On Apr 29, 2012, at 9:19 PM, Ciara Ledero wrote: > This is my code for running a samtools command internally, via Galaxy: > > > open INP,"< $ARGV[0]" > or die "Cannot open file: $!"; > > $file = "$ARGV[1]"; > > open OUT, "> $file" > or die "Cannot open file: $!"; > > @out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[0] 2>&1`; > > print OUT @out; > > close INP; > close OUT; > > The 2>&1 is used to redirect the STDERR to STDOUT. When I run this in the > console, it gives a non-empty file. But when run it in Galaxy, Galaxy can no > longer find the path. This error message is given to me. > > Traceback (most recent call last): > File "/home/applications/galaxy-dist/lib/galaxy/jobs/runners/local.py", line > 126, in run_job > job_wrapper.finish( stdout, stderr ) > File "/home/applications/galaxy-dist/lib/galaxy/jobs/__init__.py", line 618, > in finish > dataset.set_meta( overwrite = False ) > File "/home/applications/galaxy-dist/lib/galaxy/model/__init__.py", line > 874, in set_meta > return self.datatype.set_meta( self, **kwd ) > File "/home/applications/galaxy-dist/lib/galaxy/datatypes/binary.py", line > 179, in set_meta > raise Exception, "Error Setting BAM Metadata: %s" % stderr > Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found > > The weird thing is, when I remove the 2>&1 from the code and run it again in > Galaxy, I am able to get this diagnostic message: > > [samopen] SAM header is present: 66338 sequences. > > This is the reason why I added the 2>&1 in the first place, so that this > diagnostic message would be 'ignored' (since it is detected as an error). > > Now, if the other code (the one without 2>&1) is able to produce the > aforementioned diagnostic message, then I assume that it is able to at least > execute the samtools command internally. But when I add the 2>&1, galaxy can > no longer find the command. Do I need to specify a path somewhere in the > galaxy-dist?
Hi Ciara, This is most likely not the job, but Galaxy's metadata step, which uses samtools to create a BAM index (.bai) file. If you put /home/applications/samtools-0.1.7a on your $PATH before you start Galaxy, that should solve this problem. --nate > > I apologize for the very long message. > > Thanks in advance, > > CL > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
