the other course you are considering. Part of the course
could include installing Galaxy and wrapping other tools to put into it.
We are a Python based framework
I do strongly recommend you
Thanks Jen, that's really good to know.
Cheers,
Nicole.
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Thursday, 21 March 2013 12:19 AM
To: Nicole Cloonan
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Galaxy Main jobs not running?
Hello Nicole,
The public Main Galaxy
Hello,
Apologies for the slow reply. I've moved this thread to the galaxy-user mailing
list because it centers on using Galaxy rather than developing it.
2. deleted the first files, like the first fastq files, but I'm affraid to
have an error messages
Deleting your fastq files after you
On Thursday, February 21, 2013, wrote:
Further, when I try “register” I add an email address and password, but
the system still doesn’t log me in
** **
Maybe this is a database configuration issue?
** **
I didn’t think I’d need to state any specific entries in universe as I am
Dikla,
After refreshing the browser, the most up-to-date view of the history should
definitely be available. Are you positive you're looking at the same history
in both places? I would verify that there's nothing in Saved Histories that
looks like what you're expecting.
-Dannon
On Feb 13,
Hello Oya,
This wiki has links to where you can add yourself to the list.
http://wiki.galaxyproject.org/MailingLists#Subscribing_and_Unsubscribing
Other general info about mailing lists:
http://wiki.galaxyproject.org/Support#Mailing_Lists
Best,
Jen
Galaxy team
On 2/13/13 11:07 PM, Oya
Hello Milad,
I am not sure if you are using the public Galaxy Main server
(https://main.g2.bx.psu.edu) or your own local computer, or if the jobs
are yellow and running or still grey and in the waiting-to-run stage.
If using Galaxy Main, and if actually running (dataset is yellow), this
Shahid Beheshti's university of Medical Science
From: Jennifer Jackson j...@bx.psu.edu
To: Milad Bastami mi.bast...@yahoo.com
Cc: galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edu
Sent: Tuesday, February 12, 2013 6:56 PM
Subject: Re: [galaxy-user
Hi John,
The current link is:
http://wiki.galaxyproject.org/FTPUpload
We changed our wiki base and many of the older links do not redirect.
I'll let our wiki admin Dave know about this and see what can be done.
If this comes up again soon, the base always redirects to
Hi,
I've put together some exempels for activating and using the api. You can find
them here:
http://geertvandeweyer.zymichost.com/index.php?page=readid=29
Best regards,
Geert vandeweyer
Op 16-jan.-2013 om 02:52 heeft neil.burd...@csiro.au het volgende geschreven:
Hi
Sorry if these
Geert, this is great stuff!
One small correction -- the API is enabled by default as of revision
7022:8376ad08ae41 (April 2012).
-Dannon
On Jan 16, 2013, at 1:17 AM, Geert Vandeweyer geertvandewe...@gmail.com wrote:
Hi,
I've put together some exempels for activating and using the api.
Neil,
.../api/workflows is not a path in the galaxy directory, but a URL
that you should access over HTTP. For example, if you login to Galaxy
Test, and then access https://test.g2.bx.psu.edu/api/workflows you
will get a json dict of all of your workflows, including the workflow
id that you are
You are probably seeing the mtDNA re-sequencing datasets associated
with this paper:
http://genomebiology.com/2011/12/6/R59
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Jan 4, 2013 at 10:46 AM, Sun, Wenping [USA] sun_wenp...@bah.com wrote:
Hello,
It is good
To be clear, your admin user still works on this instance but another one does
not? If this is the case, can you log in as the admin user (and, if not,
simply register a new user and make it an admin) and take a look at the user
list in the admin panel?
To get to the user list when in Galaxy,
The root size for the worker nodes doesn't matter. The only thing
relevant to Galaxy here are the available compute units and memory.
The only storage and working space used is actually attached to the
master node (the EBS volume you configure at initial launch) and
shared over NFS with the
It looks like you've worked on both the public galaxy site we provide
(main.g2.bx.psu.edu) and your own cloud instance. Data on the public instance
won't be automatically migrated to the cloud instance and vice versa.
All work done on the cloud site will remain there and persist after
Hello Dominique,
Would the tool 'NGS: QC and manipulation - Barcode Splitter' meet your
needs? Please see the tool's help for usage.
Another option is to first covert the file to tabular with 'FASTA
manipulation -FASTA-to-Tabular', then use the 'Filter and Sort -
Filter' tool. The match
Hi Dominique,
This means that there were no results. My fault - the Filter tool is the
wrong choice. The Select tool, as you were starting with, is better for
this case. The issues you had originally were most likely with format or
the regular expression. So, be sure to do the following this
Hello Sachit,
Instructions for setting up local indexes are in our wiki here:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
Bowtie2 is not specifically listed, but the instructions for Bowtie and
Bowtie2 are nearly identical. The same indexes are used for Bowtie2 and
Tophat2. When
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
That's just the section demarcation stating that everything following (until
the next such bracketed line) is a property of the 'server:main' section --
there should be no need to change that, though you can certainly change any of
the properties within the section as needed.
-Dannon
On Nov
On Nov 7, 2012, at 5:47 AM, Diam Hsu wrote:
Dear Sir or Madam,
I used to use Galaxy to analyze NGS data, but these two days I could't login
my Galaxy account, it also told me that my account has been marked deleted,
and asked me to contact the Galaxy administrator to restore my
Hello Kshama,
We would like to help. I looked for an account under your email address
kasw...@masonlive.gmu.edu on the public Main Galaxy instance at
http://main.g2.bx.psu.edu (http://usegalaxy.org), and did not find one,
so I will tell you how to check for the data yourself, then you can
Thanks Jen. But it looks like the datatype was already set to fasta.
I tried setting it again and saving but it didn't seem to help.
Is there anything else I can try?
thanks,
Greg
On Tue, Oct 9, 2012 at 9:10 PM, Jennifer Jackson j...@bx.psu.edu wrote:
Hi Greg,
Nice pic, it helps! My guess
Looking at your screenshot, you have Use a built-in index selected. If you
change this to Use one from the history, do you see your fasta file listed?
-Dannon
On Oct 10, 2012, at 9:02 AM, greg margeem...@gmail.com wrote:
Thanks Jen. But it looks like the datatype was already set to fasta.
Yes that was it! I knew I was missing something obvious.
Thanks,
Greg
On Wed, Oct 10, 2012 at 9:06 AM, Dannon Baker dannonba...@me.com wrote:
Looking at your screenshot, you have Use a built-in index selected. If you
change this to Use one from the history, do you see your fasta file
Hi Greg,
Nice pic, it helps! My guess is that the datatype is not assigned as
fasta. To do this, click on the pencil icon for the custom reference
genome dataset (#1) to bring up the Edit Attributes forms in the center
panel. Then click on the Datatype tab and change this to be fasta
and
Hi Anatoliy,
If you're going to keep that cluster alive continuously, just set it up as
per the page whose link you provided and you should be ok. If you plan on
having multiple users have their own cloud clusters
with Galaxy, you'll probably want to do what I suggested in my previous
email.
Good
Hello Kenneth,
Are you using BLAST+ in a local install or cloud instance? The problem
may be that the query dataset needs to have the datatype assigned as
fasta. To do this, click on the pencil icon for the dataset to reach
the Edit Attributes form. Then either scroll down to (or click on the
Hi Kenneth,
Yes, target databases require indexes and *.loc file set-up. Please see
this wiki for details. For Genbank data such as NR, FTP the pre-built
indexes and use those (generating them with formatdb is not necessary).
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
See the
Hi Kenneth,
It is likely that the path is wrong in the .loc file. It has to point to
the actual files, not just the directory. Inside here
/9720/genome_references/ncbi/nr-protein-db
is where all the nr.* files are? In that case, the path should be
Added: worker nodes are now submit hosts as well:
https://bitbucket.org/galaxy/cloudman/changeset/b4c66783b42fb559b35b689363b34826d00ced34
This will be generally available with the next release of CloudMan is made
(however, there is no immediate plans for doing so as quite a bit of other
details
You probably need to sudo to sgeadmin (cloudman guys correct me if you
have this setup differently).
I don't see any reason not to make worker nodes submit hosts by
default in a future cloudman release.
-- jt
On Thu, Sep 13, 2012 at 4:17 PM, greg margeem...@gmail.com wrote:
As a follow up I
This is slightly different from Masaki's question since you cannot
access Galaxy from the same machine that it's running on. What are
Galaxy's host and port settings in universe_wsgi.ini?
-Scott
- Original Message -
Hi all
I've installed Galaxy on my Mac. The sh run.sh, run but
--
Message: 6
Date: Wed, 15 Aug 2012 11:28:37 -0700
From: Jennifer Jackson j...@bx.psu.edu
To: Mahtab Mirmomeni m.mirmom...@student.unimelb.edu.au
Cc: galaxy-u...@bx.psu.edu
Subject: Re: [galaxy-user] Galaxy toolshed-vcftools
Message-ID: 502bea55.3090...@bx.psu.edu
Content-Type: text/plain; charset
Hello Mahtab,
Some vcftools are in development status on our test server under VCF
Tools at:
http://test.g2.bx.psu.edu/
Adding these and others (including the ones you mention) to the Tool
Shed is under consideration by the Galaxy team, but a firm timeline is
not set at this time. If your
Hello,
Nice catch! I made the corrections (this time) but next time we
encourage you to jump right in and contribute to the wiki directly!
Create an account and become an editor...
http://wiki.g2.bx.psu.edu/VettedEditorGroup
Feel free to double check big content edits/changes you are thinking
Hello Robby,
It sounds like you are using the Galaxy instance run by the Huttenhower
Lab at Harvard? At this link?
http://huttenhower.org/galaxy/
If so, then at the bottom of the home page is a link you can use to
contact the lab members about issues with the instance. (They probably
have
On Jun 16, 2012, at 7:38 PM, Jayaraman, Shyam wrote:
Hi,
My username is shyamsundar19...@gmail.com
Galaxy main is not running jobs since today morning. They stay queued (gray)
forever. I deleted and then re queued them twice. Still nothing.. Is the
server down or is something wrong
...@gmail.commailto:kristen.r...@gmail.com
Cc: galaxy-u...@bx.psu.edumailto:galaxy-u...@bx.psu.edu
Subject: Re: [galaxy-user] Galaxy Reference Genome
Hello Kristen,
Our RNA-seq tutorial and FAQ can help out with the general workflow:
https://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
https
and I terminated a created from the beginning new instanced for the last
several hours (at least 5 different instances). All don't work.
Lilach
2012/6/14 Lilach Friedman lilac...@gmail.com
Hi,
Can somebody please help me?
I'm trying for hours to connect to Galaxy on Amazon EC2. I did
Hello Kristen,
Our RNA-seq tutorial and FAQ can help out with the general workflow:
https://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
https://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq
And an iGenomes reference annotation GTF dataset for mm9 is in the
Shared
Hi Lilach,
It seems you ran into a bug that was introduced in the most recent CloudMan
update. It's been fixed now.
If you still have your instance up, the way to get around the issue is to
simply strip off '/cloud' part of the URL and you'll get to Galaxy. Any new
instances will work fine.
mailto:j...@bx.psu.edu
Date: Wed, 13 Jun 2012 16:12:27 -0700
To: Kristen Roop kristen.r...@gmail.com mailto:kristen.r...@gmail.com
Cc: galaxy-u...@bx.psu.edu mailto:galaxy-u...@bx.psu.edu
Subject: Re: [galaxy-user] Galaxy Reference Genome
Hello Kristen,
Our RNA-seq tutorial and FAQ can help out
Todd,
There's not an ideal solution for your situation. My suggestion:
(a) set up a cloud instance with your tools + a Page and use the
share-an-instance feature so that others can access your data, tools,
histories, and page in a single place ( http://wiki.g2.bx.psu.edu/Admin/Cloud );
(b) put
Hi Todd,
[Not sure if this is better suited to galaxy-dev or -user, so I'm sending
to both].
galaxy-user is most appropriate for this question because it related to usage
of Galaxy; galaxy-dev is for local installation and tool development questions.
My question is - can I create a
Hello L-A,
Galaxy is open-source for all components, the license is here:
http://bitbucket.org/galaxy/galaxy-central/src/3f12abbd2394/LICENSE.txt
And in case you haven't seen this wiki, section 3 lists some preferred
link URLs:
http://wiki.g2.bx.psu.edu/Citing%20Galaxy
We'll send more
Hello Jen,
That helped a lot, thank you! I didn't know the license also applied to
the images.
Best,
L-A
Le 11/04/2012 15:45, Jennifer Jackson a écrit :
Hello L-A,
Galaxy is open-source for all components, the license is here:
Hello Hong,
There is likely a problem with the formatting of your input file. BED
and GFF format are very different, and this may be the problem. You will
want to input a strict BED6 file to this tool:
http://wiki.g2.bx.psu.edu/Learn/Datatypes#Bed
for the reply. I'll try BED6 and see in Galaxy.
I would also want to try ENSEMBL API, because one of our publication is based
on ENSEMBL database.
Best,
Hong Xu
From: Jennifer Jacksonj...@bx.psu.edu
Reply-To:
To: hongxuhon...@zju.edu.cn
Subject: Re: [galaxy-user] Galaxy Server running error
Hong:
I'm forwarding this to our official user mailing list. Please, use it in the
future for your inquiries.
Thanks!
anton
Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org
On Apr 3, 2012, at 4:37 PM, xu hong wrote:
Hi Anton,
I'm a biological student using Galaxy sever
Hi David,
I don't know if you are still having this problem or not, but I did a
web search and found this thread on seqanswers from 2/16 that seems like
a good match to the problem you were having:
http://seqanswers.com/forums/showthread.php?p=65085
These scientists resolved the problem by
Hi,
I've found that I need to be really aggressive with forcing a purge
refresh of the browser when changing things like static/welcome.html and
static/images/whatever.png. It might be a function of the nginx
light-weight HTML renderer within Galaxy caching things on top of the
normal caching.
Hi Peera,
I downloaded the file, stripped off extra comment lines (extra two at
top starting with #! and one at bottom ##). I loaded this to Galaxy
as text, and when I attempted to set datatype as GFF3 ran into the
metadata issues.
This links at GMOD have a GFF3 format specification:
On Sun, Mar 4, 2012 at 6:34 PM, Hemarajata, Peera hemar...@bcm.edu wrote:
Dear all,
I’m been trying to get Galaxy to recognize this GFF from NCBI (
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Lactobacillus_reuteri_JCM_1112_uid58875/NC_010609.gff)
but it failed to recognize the format after I
Hello all,
Did this issue get resolved?
If Sandrine was right about there being an off by one error in GI number in
the BLAST tabular output, it could be a bug in 'legacy' blastall command.
I say 'legacy' BLAST because that's what Galay's NGS 'megablast' tool
is using internally (as opposed to
Hello Rita,
The UCSC Table Browser has a limit on the amount of output that can be
extracted in any single query. Without seeing your history, my initial
suspicion is that both of the queries timed out, the first sooner than
the last.
Comparing the number of items between the original UCSC
Dear Sandrine,
Thanks for pointing out this issue.
The BLAST databases we have on Galaxy are from last year, while those on
NCBI website are the latest (Jan 2012). As pointed out on NCBI website (
http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html), it appears that each
time any change is made
Hello Eric,
There are a few choices:
flagstat
BAM Index Statistics
SAM/BAM Alignment Summary Metrics
Use Options - Show Tool Search and enter the tool name (in the left
tool panel) to locate these and other tools quickly.
Best,
Jen
Galaxy team
On 12/8/11 4:02 PM, Eric Guo wrote:
Hello,
Hello Sheena,
Our apologies, Cufflinks was updated to version 1.3.0 this week and we
did a poor job of giving notice to our community.
You can expect to see a tweet and a news item today and an updated wiki
by the end of the week.
Again, we are very sorry that you had to discover this on
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