Hi Bjorn and Hans,

We are running Galaxy on our local webserver, so there is no job
scheduler.  Instead, we are using the localJobRunner configuration in the
job_conf.xml

<?xml version="1.0"?>
<job_conf>
    <plugins>
        <plugin id="local" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="8"/>
        <plugin id="multilocal" type="runner"
load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
    </plugins>
    <destinations default="local">
        <destination id="local" runner="local"/>
        <destination id="multicore6" runner="multilocal">
          <param id="local_slots">6</param>
        </destination>
    </destinations>
    <tools>
    <tool id="bowtie2" destination="multicore6" />
    <tool id="spades"  destination="multicore6" />
    <tool id="bbmap_1"  destination="multicore6" />
    <tool id="iuc_pear"  destination="multicore6" />
    <tool id="abyss-pe"  destination="multicore6" />
    <tool id="fastq_groomer_parallel"  destination="multicore6" />
    </tools>

    <handlers>
        <handler id="main"/>
    </handlers>
</job_conf>

Also, normally, we run galaxy in the daemon mode, but recently to help
debug this issue, we have been running galaxy in interactive mode in a
screen session.

@Hans - The processes run under the galaxy user and everything seems to run
fine.  I am trying to get a concrete example, but run.sh usually crashes
during our trimming/assembly steps for NGS data.  Sometimes these workflows
run to completion, but sometimes they crash the run.sh process.  When
run.sh crashes, the individual running programs keep running as the galaxy
user.  We cannot restart galaxy until we manually kill those running
processes.  Here are what the running processes look like on the system.

galaxy         21162  99.4  0.0  2432784    616 s014  R     2:08PM
1425:10.57 seqtk seq -q 0 -X 255 -l 0 -Q 33 -s 11 -f 1.0 -L 0 -1
/Users/galaxy/data_galaxy/test_BACs/all-merged.interleaved.fq
galaxy         21159  99.4  0.0  2432784    616 s014  R     2:08PM
1425:16.72 seqtk seq -q 0 -X 255 -l 0 -Q 33 -s 11 -f 1.0 -L 0 -2
/Users/galaxy/data_galaxy/test_BACs/all-merged.interleaved.fq
galaxy         21118  92.5  0.5  3015188 367852 s014  R+    2:07PM
791:21.54 python ./scripts/paster.py serve universe_wsgi.ini
galaxy         21160   0.0  0.0  2433640   1044 s014  S     2:08PM
0:00.01 /bin/sh
/Users/galaxy/galaxy-dist/database/job_working_directory/002/2180/galaxy_2180.sh
galaxy         21157   0.0  0.0  2433640   1044 s014  S     2:08PM
0:00.01 /bin/sh
/Users/galaxy/galaxy-dist/database/job_working_directory/002/2179/galaxy_2179.sh
galaxy         21113   0.0  0.0  2433640   1000 s014  S+    2:07PM
0:00.00 sh run.sh


Thank you for the help,
-Hans
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