John, that's seems great.
I will read this stuff and see if I can use it (The bed format isn't that
essential, bowtie can bam instead).
If it wont work I will try the other solution which doesn't need to change
the galaxy own code (Creating hundreds of workflow run, linking to their
outputs and r
Hi Russell,
also keep in mind, that Cheetah is just python. Maybe you can try to do
something like that:
$text.strip() or str($text).strip()
Cheers,
Bjoern
> I want to add a filter to strip whitespace and newlines from a text
> input box so I can pipe the sanitized string to a command.
>
> Doc
Also, do I have make all the reference files executable?
On Wed, Feb 13, 2013 at 6:39 AM, Sachit Adhikari <
sachit.techner...@gmail.com> wrote:
> I downloaded the entire directory of UCSC for the reference gnome of
> Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference
> gno
I downloaded the entire directory of UCSC for the reference gnome of
Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference
gnome. I found a directory: Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index
with the files:
genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2 genome.r
I think the hg clone link on the news brief is incorrect:it states: hg clone https://bitbucket.org/galaxy-dist#stableProbably should be hg clone https://bitbucket.org/galaxy/galaxy-dist#stableThon
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Hi,I had created a trackster vizualization that had not finished indexing yet, and I decided to change it into a circster visualization.I then added a few more BAM files and tried to save the visualization and now it just hangs there...no errors in the logs so far, but no saving of the visualizatio
Hi Chun-Yuan,
Sorry to see you're running running into so much trouble. The reality of
the situation is that the Update Galaxy button in CloudMan is currently
broken due to the changes in Galaxy that make the updates a rather manual
process. For the past several weeks, the team has been working on
Bodged using string functions :-)
set $data = ''.join([line for line in ($seq_source_type.seq_paste.split()) if
line[0] != ">"])
Removes the fasta header line and any white-space so I can pipe sequence
directly to blastn.
Means users can quickly paste in a bit of sequence for blasting without f
I don't think there's one in a toolshed but someone's clearly done some
work on it at http://galaxy.cbiit.cuhk.edu.hk/
Perhaps you may be able to convince them of the many benefits of
contributing back to the community by sharing some of their tool code?
On Wed, Feb 13, 2013 at 12:32 PM, Jorge
Dear all,
Is there a repository where I can finnd SOAPdenovo tool wrappers for
Galaxy? I would like to install this tool in our local Galaxy server.
Thanks,
Jorge
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Matthew,
This is related to the version of grep called by Galaxy. GNU grep presents the
issue while BSD grep works as expected. I haven't really dug much, but this
could probably be addressed by handling input parameters better in the tool
wrapper, if you want to take a look.
-Dannon
On Fe
Hi Russell,
There may be a better way, but this works for me in the Toolfactory to
create space and special character free names?
On Wed, Feb 13, 2013 at 11:22 AM, Smithies, Russell <
russell.smith...@agresearch.co.nz> wrote:
> I want to add a filter to strip whitespace and newlines from
Regarding this issue (
https://trello.com/card/filter-and-sort-select-tool-not-dealing-with-special-characters-right/506338ce32ae458f6d15e4b3/572
):
No bug is apparent when using an up-to-date local instance of Galaxy (local
history on Trello card). However, when using the Galaxy public server the
I want to add a filter to strip whitespace and newlines from a text input box
so I can pipe the sanitized string to a command.
Documentation is a bit sparse (and my Python a bit basic) so does anyone have
an example?
Perhaps there's a better way of doing it - regex maybe?
Any ideas?
Thanx,
--R
> So we did the following:
> Downloaded the data
> Added the paths to .loc file
> restarted galaxy
>
> We still are getting the following error:
>
> 2: Extract Genomic DNA on data 1
> empty
> format: fasta, database: hg19
> 56 warnings, 1st is: Chromosome by name 'chr22' was not found for build
Hi Amanda,
the tools directory is also tracked and updated in mercurial. But only
the tools that are shipped with galaxy. If you have inserted your own
tools, they want be affected. If you modified galaxy tools that are part
of main galaxy, than you will probably get a merge conflict. But
mercuria
Since I can't find this on any of the wikis: when updating Galaxy
through mercurial, is the tools directory affected? Our instance has
backups of the directory, but I want to know whether I will have to
take care of them when I pull down the latest release.
Thanks in advance.
--
Amanda Zuzolo
Bi
Hi,
I have followed, carefully, the instructions posted in:
http://wiki.galaxyproject.org/Admin/Data%20Integration
Yet, despite my best efforts when I get, say all exons from hg19 build and
try to their fetch sequences, galaxy tells me that the sequences for hg19
are not there
I find this surpri
Hi all,
I have problems with datasets that were linked into Galaxy data libraries (as
Admin: "Add datasets", select "Upload files from filesystem paths" and "Link to
files without copying to Galaxy"). Those files cannot be looked at, downloaded
or viewed in a genome browser.
Errors in the brow
I don't believe you can, although it should be possible to extend
upload to provide that information. However, is there no header you
can use in your filetype to detect it?
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Mon, Feb 11, 2013 at 10:51 PM, David Angot wrote:
>
You cannot directly couple different workflows.
But you could indeed copy all outputs of the different workflows into
one history, and create a separate workflow with your tool to work on
all those input files.
Cheers,
Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 2
Hagai,
Jorrit Boekel and I have implemented essentially literally what you described.
https://bitbucket.org/galaxy/galaxy-central/pull-request/116/multiple-file-datasets-implementation
Merge this in to your Galaxy tree
https://bitbucket.org/jmchilton/galaxy-central-multifiles-feb2013.
Switch use
Thanks for your answer.
I figured that there is an option to run a workflow on multiple files, but
I can't merge the outputs afterwardsl. I would like the workflow to return
one final output.
But you gave me another idea.
Can I somehow tell one workflow to run on other workflow output?
If this can
Hi Hagai,
Actually, using a workflow, you are able to select multiple input files,
and let the workflow run separately on all input files.
I would proceed by creating a data library for all your fastq files,
which you can upload via FTP, or via a system directory.
You can use a sample of your
Hi,
I'm looking for a preferred way of running Bowtie (or any other tool) on
multiple input files and run statistics on the Bowtie output afterwards.
The input is a directory of files fastq1..fastq100
The bowtie output should be bed1...bed100
The statistics tool should run on bed1...bed100 and ret
Thanks Dannon.
BR
Zeeshan
On W7-Feb 12, 2013, at 12:22 PM, Dannon Baker wrote:
> Yes, you use the same image for both masters and the workers.
>
> -Dannon
>
> On Feb 12, 2013, at 5:46 AM, Zeeshan Ali Shah wrote:
>
>> Thanks Enis,
>> The paper is good , i was looking something like it.
>
Hello joachim,
Thanks for reporting this. I've added a Trello card for this issue:
https://trello.com/card/galaxy-reports/506338ce32ae458f6d15e4b3/610
Greg Von Kuster
On Feb 12, 2013, at 6:05 AM, Joachim Jacob |VIB| wrote:
> Hi all,
>
>
> Running ~/galaxy-dist/run_reports.sh brings up the G
Yes, you use the same image for both masters and the workers.
-Dannon
On Feb 12, 2013, at 5:46 AM, Zeeshan Ali Shah wrote:
> Thanks Enis,
> The paper is good , i was looking something like it.
>
> Ok, I will use CBL , just a small query :
>
> we use CBL for cloud man purpose, i think yes .
Hi all,
Running ~/galaxy-dist/run_reports.sh brings up the Galaxy Reports
interface on poort 9001.
When clicking on 'Jobs per user' -> picking a user -> picking a month ->
and clicking on 'State' in the bar at the top, clears the screen.
Thanks,
Joachim
--
Joachim Jacob
Rijvisschestraat
Thanks Enis,
The paper is good , i was looking something like it.
Ok, I will use CBL , just a small query :
we use CBL for cloud man purpose, i think yes . Should we use the same Image
for workers and enable cloudman script to use that one for launching nodes ?
BR
Zeeshan
On W7-Feb 11, 2
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