Hi,
I'm running:
planemo shed_update --check_diff --shed_target toolshed
and get a python error message (see below).
shed_diff and shed_lint are working fine.
planemo, version 0.12.2
Best,
Alexander
Traceback (most recent call last):
> File "/usr/local/bin/planemo", line 11, in
> sys
And the corresponding pull request:
https://github.com/galaxyproject/tools-devteam/pull/173
The BWA github-repo is newer than what is on the toolshed, right? When do
you update the toolshed?
Best,
Alexander
2015-06-26 22:17 GMT-05:00 Alexander Vowinkel
:
> FOR GOD'S SAKE SEARCH THE ARCHIVE !!!
FOR GOD'S SAKE SEARCH THE ARCHIVE !!!
http://dev.list.galaxyproject.org/Database-Build-td4140140.html
https://github.com/galaxyproject/tools-devteam/blob/master/tools/tophat2/tophat2_wrapper.xml#L313
2015-06-26 21:58 GMT-05:00 Alexander Vowinkel
:
> Hi,
>
> as many of you probably know by now,
Hi,
as many of you probably know by now,
I have a tool that creates an output collection
by discovering the datasets in this collection
like propsed there: [1]
Specifically I have a fastq input with set build
information (a ref genome).
The output is a collection of fastq files.
After I managed t
The second link leads to an endpoint that does exactly that.
M.
On Fri, Jun 26, 2015 at 4:43 PM Ryan G wrote:
> What if the data is not in the history? Ie we received ngs data from an
> external source and copied it to a location on our server. I now want to
> link to it in Galaxy.
>
> What I
What if the data is not in the history? Ie we received ngs data from an
external source and copied it to a location on our server. I now want to link
to it in Galaxy.
What I was doing previously was entering the file system path through the UX
but we want to automate this a bit and have a s
History Dataset Association. i.e. if you already have the dataset in
history you can very easily import it to a data library.
M.
On Fri, Jun 26, 2015 at 1:23 PM Ryan G wrote:
> What is HDA?
>
> Sent from my iPhone
>
> On Jun 26, 2015, at 1:10 PM, Martin Čech wrote:
>
> Hello Ryan,
>
> for inte
What is HDA?
Sent from my iPhone
> On Jun 26, 2015, at 1:10 PM, Martin Čech wrote:
>
> Hello Ryan,
>
> for interacting with libraries through the Bioblend:
> http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.libraries
>
> for loading data to libraries f
Hello Ryan,
for interacting with libraries through the Bioblend:
http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.libraries
for loading data to libraries form the Galaxy's system (e.g. after FTP
upload, or when admin):
https://github.com/galaxyproject/gala
By browsing the api code, I discovered library_contents.py that looks like
it should be used. Why this and not folder_contents.py? There seems to be
overlap of these two. I would expect to upload files to folders within
libraries...
On Thu, Jun 25, 2015 at 2:43 PM, Ryan G wrote:
> Hi all - I
I have the same problem with CAS under REMOTE_USER, it's pretty annoying.
If you're just using LDAP authentication, you can switch over to the
recently added built-in LDAP authentication, and this problem should go
away for you
Ciao,
Eric
2015-06-26 9:24 GMT-05:00 Erwan DELAGE :
> Dear all,
>
>
Dear all,
We have a galaxy instance that uses LDAP for authentication and it works fine.
The only problem is that a new history is created each time a user log in.
When we disable LDAP to use the classical authentication method, the problem
goes away.
Any idea of what could happen here ?
Tha
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