Re: [galaxy-dev] python subprocess OSError when running bwa-mem

2017-05-24 Thread Hans-Rudolf Hotz
Hi run.sh On 05/24/2017 10:51 AM, Georgios Nikolis wrote: Hi Hans-Rudolf, many thanks for pointing me to the right direction. samtools was installed, it was indeed a problem with $PATH. There are actually path setting scripts provides with the tools, also for samtools, e.g. database/dependencie

Re: [galaxy-dev] python subprocess OSError when running bwa-mem

2017-05-24 Thread Georgios Nikolis
Hi Hans-Rudolf, many thanks for pointing me to the right direction. samtools was installed, it was indeed a problem with $PATH. There are actually path setting scripts provides with the tools, also for samtools, e.g. database/dependencies/samtools/0.1.19/devteam/package_

Re: [galaxy-dev] python subprocess OSError when running bwa-mem

2017-05-21 Thread Hans-Rudolf Hotz
Hi Georgios I am just guessing here, but the error looks familiar: Do you have samtools installed? and is it in $PATH? (for a similar case, see: https://biostar.usegalaxy.org/p/19938/ ) Regards, Hans-Rudolf On 05/19/2017 10:03 AM, Georgios Nikolis wrote: Dear all, we are currently working o