Hi,
How can I create a folder inside another library folder?
I tried:
lib_create_data = {
'name':'mm9',
'create_type': 'folder',
}
submit(api_key, api_url + "libraries/%s/contents" % library_id,
lib_create_data, retur
Hi,
I have tried to use tasks with tophat2, but I got the following bug.
> multi.py +153
msg = 'nothing to merge for %s (expected %i files)' \
% (output_file_name, len(task_dirs))
This occurs because tophat2 tool uses from_work_dir feature to get the
output files.
But on
That's a great idea.
I have used data libraries from the api.
Can I set a data library file as the input for a tool using the browser?
Hagai
On Thu, Apr 4, 2013 at 5:31 PM, Hans-Rudolf Hotz wrote:
>
>
> On 04/04/2013 04:10 PM, Hagai Cohen wrote:
>
>> Hi,
>> Is
Hi,
Is is possible to configure gene annotation file files inside galaxy per
genome internally?
As in bowtie indices or something similiar.
I don't want to upload the ucsc constant gtf files on each history I need
them.
Thanks for the help,
Hagai
___
1:4770447-4781119>
chr149984769194991695.9322.77
http://genome.ucsc.edu/cgi-bin/hgTracks?db=m9&position=chr1:4798-4316<http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=chr1:4792498-4803416>
I hope this might be useful for others as well.
Hagai
On Mon, Mar 18, 2013 at 6:14
Hi,
How is it possible to change the deafult display ratio in galaxy?
(The ratio between the tools, center & history)
Thanks,
Hagai
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rCell function here: static/scripts/mvc/data.js, but
I didn't succeed in changing it to add links to the html.
What am I doing wrong?
Thanks,
Hagai
On Sun, Feb 3, 2013 at 1:06 PM, Hagai Cohen wrote:
> Right.
> I will convert it to text, allowing only simple links ( with href onl
You can change the bowtie wrapper to save the stderr of the bowtie part.
The command line is (bowtie2_wrapper.py):
cmd = 'bowtie2 %s -x %s %s %s | samtools view -Su - | samtools sort -o - -
> %s'
Change it to something like:
cmd = 'bowtie2 %s -x %s %s %s 2> bowtie_stderr_filename | samtools view -
derstand the galaxy code there.)
The difference between tool which accepts input file and a tool which
accepts multi-input-file is nice.
Currently, I'm gone use this. I hope the official release will have similar
feature in the future.
Thanks,
Hagai
On Wed, Feb 13, 2013 at 9:56 AM, Hagai
> http://www.bits.vib.be
> @bitsatvib
>
> On 02/12/2013 04:31 PM, Hagai Cohen wrote:
>
>>
>> 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 work
> Rijvisschestraat 120, 9052 Zwijnaarde
> Tel: +32 9 244.66.34
> Bioinformatics Training and Services (BITS)
> http://www.bits.vib.be
> @bitsatvib
>
>
> On 02/12/2013 04:02 PM, Hagai Cohen wrote:
>
>> Hi,
>> I'm looking for a preferred way of runni
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
Hi,
There are couple of Linux shells: bash, sh, zsh, csh. etc
I would like to know if Galaxy is written to be supported on a specific one
or it is written to support any linux shell?
I'm asking this, because I want to add some features and I want to know
what shell should I support?
Or should writ
loaded tabular file
> will be executed by the .html call, with complete access to everything
> in the Galaxy browser window (like your session cookies).
>
> --
> James Taylor, Assistant Professor, Biology/CS, Emory University
>
>
> On Tue, Jan 29, 2013 at 7:18 AM, Hagai Cohen
, Hagai Cohen wrote:
> Hi,
> I have a tool which outputs a csv file with links.
> When I press the eye icon - I would like these links to be shown as links
> in the browser.
> It is possible?
>
> Thanks,
> Hagai
>
Hi,
I have a tool which outputs a csv file with links.
When I press the eye icon - I would like these links to be shown as links
in the browser.
It is possible?
Thanks,
Hagai
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in you
Hi,
is it possible that when I rerun a tool it will also rerun the tools that
depends on it?
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Hi,
I have a problem with my galaxy local installation working with a cluster.
On the server my galaxy dir path is X, but on the cluster it is Y (same
directory but different soft links).
Is it possible to config the path of the galaxy installation (GALAXY_DIR)
which will be send to the nodes?
Th
but here is the full
> context of how I create such a file if that is of interest:
>
> https://github.com/jmchilton/cloudbiolinux/blob/deploy/cloudbio/deploy/galaxy.py
>
> -John
>
> On Mon, Jan 7, 2013 at 3:37 AM, Hagai Cohen wrote:
> > Hi,
> > I would like to auto cr
Hi,
I would like to auto create users on my local Galaxy instance.
I saw that in the "create user" on the API, I should enable use_remote_user
(which as I understand means that I have to use Apache or nginx).
Is there another way besides using Apache to create users automatically?
Thanks,
Hagai
_
Hi,
I'm trying to use the API for showing workflow info which should be
something like:
/api/workflow/
But I'm getting the following error:
.../galaxy-dist/lib/galaxy/webapps/galaxy/api/workflows.py", line 80, in
show
label_name = step.tool_inputs['name']
TypeError: 'NoneType' object has no at
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