Hi Jen,
First of all, please accept my sincere apology that I forgot to
change the email title and made a mess
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
else in
the workflow editor. As my ultimate purpose is to share my workflow
with
someone else. If they see three steps with the same displayed name and
do
not have the related knowledge, they will get lost.
To help myself to explain well, please see the attached illustration.
Best regards!
Jun
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To: galaxy-user@lists.bx.psu.edu
Subject: galaxy-user Digest, Vol 86, Issue 17
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Today's Topics:
1. Question about Extract intron sequences from [gtf file] +
[genome FASTA file] (??)
2. Re: Question about Extract intron sequences from [gtf file] +
[genome FASTA file] (Jennifer Jackson)
3. Re: customize tool display in the workflow (Jun Fan)
4. Re: customize tool display in the workflow (Jennifer Jackson)
5. Very very slow response when a class is using Galaxy from a
computer room in the university (Ido Carmel)
Message: 1
Date: Wed, 21 Aug 2013 00:29:56 +0800
To: <galaxy-user@lists.bx.psu.edu>
Subject: [galaxy-user] Question about Extract intron sequences from
[gtf file] + [genome FASTA file]
Message-ID: <blu176-ds19b84f8b1d1040db7aa3e5c4430@phx.gbl>
Content-Type: text/plain; charset="gb2312"
Dear Jen,
I am not much of a Galaxy user yet. Some days ago I know something
about
Galaxy and found it a really wonderful tool. And I am confused by a
simple
question regarding how to extract intron sequences from [gtf file];
Here is a simple of a gtf file:
1 Cufflinks transcript 3 22 1000 + . gene_id "CUFF.26";
transcript_id "CUFF.26.1";
1 Cufflinks exon 3 22 1000 + . gene_id "CUFF.26";
transcript_id
"CUFF.26.1"; exon_number "1";
1 Cufflinks transcript 10 40 1000 - . gene_id "CUFF.204";
transcript_id "CUFF.204.1";
1 Cufflinks exon 10 15 1000 - . gene_id "CUFF.204";
transcript_id
"CUFF.204.1"; exon_number "1";
1 Cufflinks exon 30 40 1000 - . gene_id "CUFF.204";
transcript_id
"CUFF.204.1"; exon_number "1";
I want to extract intron from the [gtf] file. I found 2 ways may
solve the
question but it is both useless;
1. I use (Filter and Sort) -> Filter to cut the [gtf] file into 2
files such
as the follows:
File A ( contain transcript ):
1 Cufflinks transcript 3 22 1000 + . gene_id "CUFF.26";
transcript_id "CUFF.26.1";
1 Cufflinks transcript 10 40 1000 - . gene_id "CUFF.204";
transcript_id "CUFF.204.1";
File B ( contain exon):
1 Cufflinks exon 3 22 1000 + . gene_id "CUFF.26";
transcript_id
"CUFF.26.1"; exon_number "1";
1 Cufflinks exon 10 15 1000 - . gene_id "CUFF.204";
transcript_id
"CUFF.204.1"; exon_number "1";
1 Cufflinks exon 30 40 1000 - . gene_id "CUFF.204";
transcript_id
"CUFF.204.1"; exon_number "1";
Then I use (Operate on Genomic Intervals)->Subtract to subtract File B
from
File A Return Non-overlapping pieces of intervals. I thought it will
return
a file containing intron But the result is an empty file;
2. I convert [gtf] file to [Bed] file ,and use (Extract
Features)->Gene BED
To Exon/Intron/Codon BED, and it return the same result, an empty
file.
I think it must be something wrong with my thoughts. So I really need
your
help. Thank you very much.
sincerely yours,
John
URL:
<http: lists.bx.psu.edu="" pipermail="" galaxy-="" user="" attachments="" 20130821="" 0686d76a="" attachment-0001.html="">
Message: 2
Date: Tue, 20 Aug 2013 10:45:52 -0700
To: ?? <zhusy88@msn.cn>
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Question about Extract intron sequences
from [gtf file] + [genome FASTA file]
Message-ID: <5213AB50.1070805@bx.psu.edu>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
Hello,
There appears to be something odd with the formatting of the GTF file
- the
exon counts are off in the second transcript's first exon. The
exon_number
"1" should be "2" (remember to count reverse, is on the negative
strand).
But that is a side issue. There are other things that do not quite
make
sense, but the entire dataset was not shared.
Run this again, but do the following:
1 - make sure the files are in interval format and that the column
assignments are correct (click on the pencil icon)
2 - Use strand assignment or better, separate (+) and (-) stranded
transcripts into two files, at the start and run the query in two
workflows
from there. Some GOPS tools work best this way.
Also, be aware that some of these transcripts will not have intron
output.
For example, the first transcript in your example is a single exon
transcript. Also, if you have genes with overlapping variant
transcripts,
these will interfere with the query (you will lose introns or
fractions of
introns), but I don't know how large of a dataset you are working
with. If
you want to pull out data per transcript, the tools in the group
"Filter and
Sort" can be used to subset GFF/GTF files.
The last query that you ran is the ideal way to run to obtain this
information in Galaxy, but the GFF to BED converter creates a BED6,
not a
BED12 file, and this is why the tool produced no output (see the tool
form
for required input). Having this tool accept GTF formatted input might
be
something to consider as an enhancement - I will run it by our
development
team and open a Trello ticket as appropriate.
Another method, which may not be available to you, (from looking at
the
chromosome identifiers - these are not UCSC chrom IDs) -- but could
help in
the future or others now, is to use the UCSC Table browser. It goes
something like this:
1 - Click on "display at UCSC Main" for a GTF dataset, this loads the
data
as a custom track, default display in assembly viewer
2 - Once in UCSC, at the top bar, pick Tools -> Table Browser
3 - In the Table Browser, change track group to "Custom Tracks" and
the user
track you just loaded will be there
4 - Change region = genome, then output = bed, and make sure "Send
output to
Galaxy" is checked, submit
5 - On the next form, you will be given a list of regions to output in
the
BED6 output, Introns are one of them
Best,
Jen
Galaxy team
--
Jennifer Hillman-Jackson
http://galaxyproject.org
URL:
<http: lists.bx.psu.edu="" pipermail="" galaxy-="" user="" attachments="" 20130820="" 578f6f21="" attachment-0001.html="">
Message: 3
Date: Tue, 20 Aug 2013 17:34:24 +0100
To: <galaxy-user@lists.bx.psu.edu>
Subject: Re: [galaxy-user] customize tool display in the workflow
Message-ID: <001201ce9dc3$21917f10$64b47d30$@qmul.ac.uk>
Content-Type: text/plain; charset="us-ascii"
Hi Jennifer,
Many thanks for your reply. Unfortunately I am not clever to
figure
out how to using the existing workflow dataset renaming functions. I
only
know how to rename a dataset within history. Could you show me how to
do
this? I have attached a screen shot of my workflow. You can see that I
have
only managed to add annotation/notes to this step. Ideally I would
like to
have the step with the label of "mzidLib:PostProcessing FDR" in the
graphic
view. From other thread, someone mentioned to use ${method} in the
label, I
failed to apply this trick.
Best regards!
Jun
Message: 3
Date: Mon, 19 Aug 2013 10:18:32 -0700
To: Jun Fan <j.fan@qmul.ac.uk>
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] customize tool display in the workflow
Message-ID: <52125368.1060308@bx.psu.edu>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
Hi Jun,
I asked Dannon (our workflow lead developer) and he suggested just
using the
existing workflow datastet renaming functions. These are in the right
panel
when you click on a dataset within the workflow editor (as you
probably
know).
Inherited naming is not something that is currently being worked on,
but you
can always start a Trello card and see if it gathers votes or the
attention
of a contributor from the larger development community:
http://wiki.galaxyproject.org/Support#Galaxy_Issue_Board
Take care,
Jen
Galaxy team
--
Jennifer Hillman-Jackson
http://galaxyproject.org
URL:
<http: lists.bx.psu.edu="" pipermail="" galaxy-="" user="" attachments="" 20130819="" 8dca342d="" attachment-0001.html="">
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Message: 4
Date: Tue, 20 Aug 2013 11:34:47 -0700
To: Jun Fan <j.fan@qmul.ac.uk>
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] customize tool display in the workflow
Message-ID: <5213B6C7.5030800@bx.psu.edu>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
Hi Jun,
You are very close - just click on the "create" button within the
"Edit Step
Actions" box and it will expand, where you can then enter the new
custom
name. It will look something like this:
The other post you are referring to is a method to name the output
dataset
based on the input datasets name. You can certainly try this out and
see if
it is useful.
Hope this helps,
Jen
Galaxy team
trick.
--
Jennifer Hillman-Jackson
http://galaxyproject.org
URL:
<http: lists.bx.psu.edu="" pipermail="" galaxy-="" user="" attachments="" 20130820="" 3406f040="" attachment-0001.html="">
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Message: 5
Date: Wed, 21 Aug 2013 14:39:18 +0300
To: galaxy-user@bx.psu.edu
Subject: [galaxy-user] Very very slow response when a class is using
Galaxy from a computer room in the university
Message-ID:
<cagybphdue95okm5dhtewpprogcbr1tupczfxrjebdjpqgeeqdg@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear Sir/Madam,
My Name is Ido Carmel, I am teaching the course titled "Advanced
bioinformatics" in the Faculty of Agriculture in the Hebrew University
(Israel).
This year (around May), I used the Galaxy platform on the internet in
a
hands-on session about NGS data analysis. The session took place in
one of
the University computer classes with six students participating.
For some reason, the Galaxy response was very very slow. It was slow
when
the students were signing up and also when the students were
practicing very
lightweight jobs that usually perform immediately such as "Fastq
trimmer" or
"fastq summary" statistics.
Does the slow response was something seasonal or temporal?
Alternatively, does the response is related to the fact that the
students
were in one computer room (and possibly all the queries were sent from
the
same proxy server)?
I am teaching this course next year, do you have any advice/solution
for me?
Best Regards,
Ido Carmel
--
Ido Carmel, Dr. Yael Heifetz Lab,
Robert H. Smith Faculty of Agriculture Food and Environment, The
Hebrew
University, POB 12, Rechovot, Israel.
Tel: (+)972-8-9489222
URL:
<http: lists.bx.psu.edu="" pipermail="" galaxy-="" user="" attachments="" 20130821="" 38e4989b="" attachment-0001.html="">
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