Re: [galaxy-dev] Unable to set BAM Metadata
Thanks for the reply! I'll try that one. I'll come back if the problem still persists. Cheers, 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/
Re: [galaxy-dev] Unable to set BAM Metadata
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] 21`; print OUT @out; close INP; close OUT; The 21 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 21 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 21 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 21) 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 21, 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/
Re: [galaxy-dev] Unable to set BAM Metadata
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] 21`; print OUT @out; close INP; close OUT; The 21 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 21 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 21 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 21) 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 21, 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/
