An idea for sharing tools
by James Casbon
Hi Everyone,
I have an "I want a pony" idea that I would like to kick onto the mailing list:
It would be great if there was a way for sharing tool definitions between users.
At the moment, the main repo is maintained by the galaxy team, and
that is fine and makes sense. However, I'm sure there is a lot of
duplicated work between the users when adding other tools in. For
example, there was a conversation the other day about adding in awk.
Someone had already done this, so the best idea would be if I could
pull in that definition and enable it with minimum effort. I have
already added tools (exonerate, restriction mapper, etc, etc) that may
be of use to other people. Not sure the best way to go about this,
but if my understanding of mercurial is right, we can simply offer
another repo for people to pull changes from.
If this is of interest to you, please can you reply? If we get enough
interest and preferably some support of the core team, I could set up
a free repo at, e.g., bitbucket and add users to it. Or perhaps there
is a better way (eg patches submitted to trac)? Another question is
what kind of tools would the core team accept for inclusion in the
main dist?
Cheers,
James
12 years, 4 months
Fwd: [Genome] Stitch MAF blocks given a set of genomic intervals
by Stein Aerts
Dear Galaxy,
I was wondering whether I might be able to get the source of the
online feature "Stitch MAF blocks", to use locally?
Thanks you so much, in advance!
Best regards,
Stein Aerts
VIB, Belgium
Begin forwarded message:
> From: Brooke Rhead <rhead(a)soe.ucsc.edu>
> Date: Sat 31 Jan 2009 01:09:25 GMT+01:00
> To: Stein Aerts <stein.aerts(a)med.kuleuven.be>
> Cc: genome(a)soe.ucsc.edu
> Subject: Re: [Genome] Stitch MAF blocks given a set of genomic
> intervals
>
> Hello Stein,
>
> There is not a tool to do this in the Kent source tree. From one of
> our developers:
>
> ---
> We don't have good tools to do this, partially because the
> transformation isn't necessarily possible (not all maf's can be
> converted to a global alignment like FASTA is, and also maf blocks
> don't necessarily contain all the sequence that are in the species).
>
> The user may grab the corresponding sequences using the maf, and run
> their own global aligner (e.g. clustalw, MUSCLE).
> ---
>
> You might be able to get Galaxy's source for this. If you haven't
> already contacted them, their helpdesk address is galaxy-user(a)bx.psu.edu
> .
>
> --
> Brooke Rhead
> UCSC Genome Bioinformatics Group
>
>
> On 01/30/09 03:25, Stein Aerts wrote:
>> Hi,
>> I am looking for a standalone solution to extract MAF blocks and
>> then 'stitch' those together for each species into a fasta file,
>> starting from a genomic interval of one species? Galaxy has this
>> feature online so I was wondering whether there is a script or
>> similar code in the Kent source (or a combination of scripts) to
>> accomplish this locally in an efficient way?
>> Many thanks in advance,
>> Stein Aerts
>> Belgium
>> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
>> _______________________________________________
>> Genome maillist - Genome(a)soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>
Stein Aerts, PhD
Laboratory of Neurogenetics
VIB-KULeuven
Belgium
http://perswww.kuleuven.be/~u0038182/
http://med.kuleuven.be/cme-mg/lng/
12 years, 8 months
display at UCSC main (gbrowse)
by Rochak Neupane
When a data is in BED format or Customtrack and build is on of ucsc, a link
shows up with a link to "display at UCSC main".
I was wondering if this would be possible to do with gbrowse for data in Gff
or Gff3.
I added gbrowse links to: tool-data/shared/gbrowse/gbrowse_build_sites.txt
for data in gff format, lib/galaxy/datatypes/interval.py has add_display_app
in it, but I was not able to get a link on my dataset.
What exactly do I have to do to get a link to "display in Gbrowse"?
thanks!
rochak
12 years, 8 months
strange behavior with Job-queue
by Assaf Gordon
Hello,
On a local galaxy server, I've got into a strange situation:
Several jobs are marked as "new", but non are starting.
I've stop and re-started the server, and got the following message:
-----
galaxy.jobs.runners.local DEBUG 2009-01-26 19:29:00,829 5 workers ready
galaxy.jobs.schedulingpolicy.roundrobin INFO 2009-01-26 19:29:00,829
RoundRobin policy: initialized
galaxy.jobs INFO 2009-01-26 19:29:00,829 job scheduler policy is
galaxy.jobs.schedulingpolicy.roundrobin:UserRoundRobin
galaxy.jobs INFO 2009-01-26 19:29:00,829 job manager started
galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7886 is still in
new state, adding to the jobs queue
galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7893 is still in
new state, adding to the jobs queue
galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7896 is still in
new state, adding to the jobs queue
galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7902 is still in
new state, adding to the jobs queue
galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7904 is still in
new state, adding to the jobs queue
galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7905 is still in
new state, adding to the jobs queue
galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7906 is still in
new state, adding to the jobs queue
galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7907 is still in
new state, adding to the jobs queue
galaxy.jobs DEBUG 2009-01-26 19:29:00,952 no runner: 7908 is still in
new state, adding to the jobs queue
galaxy.jobs INFO 2009-01-26 19:29:00,971 job stopper started
-----
But even after a server restart - no jobs are starting (I've waited for
about a minute after restart).
Is there any configuration setting that can cause these jobs to start if
I restart the server? (or cause the 'stale' jobs to be deleted?)
Thanks,
Gordon.
12 years, 8 months
Two usability questions
by Assaf Gordon
On my local galaxy server:
1. Is there a way to limit number of concurrent jobs PER user ?
That is - if one user started a workflow with 30 steps,
Executing only one (or two or three) jobs of that user,
instead of all his jobs hogging the job-queue (and causing other users'
jobs to wait).
2. Is there a way to force users to login?
Prevent un-logged in users from running jobs ?
Thanks,
Gordon.
12 years, 8 months
file format on biomart imported data
by Rochak Neupane
Hello,
When importing BioMart data from galaxy, the format is always "text". In the
"Results" page in BioMart where it says "Export al results to Galaxy, the
only available format is "TSV".
Export all results to Galaxy HTMLCSVTSVXLS Unique results only
Should this not make the data imported to galaxy to be "tabular"? With the
default "text" format, I cannot view the data within galaxy, I have to
download it first then open in an editor. Only when the I change the data
type to "tabular" do I get to view the data within galaxy. I downloaded
same data as both "text" formatted and "tabular" formatted and there are no
differences between the files.
It would be better if galaxy could automatically change the datatype to
"tabular" when getting data from biomart.
When sequences are imported, perhaps galaxy can detect it as such and apply
the "fasta" format. Biomart always exports sequences in fasta format but in
galaxy this also comes out as text.
Thanks.
Rochak
12 years, 9 months
Help with adding new datatype
by Chris Cole
Hi,
I'm confused on how to add a new datatype. I've read the
http://g2.trac.bx.psu.edu/wiki/AddingDatatypes wiki page, but it isn't
clear what I need to do for a completely new type.
Specifically, I want to add a gzip tool to compress and uncompress files
to help up/downloading of large files. I've added the following line to
the datatypes_conf.xml:
<datatype extension="gz" type="galaxy.datatypes.images:Gzip"
mimetype="application/gzip" display_in_upload="true"/>
But I am stumped as to where I should add the additional information as
per step 3. on the wiki page. Can someone help, please? BTW I do code,
but not in python.
Thanks,
Chris
12 years, 9 months
Lost sequence info on update
by Chris Cole
Hi,
I've recently done an svn update on my local Galaxy install, which all
seemed to go well. However, in the history pane, the information for
fasta and solexafastq files no longer details the number of sequences in
the file, it only gives the size of the file. How do I get back the
sequence information for those file types?
Thanks,
Chris
12 years, 9 months
[patch] much more efficient fasta tools
by James Casbon
Hi everyone,
I got bored waiting around for the fasta tools to finish so I improved
the length filter and fasta to tabular scripts. On a reasonable data
set these were taking over ten minutes with the old version. With
this version its a few seconds.
The improvement comes from not reformatting the data, caching it in
memory or building a hash. All of these are unnecessary for these
tasks IMO.
cheers,
James
12 years, 9 months
