Hi,
"Summary Statistics" is ok, but before you need to use the tool 'Compute
sequence length'.
Ciao,
Bjoern
Am 23.05.2014 13:29, schrieb Dominique Cowart:
Hello,
I am attempting to use Galaxy to calculate the mean sequence read
length and identify the range of read lengths for my 4
Hi Anna,
you can unsubscribe yourself, following the steps on:
https://wiki.galaxyproject.org/MailingLists#Subscribing_and_Unsubscribing
Cheers,
Bjoern
Am 21.05.2014 01:37, schrieb Anna J.:
please delete me from the mailing list
_
Hi Kaz,
you are searching for GATK tools, right? Please have a look at the GATK
suites in the Tool Shed.
Cheers,
Bjoern
Am 12.04.2014 00:16, schrieb KS:
Dear all,
I can't find either of Table Recalibration or Base Recalibrator on
usegalaxy public server. I am defident this is right place to
Hi,
we are currently working on one pipeline. I can share if you are
interested, but its not yet finished, parameter wise, but all tools
should be there.
We tried to stick to the GATK2 best-practise guide and are using snpeff
for annotation.
Cheers,
Bjoern
Am 15.03.2014 01:55, schrieb Mat
Hi Chetan,
try to use the feature to create file4.txt ...
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cconfigfiles.3E_tag_set
Cheers,
Bjoern
Am 04.03.2014 15:04, schrieb do kadya:
Respected Sir / Ma'am,
'x' tool having 3 commands,
1) command takes files from path. ex
perl
n all of my try .bai file is 0 KB.
I need to upload because my 'x' program is not accepting normal BAM
format hence it needs Indexed BAM.
Waiting for positive reply.
On Tue, Feb 25, 2014 at 1:08 PM, Björn Grüning
wrote:
Hi Do,
the link I send you yesterday, contains a section about li
Hi Do,
the link I send you yesterday, contains a section about linking file.
Have a close look at the upload form in the admin section. There should
be an option to link the file into Galaxy.
As a side note, I really think you will need an additional harddrive,
100GB free space would be not en
Hi Do,
If you are running a loacl instance and you are admin you can use the
data library and upload or even better link your data into a data library.
https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
Cheers,
Bjoern
Hi,
I am unable to upload more than 3 GB data from
Hi,
I think you should start here:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Furthermore, Peters Blast wrappers are always a good start to learn
writing Galaxy Tools.
https://github.com/peterjc/galaxy_blast
Here you can find a variety of small to complex wrappers:
https://g
Hi Mathew,
I have a mapper (bismark) and my own tools (+wrapper) and was able to do
an entire analysis with it. The bismark wrapper is in the toolshed. The
other tools can be found in my github repository.
https://github.com/bgruening
galaxytools and methtools
Hope that helps,
Bjoern
> Do we h
Hi Wang,
please check if your fastq file is associated with the correct fastq
format, fastqsanger probably.
Cheers,
Bjoern
> Hi,
>
> I just notice that NGS FASTQ Trimmer by 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 Ketan,
have you installed your tool via the Tool Shed?
If so, than you need to delete the old revision of your tool.
Cheers,
Bjoern
> Hi,
>
>
> I renamed my tool name in but when I restart Galaxy
> server, I see a dropdown in front of the tool title with two versions
> with same value. Whe
Hi Ketan!
it sounds like your input is sanitized. You can disable it for your
whole wrapper or you can write a special sanitizer for your input field:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set
Cheers,
Bjoern
> Hi,
>
>
> In a test tool that I am worki
Hi Larry,
you can build custom genomes in Galaxy.
More details in the Galaxy wiki:
https://wiki.galaxyproject.org/Learn/CustomGenomes
Cheers,
Bjoern
> Hi
>
>
> I have a question about the use of BedTools in Galaxy. I am trying to
> obtain a graph or table of the number of RNA reads mapped to
Hi all,
over the last month we developed a new version of GATK2 wrappers and are
now seeking for testers, users and overall feedback.
We are currently targeting GATK 2.8. One of the big issues with GATK2 is
the new licence. Because of that we can't install GATK2 with the
wrappers, but we hope we
Hi Catheryn,
for ChIP-seq analysis, normalisation and BAM file correlation we use
deeptTools. Here you can read more about it:
https://github.com/fidelram/deepTools
And here is the toolshed repository:
http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools
Cheers,
Bjoern
> Dear Galaxy,
>
>
Hi Jorge,
> My name is J.Braun and I am a new user of galaxy... It is a great tool
> for biologists. I have some questions and I would appreciate you could
> help me.
>
> 1) can I make a blast in Galaxy?
Yes!
> 2) If so, can I download blast in galaxy?
Yes!
> 3) If so, can I set up blast in
Hi Simon,
I had that error before, not with trackster ... somewhere else. I think
it's an error of one of these UCSC tools and it occurs if you supply
empty files. Can you check that none of your file is empty? Or your file
will be automatically converted during trackster visualisation and that
is
Hi Claudio,
did you installed Augustus with the ToolShed?
The env variable $AUGUSTUS_SCRIPT_PATH need to be set and point to the
augustus wrapper folder containing the extract_features.py script.
Hope that helps!
Bjoern
> Hello,
>
>
> I am trying to use the genome Annotation tool Augustus on m
Hi Thanh,
under "FASTA manipulation" I have one tool das is called "RNA/DNA
converter". If it is not available in your instance you need to install
the FASTX-toolkit wrappers. These are available in the Tool Shed.
Hope that helps,
Bjoern
> Hi all,
> I want to to map my sequencing reads to miRN
Hi Xiao,
can you show us the complete wrapper XML script?
Thanks,
Bjoern
>
>
> -- Forwarded message --
> From: XiaoTao Jiang
> Date: 2013/9/2
> Subject: About empty no peek problem
> To: galaxy-user-requ...@lists.bx.psu.edu
>
>
> Dear all
>
>
> Today I embed one of my R sc
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 Sachit,
we are working currently on a DESeq2 wrapper. Not yet finised sorry.
There is also a edgeR Test repository from Ross Lazarus under:
http://testtoolshed.g2.bx.psu.edu/view/fubar/edger_test
Work is in progress, help is welcome!
Ciao,
Bjoenr
> Hi,
>
>
> These are the R libraries. Have
Am Donnerstag, den 06.06.2013, 15:19 -0400 schrieb Sébastien Boisvert:
> On 06/06/13 02:58 PM, Björn Grüning wrote:
> > Am Donnerstag, den 06.06.2013, 14:42 -0400 schrieb Sébastien Boisvert:
> >> On 06/06/13 02:32 PM, James Taylor wrote:
> >>>> I want to add Ray
Am Donnerstag, den 06.06.2013, 14:42 -0400 schrieb Sébastien Boisvert:
> On 06/06/13 02:32 PM, James Taylor wrote:
> >> I want to add Ray (a scalable de novo assembler for genomes and
> >> metagenomes)
> >> to Galaxy.
> >
> > And I really want you to do this!
>
> So we are at least two !
Joining
Hi Chunyu,
can you provide us with a small, reproducible example?
Thanks,
Björn
> Actually, the file is all tab-delimited, from beginning to end.
> It has no problem uploading larger data. Seems to be bug somewhere?
> Chunyu
>
>
> On Mon, May 13, 2013 at 12:45 PM, James Taylor
> wrote:
>
Hi Els,
try the tool 'Group data by a column and perform aggregate operation on
other columns.' And choose 'count' or 'count distinct.
Hope that will work.
Happy research!
Bjoern
> Dear all,
>
>
>
> I am a Phd student working on chicken genomics, with limited
> experience in the bio-informat
ol RepeatMasker:
>
> An error occurred running this job: Epilog : job finished at jeu.
> janv. 31 14:39:16 CET 2013
> /work/galaxy/database/pbs/galaxy_4134.sh: line 13: Erreur de syntaxe
> près du symbole inattendu « ;; »
> /work/galaxy/database/pbs/galaxy_4134.sh: line 13: `
manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
--
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
D-79104 Freiburg i. Br.
Te
Hi Sachit,
bismark is not yet in any official toolshed. It is in the test-toolshed
and there are reasons for it :)
Try to apply that patch and it should work:
https://bitbucket.org/BjoernGruening/galaxy-central-bismark/changeset/446c309fe6d346362ad0bcc29a216121553dd361
Cheers,
Bjoern
> I am get
uot;reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please
Hi Bernardo,
> Hello Galaxy community,
>
>
> I would like to know if there is any available tool in Galaxy for
> automated gene annotation. I need gene annotation in GTF or GFF3
> format to run CuffDiff on a RNA-Seq project that we are.
We have a tool, that annotates your prokaryotic genome, th
e code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
--
Björn Grüning
Albert-Ludwigs-Universität Fre
;
> On Mon, Oct 8, 2012 at 8:08 AM, Björn Grüning
> wrote:
> Hi David,
>
> please do not hijack a different thread :)
> If you are analysing Bisulfite data i would recommend to have
> a look at
> http://www.bioinformatics.babraha
Hi David,
please do not hijack a different thread :)
If you are analysing Bisulfite data i would recommend to have a look at
http://www.bioinformatics.babraham.ac.uk/projects/ ... especially at
bismark.
We have written a wrapper for bismark, its still in testing phase but if
you like to try it ou
Hi Sachit,
you need to install such tools by yourself, unless you are using some
new tools from the toolshed. For example the ncbi-tools or BWA from the
toolshed are capable of installing all dependency automatically.
In the future the plan is to move all heavy tools to the toolshed with
automatic
Hi Yan,
have a look at the blast2GO wrapper in the toolshed. If you already have
gene-ids you can download the GO in an appropriate format and intersect
with your ids.
Hope that works,
Bjoern
> Hi everyone,
>
>
>
> I got a list of differentially expressed genes from my RNA-seq data.
> Is the
o manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
--
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
D-79104 Freiburg
laxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
--
Björn Grüni
Hi Irene,
> Hi,
> I deleted several jobs from my history (and purged history as well), however
> the used space on history hasn't changed.
> What is the limit of Gb that can e stored?Can this be updated when files are
> deleted permanently
Have a look @
allow_user_dataset_purge = False
in
Hi Norbert,
please have a look at the FTP-Upload feature from galaxy.
The idea is that every user gets an FTP folder in which he can upload
data. If you create such a directory you can probably link your data in
such directories and galaxy will offer them to the users in the upload
tool.
Hope tha
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
--
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
laxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
--
Björn Grüning
Alber
y Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
--
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceut
Hi Efthymios,
it should work as you expected. The server and the processes should run
even if you close the browser. All you need is to keep the server (local
instance ...) running.
Cheers,
Bjoern
> Dear Galaxy users,
>
> I have installed a local Galaxy instance on a server and I use it to
> ru
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