Probably nothing wrong with the script, but my hunch is that the original $PATH
setting you did for the galaxy user doesn't persist to this script's
environment because it uses a non-login shell. I'm definitely not a CentOS
expert, but there's probably another file used for settings like this in
non-login shells. You could also just set those variables in that
/etc/init.d/galaxy script, I'm betting.
-Dannon
On Feb 5, 2013, at 12:55 PM, Hakeem Almabrazi <halmabr...@idtdna.com> wrote:
> Thank you Dannon for pointing me to the right direction. I have been using a
> script suggested in one of this forum to start it "service galaxy
> start/stop". I never thought that would be a source of issue since it is
> calling "run.sh" script anyway. However, I just tried "sh run.sh" and I did
> not see this issue at all.
>
> Here is part of the /etc/init.d/galaxy script I am using to start and stop
> the server
>
> .........
> #!/bin/bash
>
> SERVICE_NAME=galaxy
> RUN_AS=galaxy
> RUN_IN=/usr/local/galaxy/galaxy-dist
>
> #--- main actions
>
> start() {
> echo "Starting $SERVICE_NAME... "
> cmd="cd $RUN_IN && sh run.sh --daemon"
> case "$(id -un)" in
> $RUN_AS)
> eval "$cmd"
> ;;
> root)
> su - $RUN_AS -c "$cmd"
> ;;
> *)
> echo "*** ERROR *** must be $RUN_AS or root in order
> to control this service" >&2
> exit 1
> esac
> echo "...done."
> }
>
> ...................
>
> So what does that mean? Is there something wrong with this script?
>
> Thank you...
>
>
> -----Original Message-----
> From: Dannon Baker [mailto:dannonba...@me.com]
> Sent: Tuesday, February 05, 2013 11:37 AM
> To: Hakeem Almabrazi
> Cc: Galaxy Dev
> Subject: Re: [galaxy-dev] Error! Sam-to-bam samtools command not found
>
> Hakeem,
>
> What's going on here is that the BAM metadata setting function doesn't use
> the normal dependency methods and thus doesn't read 'env.sh' (which does look
> correct), requiring 'samtools' to be available on the path of the galaxy
> user. How are you executing galaxy itself? Are you positive that at launch,
> samtools is in the PATH? One simple way to inject this basic dependency
> would be to add it to the PATH in run.sh itself, as galaxy loads.
>
> -Dannon
>
>
>
>
> On Feb 5, 2013, at 12:17 PM, Hakeem Almabrazi <halmabr...@idtdna.com> wrote:
>
>> Hi,
>>
>> I installed a local galaxy on Centos 6 and I followed the instructions on
>> how to install samtools/bwa/bowtie found
>> herehttp://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup.
>>
>> I setup the correct env. for these programs correctly. Since I have no
>> issues with the bwa and bowtie so I assumed I got everything correctly but
>> that was not true since I keep getting the following error when I try
>> Sam-To-Bam...
>> .............
>> galaxy.jobs.runners.local DEBUG 2013-02-05 10:37:36,053 execution of
>> external set_meta for job 62 finished
>> galaxy.jobs DEBUG 2013-02-05 10:37:36,070 Tool did not define exit code or
>> stdio handling; checking stderr for success
>> galaxy.datatypes.metadata DEBUG 2013-02-05 10:37:36,101 setting metadata
>> externally failed for HistoryDatasetAssociation 76: Error Setting BAM
>> Metadata: /bin/sh: samtools: command not found
>> galaxy.jobs.runners.local ERROR 2013-02-05 10:37:36,134 Job wrapper finish
>> method failed
>> Traceback (most recent call last):
>> File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line
>> 156, in run_job
>> job_wrapper.finish( stdout, stderr, exit_code )
>> File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 412,
>> in finish
>> dataset.datatype.set_meta( dataset, overwrite = False ) #call
>> datatype.set_meta directly for the initial set_meta call during dataset
>> creation
>> File "/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line
>> 213, in set_meta
>> raise Exception, "Error Setting BAM Metadata: %s" % stderr
>> Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
>> galaxy.datatypes.metadata DEBUG 2013-02-05 10:37:36,239 Cleaning up external
>> metadata files
>> ............
>>
>> * Samtools is in the path: >echo $PATH
>> /usr/local/galaxy/galaxy_env/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/java/latest/bin:/usr/local/scripts:/usr/local/galaxy/software/samtools/0.1.16/bin/:/usr/local/galaxy/software/bwa/0.2.6/bin/:/usr/local/galaxy/software/bowtie/0.12.7/bin/:/usr/local/galaxy/software/fastx/0.0.13/bin/:/usr/local/galaxy/software/ncbi-blast/2.2.27/bin/:/usr/local/galaxy/software/lastz-distrib/1.02.00/bin/
>>
>> * I setup the env.sh as recommended. >more
>> //usr/local/galaxy/software/samtools/0.1.16/env.sh
>> #Configure PATH to Samtools binaries
>> PATH="/usr/local/galaxy/software/samtools/0.1.16/bin/:$PATH"
>> export PATH
>>
>> * And here what I have in the bin:> ls -lh
>> /usr/local/galaxy/software/samtools/0.1.16/bin/
>> total 1.5M
>> -rwxr-xr-x 1 galaxy galaxy 2.4K Jan 29 12:53 blast2sam.pl
>> -rwxr-xr-x 1 galaxy galaxy 2.1K Jan 29 12:53 bowtie2sam.pl
>> -rwxr-xr-x 1 galaxy galaxy 19K Jan 29 12:53 export2sam.pl
>> -rwxr-xr-x 1 galaxy galaxy 4.9K Jan 29 12:53 interpolate_sam.pl
>> -rwxr-xr-x 1 galaxy galaxy 5.9K Jan 29 12:53 novo2sam.pl
>> -rwxr-xr-x 1 galaxy galaxy 2.0K Jan 29 12:53 psl2sam.pl
>> -rwxr-xr-x 1 galaxy galaxy 7.7K Jan 29 12:53 sam2vcf.pl
>> -rwxrwxr-x 1 galaxy galaxy 1.4M Jan 29 12:53 samtools
>> -rwxr-xr-x 1 galaxy galaxy 14K Jan 29 12:53 samtools.pl
>> -rwxr-xr-x 1 galaxy galaxy 2.7K Jan 29 12:53 soap2sam.pl
>> -rwxr-xr-x 1 galaxy galaxy 2.7K Jan 29 12:53 wgsim_eval.pl
>> -rwxr-xr-x 1 galaxy galaxy 2.4K Jan 29 12:53 zoom2sam.pl
>>
>> * I could ran the samtools from anywhere in the system including
>> from "galaxy" account.
>>
>> * I looked at this thread which the guy has similar problem but he
>> was trying to set it up in a cluster and installing it on Ubunto. I read
>> the whole thing and tried everything in there but no luck....
>> http://gmod.827538.n3.nabble.com/Exception-Error-Setting-BAM-Metadata-bin-sh-samtools-not-found-td3915349.html
>>
>> * I have installed R and Python/rpy and set their env. as required
>> (I THINK) assuming this might be a cause but I do not see anything in the
>> error log that will indicate that...
>>
>> Can anyone help in debugging this issue please?
>>
>> Thanks
>>
>> hakeem
>>
>>
>>
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