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 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.
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
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
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
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
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
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
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
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,
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
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