/galaxy_blast/issues/39
Thanks,
Peter
On Mon, Apr 28, 2014 at 5:25 PM, Scott W. Tighe scott.ti...@uvm.edu wrote:
Dear Wayne
Here is the error message I get back.
Server Error
Your request could not be processed due to a problem on our Web server. This
could be a transient problem, please try
On Mon, Apr 28, 2014 at 9:01 PM, Scott Tighe scott.ti...@uvm.edu wrote:
Peter
Thank you for your detailed response and I should have noted that I was
using the Main Public Galaxy. Thank you for confirming that it is down!
I appreciate your input!
Scott
Hi Scott,
Galaxy is back for me now
://biostar.usegalaxy.org/u/333/ - old ISP based email address
https://biostar.usegalaxy.org/u/337/ - old ISP based email address
https://biostar.usegalaxy.org/u/394/ - my Google mail address
Thanks,
Peter
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On Thu, Apr 24, 2014 at 2:40 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
I see that https://biostar.usegalaxy.org is live now, with lots of
content mined from the galaxy-user mailing list (which may or may not
result in this email starting a new question? We shall see
On Fri, Mar 14, 2014 at 9:58 AM, Elvio Pederzolli
epede...@bigpond.net.au wrote:
Hi there can you please unsubscribe me from all Galaxy lists please
Thank you
Elvio Pederzolli
You should be able to unsubscribe yourself here:
http://lists.bx.psu.edu/listinfo/galaxy-user
Regards,
Peter
(CC'd).
It sounds like your problem is inside your own Perl script?
Perhaps within Galaxy there is a problem with the Perl
environment variables defining where to find Perl libraries...
Peter
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run as a different Linux user?
Peter
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, why not pass in the environment
variable name without the dollar?
Peter
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and running! #usegalaxy
https://twitter.com/galaxyproject/status/425314813946773504
However, it still seems to be a bit slow to load for me...
Peter
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the tabular output from BLAST with
this sequence filtering tool:
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
e.g. If you want to remove transcripts which seem
to be mitochondria, you could BLAST against a
mitochondrial database, and take only the sequence
with no hits.
Regards,
Peter
This tool of mine might do what Seung Hee wanted,
but I have not tried it on very large Illumina datasets:
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip
Regards,
Peter
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the video you posted at the youtube,
but still couldn't find it. Do you know what I miss here? Thanks.
Best,
Peter
-Original Message-
From: Brad Chapman [mailto:chapm...@50mail.com]
Sent: September-18-13 8:44 PM
To: Peter Huang; galaxy-user@lists.bx.psu.edu
Subject: RE: [galaxy-user] add
this is a special constant, and
give people just one place to change the code?
Any help appreciated. I'm a little out of my depth here.
Ha ha, good pun.
Peter
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Hi Brad,
Thanks for the kind reply. So does it mean that I won't be able to add it to
our existing galaxy-dist production server as the only way to obtain it is to
clone the one you listed? Thanks.
Best,
Peter
-Original Message-
From: Brad Chapman [mailto:chapm...@50mail.com]
Sent
have a patch
name for it? Should I use hg pull or hg patch? Thanks
Best,
Peter
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folder.
Peter
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tool which acts as a wrapper.
This sounds a bit like the idea of making a workflow into a
tool (or act in a tool like manor)... but I think you'd be better
off raising this question on the Galaxy Development list:
http://lists.bx.psu.edu/pipermail/galaxy-dev/
Peter
or not to
read the details. Thanks!
1. How do I output the quality scores when converting from FASTQ to FASTA?
You can't, unless you mean converting a FASTQ file into a FASTA and
matching QUAL file?
Peter
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produced a small amount on stdout - which is not
available until the job finishes.
Peter
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if there can be complications with meta-data normally
added automatically by inspecting the finished file...)
Peter
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?
No, not the edit button.
First click on a dataset's title so it expands. You should see a snippet
of data etc plus a row of icons (save, information, reload in bottom
left of the history, and tags and annotation bottom right).
Peter
* rename the description of the file as shown within the
Galaxy interface (via edit attributes).
Peter
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this long to run?
Which FASTQ filtering tool exactly are you referring too? The one called
Filter FASTQ reads by quality score and length in the left hand column,
tool ID fastq_filter?
How big were the input files?
Peter
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On Mon, Apr 29, 2013 at 3:27 AM, Mike Dyall-Smith
mike.dyallsm...@gmail.com wrote:
Dear Peter Cock, thanks for your advice. Just to be clear, do I leave the
files within their decompressed folders or do I put all the individual files
into one folder? I assume the former, but want to be sure
be useful. I could not find any.
Thanks for any assistance, Mike DS
Don't cat anything - just download all nr.*.tar.gz files, and
decompress them. You'll have a load of files including a
special alias file called nr.pal which is how BLAST knows
how to deal with the combined 'nr' database.
Peter
without inventing quality scores (e.g. give everything score 30).
Does that help?
Peter
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server (in my case, a live on and a dev one).
Peter
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). The users' files
are all on disk (with the extension .dat regardless of the file type).
Peter
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On Tue, Nov 27, 2012 at 9:51 PM, shamsher jagat kanwar...@gmail.com wrote:
Is there an option in galaxy to combine two fastq files?
Thanks
kanwar
Yes, but what do you mean by combine? Interleave? Concatenate?
Peter
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only
get matches on one strand that is probably the correct orientation.
(one thing I know is for the sense sequence the 10th nucleotide is
always A)?
Why is that? Is this related to your library preparation?
Peter
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point you to the stdio,
regex, and exit_code tag sets documented here:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax
Using these new features you can avoid a wrapper script just to
hide stderr.
Peter
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!
The Galaxy tool Concatenate datasets tail-to-head under Text Manipulation
should work. I'm assuming you just need a simple concatenation of individual
FASTQ files, not a more complex merge dealing with duplicates or sorting.
Peter
in the public ToolShed.
Peter
P.S. Problems with local Galaxy installs are normally discussed
on the galaxy-dev list (CC'd) rather than galaxy-user list.
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/department/... ask
the local Galaxy administrator about this.
Regards,
Peter
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if there was it
wouldn't help for pushing changes or suggestion into Galaxy.
Speaking as a git user who only has to use hg for Galaxy, I just
learnt enough hg to get the basics done, and frequently consult
resources like this:
http://mercurial.selenic.com/wiki/GitConcepts#Command_equivalence_table
Peter
would be a better place.
Peter
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of discussion is normally directed to the galaxy-dev list (CC'd)
Peter
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lengths,
and then you should be able to compute some statistics about the lengths.
Peter
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.
This is most commonly used for genes made up of multiple exons, but
can even apply across references in some extreme trans-splicing cases.
Peter
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On Tue, Apr 24, 2012 at 10:24 PM, Jennifer Jackson j...@bx.psu.edu wrote:
..., using
the BLAST+ BLASTN megablast wrapper that Peter authored, in a local or cloud
instance, would be the best immediate remedy (this version has the standard
12 column output). Sequence length data could always
Hi there
I'm trying to download the screencasts referenced in the Galaxy ENCODE
paper (Blankenberg et al 2007). They appear to be on
screencast.g2.bx.psu.edu, but while that domain resolves, it doesn't
respond to HTTP requests. Does anyone know where they are currently
available?
Thanks,
Peter
On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster g...@bx.psu.edu wrote:
On Mar 24, 2012, at 7:30 AM, Peter Cock wrote:
Have you seen the README file that comes with the
Blast2GO wrapper? Perhaps the 'install from toolshed'
could be tweaked to make this kind of documentation
more visible
lists now given local Galaxy installations
are getting more common and not everyone wants to follow
the Galaxy development itself).
Peter
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On Wed, Mar 21, 2012 at 10:21 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
2012/3/21 Makis Ladoukakis makis4e...@hotmail.com:
Dear Galaxy users,
I have been trying to upload a blastable database in my local instance of
galaxy. I have used the nr database and generated all the nhr, nin, nsq
You forgot to CC the mailin list.
On Mon, Mar 19, 2012 at 12:02 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
On Mon, Mar 19, 2012 at 4:53 PM, Innocent Onsongo onson...@umn.edu wrote:
Galaxy Team,
I would like to create a workflow by combining portions of two
different workflows. How do
list, CC'd, since BLAST+ isn't event available on the public galaxy)?
Also which version of BLAST+ are you using since I recall some changes
to the tabular output IDs prior to 2.2.25 (which is what the wrappers were
tested on, I've not tried 2.2.26 yet).
Thanks,
Peter
with a GFF3 file converted
from GenBank using BioPerl, then I guess it is a Galaxy issue.
Peter
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Peter
On Wed, Jan 25, 2012 at 3:14 PM, Guru Ananda g...@psu.edu wrote:
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
in Galaxy?
Peter
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On Mon, Feb 13, 2012 at 2:17 AM, Arthur Zheng haoz...@gmail.com wrote:
On Sun, Feb 12, 2012 at 4:34 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Sun, Feb 12, 2012 at 10:28 PM, Arthur Zheng haoz...@gmail.com wrote:
Hi,
I have downloaded and installed a local instance of galaxy
on disk but point at the existing files already
on the server:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
Peter
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On Thu, Feb 9, 2012 at 9:57 PM, Jennifer Jackson j...@bx.psu.edu wrote:
Hi Peter,
It looks to me like there are versions both, with the Tool Shed version
having the more recent date stamp. But if those extra functions are not
needed, then yes, you are correct, the version included
into a local or cloud version
of Galaxy and set up using the following instructions:
http://getgalaxy.org
Hi Jen,
The NCBI BLAST wrappers used to be included as standard tools
when doing a local Galaxy server installation - and were not in
the ToolShed. Has that changed?
Peter
So it depends.
Peter
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and __cb__ which must be
short for open bracket and close bracket.
I believe that the fuzzpro tool (and perhaps others) need
to have an explicit sanitizer and valid entry in their
Galaxy wrapper XML file to allow these characters though.
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax
Peter
.
Regards,
Peter
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format that
I cannot open with these programs. What should I do?
Thanks,
Rena
Try renaming the file to end with .tsv or .txt and Excel or your text editor
should be happy.
Peter
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/DIST/docs/tutorial/Tutorial.html
http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
Regards,
Peter
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On Tue, Nov 8, 2011 at 10:26 PM, Austin Paul austi...@usc.edu wrote:
Hi Peter,
Thanks for the suggestion. For example, I have a fastq file with 50 million
reads and I want to randomly select 5 million of them. It seems biopython
would very easily select a single or a handful of reads
/showthread.php?p=49667
Peter
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of preparing
BAM files on upload.
Might this be tied to a specific version of samtools? e.g. a
possible regression?
I don't see a Sort step in your workflow, maybe that's the problem?
Please CC me on any reply, I might miss it in the list.
Jim
Thanks,
Peter
. Any suggestions?
Many thanks in advance and Cheers!
Uwe
Don't you need to escape both the and the characters here? i.e.
amp;gt; should work.
Peter
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On Mon, Oct 24, 2011 at 9:42 AM, Appelt, Uwe
uwe.app...@nct-heidelberg.de wrote:
Hi Peter,
thanks a lot for your quick reply. However amp;gt; doesn't
seem to work as well. Also, I do have to admit that two different
doesn't work exist.
Notations that are not accepted during parsing
.
For some strange reason (Peter, you're right again) all log-lines appear in
the green box.
To be expected, Galaxy captures any stdout (assuming nothing else captured
it first) and puts it in the info field.
And even more, the green box turns of course red as soon as something is
written
included.
Yes, that is good.
Peter
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to the join method
to say the description from read1 is taken (if the reads differ in their
descriptions). Mind you, the whole module seems to lack docstrings ;)
Are there any unit tests (not that Galaxy seems to insist on them)?
Peter
trying with IonTorrent data.
Peter
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bang,
it doesn't even need the Galaxy interpreter in the XML file.
For the internal script it doesn't matter at all - Galaxy doesn't
need to know.
Peter
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and they copy it onto their cloud for you.
This costs money of course, but avoids the network problem.
The other option is to check with your local computing people -
perhaps there is a cluster or local super computing group you
can get access to?
Peter
.
Peter
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local
install? (skipped
over entirely or installed but do not work?)
By that do you mean of the standard tool set in the main repository?
(Because there will be lots of Galaxy tools in the Tool Shed which are
not in the standard cloud install).
Peter
the Galaxy code does now is attempt to index the BAM file
(as a safe way to find out if is really is suitably sorted), and if that fails
sorts it by co-ordinate (which will make a new BAM file) and then
indexes the sorted version.
Peter
On Fri, Jul 1, 2011 at 4:35 PM, Sergei Ryazansky s.ryazan...@gmail.com wrote:
Thanks for answer, but I have just updated the galaxy source code and blastn
works fine! Sorry for any inconvenience :)
It was an error in the wrapper script's error handler, already fixed.
Peter
them to set up an FTP server, no luck).
Any way to do this?
Try asking the sequencing centre if the username and password can be
provided as part of the HTTP URL, then give that URL to Galaxy.
Peter
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Peter
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local
FASTA and QUAL file.
Peter
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!
That's a timely question - I was also looking for something within Galaxy
to take a text file and remove duplicate lines.
Peter
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except fastx_quality_statistics.xml
Peter
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that
Artemis doesn't like?
Thanks.
Ed
Artemis will need the BAM index file (the BAI file). It may also insist
on the normal extensions, *.bam and *.bai or *.bam.bai (but not *.dat)
Peter
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an arbitrary
number of files, but is designed for input files containing the same
column structure.
Is there a better way to do this with Galaxy as it stands?
Alternatively, would adding an option to the Join two Datasets tool
not to bother with the redundant column be widely useful?
Peter
recently? If they are already using Illumina's CASAVA v1.8 pipeline
then the FASTQ files will already be in the Sanger FASTQ format:
http://seqanswers.com/forums/showthread.php?t=8895
Peter
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are a Galaxy admin, and the import from file system feature
is enabled in universe.ini then you can do this as a shared data library.
See e.g.
https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles
https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/LibrarySecurity
Peter
Great :)
Don't forget to CC the mailing list in future ;)
On Fri, Feb 25, 2011 at 4:46 PM, Amy Boddy abo...@med.wayne.edu wrote:
Thank you, these articles helped!
On Thu, Feb 24, 2011 at 5:47 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
On Thu, Feb 24, 2011 at 8:47 PM, Amy Boddy abo
this thread earlier this month
on the Galaxy dev mailing list:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-February/004344.html
Peter
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? Mappings?
If it's FASTQ files you mean, may I suggest:
http://dx.doi.org/10.1093/nar/gkp1137
and
http://en.wikipedia.org/wiki/FASTQ_format
Peter
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helpful for connecting
workflows together - one way to tackle this feature request:
https://bitbucket.org/galaxy/galaxy-central/issue/52/subworkflows
Peter
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mentioning it here rather than starting a new thread
or filing a bug..
Peter
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On Mon, Feb 21, 2011 at 9:48 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
about using SAM/BAM transcriptome mapping
(RNA-Seq) for gene finding?
Peter
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On Fri, Feb 18, 2011 at 12:35 PM, Felix Hammer hamm...@cip.ifi.lmu.de wrote:
Hi Peter,
thx for the reply.
You're right I want to display mapped RNA seq data in gBrowse.
Currently I have the data in SAM format.
Maybe I can figure out a trick using the text manipulation tools.
thx,
Felix
On Thu, Feb 10, 2011 at 6:42 PM, Peter wrote:
On Thu, Feb 10, 2011 at 6:34 PM, Stephen Taylor wrote:
Sounds like this should be added into the main release. It would save a lot
of time/disk space instead of using Groomer.
I agree. Maybe Dan can take care of it - I don't have bowtie setup
to fit on my screen
without zooming out so much that I can hardly read it. I'm using
Firefox 3.6 on Linux.
(I then got a username clash, and realised I'd already made an account
with a different email address)
Peter
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