Thanks, this helps. I was running with an interpreter and I didn't realize I
had to had the full path in there. I was expecting that $PATH which contains
the directory the script was located in to take care of it. Thanks you very
much for the clarification.
Timothy
Hello Alison,
I wanted to share with you the bitbucket ticket for the improvements to
composite datatypes. As Ross described, this would be part of a larger
project. The ability to save composite data using the floppydisc icon
would be one example an impact of the proposed change.
https://bi
I am asking for galaxy to add our VectorBase source to their public instance,
as VectorBase sourced-data (either biomart instance) may be out-of-date. The
UCSC data is even older. As EuPath has their latest release data available
from the public interface, we were interested in doing the same.
Hello Jacob,
This would be a welcomed addition to the Tool Shed. Please see this wiki
for instructions about how to submit:
http://galaxyproject.org/wiki/Tool%20Shed
Apologies for the late reply,
Best,
Jen
Galaxy team
On 6/23/11 5:59 PM, Jacob Israel Cervantes Luevano (LANGEBIO) wrote:
Hi
Nate,
For some reason, ~/galaxy-dist wasn't in my PATH. Here is the output when the
script is run from the ~/galaxy-dist directory:
[~/galaxy-dist] myuserid 03:50 PM > python ./scripts/get_platforms.py
macosx-10.6-intel-ucs2
[~/galaxy-dist] myuserid 03:50 PM >
Looks like it is set for Mac OS
I suppose what I meant to say was that since I was able to add the
metazoa.ensembl.org biomart by modifying the existing biomart xml, would
this not also work for VB's biomart instance? Or would this not be what you
are looking for?
Actually, re-reading your OP, is it that you are asking for gala
Hi Nate,
I wrote the code such that if a machine had a large local scratch space then
you could comment it out and it would go to the default setting of writing to
/tmp or whatever is defined by SGE. You are correct that the environmental
variables defined in the Galaxy startup script do not ge
Hi Scott,
For information on adding Datasource tools to Galaxy, please see:
http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources
http://www.ncbi.nlm.nih.gov/pubmed/21531983
If your resource is using software that is already Galaxy-aware, you can often
take an existing xml configuration (GALA
Hi Nate,
Thanks for the response. Here is the output:
[~] myuserid 01:34 PM > python ./scripts/get_platforms.py
/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python:
can't open file './scripts/get_platforms.py': [Errno 2] No such file or
directory
[~] my
Dannon Baker wrote:
> The 'step' in question is the actual workflow step id, since ordering of
> steps in a workflow is flexible and might be changed without realizing it by
> moving steps around in the editor. The easiest way to retrieve this
> identifier is to use the API and view the workflo
The 'step' in question is the actual workflow step id, since ordering of steps
in a workflow is flexible and might be changed without realizing it by moving
steps around in the editor. The easiest way to retrieve this identifier is to
use the API and view the workflow in question.
Here's an ex
Hello Lukasz,
This is a good idea, but perhaps it would be better to share the data in
a history where others can gain access rather than add the merged
"contamination" genomes as a native reference genome (to avoid
confusion). This would also give you control over the actual contents
for upd
Roxanne Tapia wrote:
> Is there a way to create/view histories via the api, and to associate data in
> libraries to histories?
> Then to share the histories or make them public, and build a URL to view the
> history?
Hi Roxanne.
To the first three, yes. This was added in the most recent stab
Roxanne Tapia wrote:
> Hi,
>
> I was going through the examples in the README, and everything went along
> fine until I tried to upload files from the import directory:
>
> usage: library_upload_from_import_dir.py key url folder_id file_type
> server_dir dbkey
>
> I don't understand what the
Is there a way to create/view histories via the api, and to associate data in
libraries to histories?
Then to share the histories or make them public, and build a URL to view the
history?
Roxanne Tapia
Software Developer 3
B-6, Genome Science
Bioscience Division
r...@lanl.gov
(505)665-0206
Hi,
I was going through the examples in the README, and everything went along fine
until I tried to upload files from the import directory:
usage: library_upload_from_import_dir.py key url folder_id file_type server_dir
dbkey
I don't understand what the last two arguments 'server_dir' and 'db
I was trying to use the workflow_execute.py
And I can't understand the last argument:
usage: workflow_execute.py key url workflow_id history step=src=dataset_id
So in step=src=dataset_id
step: I think equals the next step #in the history?
src: ???
dataset_id: This has to be the dataset id
Peter Cock wrote:
> On Tue, Sep 6, 2011 at 5:00 PM, Nate Coraor wrote:
> > Peter Cock wrote:
> >> On Tue, Sep 6, 2011 at 3:24 PM, Nate Coraor wrote:
> >> > Ideally, there'd just be a column on the dataset table indicating
> >> > whether the dataset is compressed or not, and then tools get a new
>
On Tue, Sep 6, 2011 at 5:00 PM, Nate Coraor wrote:
> Peter Cock wrote:
>> On Tue, Sep 6, 2011 at 3:24 PM, Nate Coraor wrote:
>> > Ideally, there'd just be a column on the dataset table indicating
>> > whether the dataset is compressed or not, and then tools get a new
>> > way to indicate whether
Hi,
when a tool outputs an unsorted bam file, the indexing fails (quietly)
and its metadata variable "bam_index" points to an inexistent file. This
causes a nasty bug when trying to import the dataset into a data library
and actually makes the library unusable unless you delete the broken
ent
Peter Cock wrote:
> On Tue, Sep 6, 2011 at 3:24 PM, Nate Coraor wrote:
> > Edward Kirton wrote:
> >> Peter wrote:
> >> > I wonder if Galaxy would benefit from a new fastqsanger-gzip (etc)
> >> > datatype?
> >> > However this seems generally useful (not just for FASTQ) so perhaps a
> >> > more
>
SHAUN WEBB wrote:
>
> Hi.
>
> I am interested in putting quotas in to effect on our local Galaxy
> server. From the admin page I can create a quota but this only seems
> to apply to disk space. I noticed on your test site you have quotas
> for concurrent jobs also. Have I missed how to set this o
Timothy Wu wrote:
> Hi,
>
> I'm trying the add tool tutorial at
> http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial . It works, but
> how do I designate the path of the tool if it's not dropped into the same
> directory as the tool config xml? Some executable may not be in the
> director
Kristen Eisenberg wrote:
> [galaxy-dev] Failure to prepare job error
>
>
>
> Hello,
>
> I'm running a Python/R tool from my Amazon Galaxy instance. To use R, I
> import a package I've installed called PypeR. My tool works fine from the
> command line, but when I try to run it on my Amazon insta
Nikhil Joshi wrote:
> Hi all,
>
> Is there a repository of pre-indexed genomes for base-space/color-space,
> bwa, bam, sam, etc...? It would be much easier than having to index them
> all ourselves :)
Hi Nik,
I've been meaning to set this up for a while now. Stay tuned for an
announcement
Shantanu Pavgi wrote:
>
> Thanks for the reply Kanwei. Is there any announcement or news feed that
> people can subscribe to know when main galaxy instance is updated. This will
> help sites which want to keep up with the PSU's main galaxy instance. Do you
> announce it on the galaxy-user list
Whyte, Jeffrey wrote:
> Thanks for the information, Nate.
>
> I installed Python as you described, and the error I get now is pasted below.
> I appreciate your help.
>
> Jeff
>
> [~/galaxy-dist] myuserid 03:06 PM > ./run.sh
> Some eggs are out of date, attempting to fetch...
> Warning: MarkupS
remy d1 wrote:
> Hello Nate,
>
> It is not easy...
>
> I think it is in this :
>
> if dataset.type in ( 'server_dir', 'path_paste' ) and link_data_only ==
> >> 'link_to_files':
> >
> > # Never alter a file that will not be copied to Galaxy's local file
> >> store.
> >
> > if
I completely agree it's a bit of an unfortunate requirement in this
case, but I'm not averse to (minor) code changes to achieve a more
polished user experience. Something like the best guess mechanism
Galaxy currently employs to recognize returning anonymous would be
fine, but I don't know where to
Joseph Hargitai wrote:
>
> Nate,
>
> could we go to the beginning of the issue:
>
> where is the galaxy env set? I've seen a few post but I can only gather
> partial info.
When running locally, the environment is the environment that is in
place when you start Galaxy. If you're starting via
On Tue, Sep 6, 2011 at 3:24 PM, Nate Coraor wrote:
> Edward Kirton wrote:
>> Peter wrote:
>> > I wonder if Galaxy would benefit from a new fastqsanger-gzip (etc)
>> > datatype?
>> > However this seems generally useful (not just for FASTQ) so perhaps a more
>> > general mechanism would be better w
Edward Kirton wrote:
> > In your position I agree that is a pragmatic choice.
>
> Thanks for helping me muddle through my options.
>
> > You might be able to
> > modify the file upload code to gzip any FASTQ files... that would prevent
> > uncompressed FASTQ getting into new histories.
>
> Right
Hi all,
Thanks for reply . I have an application to visualize some
custom datatyes inputs . i want to integrate this application with
galaxy . i have already added datatypes in my local instance of
Galaxy . Is It required to modify my application ?
Regards
shashi
On Tue, Sep 6, 2011
Chorny, Ilya wrote:
> Nate,
>
> We ran into this issue with /tmp not having enough space. We came up with a
> generic solution and were wondering if you might want to add it to
> galaxy-central. We did not want to modify SGE as it could affect other jobs
> that use the cluster.
>
> We create
Hi.
I am interested in putting quotas in to effect on our local Galaxy
server. From the admin page I can create a quota but this only seems
to apply to disk space. I noticed on your test site you have quotas
for concurrent jobs also. Have I missed how to set this or is this
functionality
Hi Shashi,
The docs for external display application could use some enhancement, but I
have provided details on the features you are asking about below.
target_frame: this is the frame where you want this external display
application to appear.
type="template": this parameter type is a cheetah
On Tue, Sep 6, 2011 at 3:33 PM, shashi shekhar wrote:
> Hi All.,
>
> I need help in understanding the xml tag for display_application. i
> don't know how all these xml tags works . can u provide me links for
> understanding those tags like
>
> target_frame
>
> type="template"
>
> viewable="False
Hi All.,
I need help in understanding the xml tag for display_application. i
don't know how all these xml tags works . can u provide me links for
understanding those tags like
target_frame
type="template"
viewable="False
http://genetrack.g2.bx.psu.edu/galaxy?filename=${encoded
On Tue, Sep 6, 2011 at 9:41 AM, Timothy Wu <2hug...@gmail.com> wrote:
> Hi,
>
> I'm trying the add tool tutorial at
> http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial . It works, but
> how do I designate the path of the tool if it's not dropped into the same
> directory as the tool confi
Here's one bad option for dealing with a bad requirement - at least it
requires no code changes...
1. create a new user called d...@where.ever.org for your Galaxy. Do
not require login in universe_wsgi.ini
2. edit welcome.html - invite visitors not wanting all the benefits of
an individual registr
Hi,
I'm trying the add tool tutorial at
http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial . It works, but
how do I designate the path of the tool if it's not dropped into the same
directory as the tool config xml? Some executable may not be in the
directory. Surely it couldn't possiblely
Hi all,
Was wondering how I can allow anonymous users to run workflows in my
local Galaxy instance, as currently users need to be logged in to run
workflows. I'd like drop this requirement in light of the intended
publication of a workflow in a journal which demands that "Web
services must not req
Hi,
I am looking for tophat xml that supports SOLID colorspace. Is it anywhere
available?
Thanks a lot.
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