Re: [galaxy-dev] /bin/sh: samtools: not found--WORKAROUND

2012-04-30 Thread Nate Coraor
On Apr 24, 2012, at 8:36 PM, Michael Moore wrote: There is apparently a persistent problem with samtools which normally lives at /usr/bin/samtools. I encountered a similar problem in Python when uploading BAM files. I did not resolve the problem. I hacked for a while on binary.py in a

Re: [galaxy-dev] /bin/sh: samtools: not found--WORKAROUND

2012-04-30 Thread Michael Moore
Yeah, I was using ['printenv| mail myaddress samtools'] inside the subprocess.Popen(['samtools'],... in upload.py. Now right before in upload.py before the subprocess was called, I had /usr/bin/ in my PATH, but inside the subprocess the story was different. I just used the symbolic link to

Re: [galaxy-dev] /bin/sh: samtools: not found--WORKAROUND

2012-04-24 Thread Michael Moore
There is apparently a persistent problem with samtools which normally lives at /usr/bin/samtools. I encountered a similar problem in Python when uploading BAM files. I did not resolve the problem. I hacked for a while on binary.py in a lib/ subdirectory and used os.system to send myself mail