Re: [galaxy-dev] How to get cleanup script to run in cron job ?

2014-11-26 Thread James Mullan
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.

[galaxy-dev] samtools: command not found in bowtie2

2014-11-26 Thread 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

Re: [galaxy-dev] samtools: command not found in bowtie2

2014-11-26 Thread Eric Kuyt
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

Re: [galaxy-dev] Egg build failed for bx_python 0.7.2

2014-11-26 Thread Dannon Baker
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

Re: [galaxy-dev] samtools: command not found in bowtie2

2014-11-26 Thread Anna Terry
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 iseegl...@googlemail.com wrote: So I actually still have a problem, (I guess the setting was still there somewhere from the bash_profile) Anyway,

Re: [galaxy-dev] samtools: command not found in bowtie2

2014-11-26 Thread Eric Kuyt
​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 iseegl...@googlemail.com wrote: yway, I am also getting the problem with samtools filter sam or bam -- Central Veterinary

Re: [galaxy-dev] samtools: command not found in bowtie2

2014-11-26 Thread Anna Terry
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

Re: [galaxy-dev] samtools: command not found in bowtie2

2014-11-26 Thread bjoern.gruen...@googlemail.com
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

Re: [galaxy-dev] samtools: command not found in bowtie2

2014-11-26 Thread 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...@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

Re: [galaxy-dev] samtools: command not found in bowtie2

2014-11-26 Thread Anna Terry
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 iseegl...@googlemail.com: