Hi Geert,
I only saw your reply just now when I checked the archive. I
can confirm that I arrived at the same solution myself via
http://stackoverflow.com/questions/3287038/cron-and-virtualenv but Thankyou
for posting your reply. stackoverflow is a great resource as well as this
one.
M
Hi,
I installed bowtie2 from the toolshed, but get the following error when I
run it:
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py",
line 129, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/home/galaxy/galaxy-dist/l
Hi Anna,
Setting your own path variables shouldn't be necessary for toolshed tools,
so probably something is wrong with the installation. could you post your
tooldependencies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/INSTALLATION.log
file?
On 26 November 2014 at 13:49, Anna Terry
Hi Anna,
you need to install samtools into your system or via the toolshed. If
you install it via the toolshed you need to create a symlink.
Lets assume you have samtools installed in:
~/tool_deps/samtools/0.19/iuc/2828727744/
than you need to create a symlink from
~/tool_deps/samtools/0.19/iuc
Hey Ryan,
Sorry this took a long while for me to get back to, again. I probably
should have pointed you here to start with, but bioblend (a nice python
layer on top of the raw galaxy API) has a much friendlier interface and is
what you'd probably want to use for this kind of script. Here's an e
Are you sure you need to build your own eggs? Outside a few
cluster-specific eggs, this is rarely the case (and not for bx-python, to
my knowledge).
The first thing I'd check is whether or not removing the eggs directory (to
force a clean start from whatever egg situation you have now) from Galax
So I actually still have a problem,
(I guess the setting was still there somewhere from the bash_profile)
Anyway, I am also getting the problem with samtools filter sam or bam
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py",
line 129, in queue
What is really weird is when running the bowtie2 tool, before it quits, I
can see samtools come up in top
On 26 November 2014 at 15:55, Anna Terry wrote:
> So I actually still have a problem,
> (I guess the setting was still there somewhere from the bash_profile)
>
> Anyway, I am also getting th
Could you try going to Admin -> Manage Installed tool shed repositories
uninstall -> reinstall package_samtools_0_1_18
On 26 November 2014 at 16:55, Anna Terry wrote:
> yway, I am also getting the problem with samtools filter sam or bam
--
Central Veterinary Institute of Wageningen UR
I just tried still the same problem.
I ran bowtie2 to test, again I saw samtools come up on top, but same error:
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py",
line 129, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File
The problem is that bowtie and Galaxy (can) use a different samtools
version. Galaxy needs samtools to create metadata for BAM files, so this
process is actually running ofter bowtie has finished.
You need a samtools version globally accessible for Galaxy. Make sure you
have smatools in your $PATH
is bash_profile the best place for this, or is somewhere else better?
Cheers
Anna
On 26 November 2014 at 16:29, bjoern.gruen...@googlemail.com <
bjoern.gruen...@gmail.com> wrote:
> The problem is that bowtie and Galaxy (can) use a different samtools
> version. Galaxy needs samtools to create met
I would use .bashrc. You can also try to symlib the default dir to the
actual /bin directory. Maybe this works for you.
2014-11-26 17:36 GMT+01:00 Anna Terry :
> is bash_profile the best place for this, or is somewhere else better?
>
> Cheers
> Anna
>
> On 26 November 2014 at 16:29, bjoern.gruen.
great, thanks
On 26 November 2014 at 16:39, bjoern.gruen...@googlemail.com <
bjoern.gruen...@gmail.com> wrote:
> I would use .bashrc. You can also try to symlib the default dir to the
> actual /bin directory. Maybe this works for you.
>
> 2014-11-26 17:36 GMT+01:00 Anna Terry :
>
>> is bash_profi
I tested all versions of setuptools available in PyPI from 0.6c11 up
to 7.0. I found that galaxy fails to fetch eggs with the following
error when setuptools > 6.0.2 (i.e., 6.1 and 7.0).
#
* Creating directory in /mnt for galaxy data
Good sleuthing Evan :)
That explains this strange error I was getting:
http://dev.list.galaxyproject.org/MarkupSafe-egg-missing-e-args-1-key-e-args-0-key-tc4666021.html
(In that case I switched to using a virtualenv)
Peter
On Wed, Nov 26, 2014 at 6:11 PM, Evan Bollig PhD wrote:
> I tested all
Hi,
I will integrate Galaxy with another system. When I logged into this system,
and clicked a link jump to Galaxy, I hope this user has already logged into
Galaxy. How to use api to deliver a session or somthing else to Galaxy?
Now, I can use api to create a new user in this system and also i
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