Errors are being output to stdout

The files don't exist and complicated by the /../../ where I don't know
which subdirectory to follow. Attached screen shot of job failing giving
the ERROR message in the web gui. I also get the same errors when
attempting to run Abys which doesn't run because it isn't installed.

galaxy@ip-10-110-143-10:/mnt/galaxyTools/galaxy-central/lib/galaxy/util$
find -name publicbuilds.txt
galaxy@ip-10-110-143-10:/mnt/galaxyTools/galaxy-central/lib/galaxy/util$ ls
aliaspickler.py   debugging.py           hash_util.py    __init__.py
lrucache.pyc   odict.pyc          streamball.py   topsort.pyc
aliaspickler.pyc  docutils_ext           hash_util.pyc   __init__.pyc
memdump.py     sanitize_html.py   streamball.pyc
backports         docutils_template.txt  heartbeat.py    json.py
none_like.py   sanitize_html.pyc  template.py
bunch.py          expressions.py         inflection.py   json.pyc
none_like.pyc  shed_util.py       template.pyc
bunch.pyc         expressions.pyc        inflection.pyc  lrucache.py
odict.py       shed_util.pyc      topsort.py






On 11/8/12 1:34 PM, "Dannon Baker" <dannonba...@me.com> wrote:

>Glad to help.  The first step would be to check and see if those files
>actually exist (and they should).
>
>If those messages are occurring on stdout and not stderr though, they
>shouldn't be causing failed jobs and something else might be wrong.
>
>-Dannon
>
>
>On Nov 8, 2012, at 1:27 PM, Scooter Willis <hwil...@scripps.edu> wrote:
>
>> Thanks! That was the explanation I was looking for and the link for how
>>to
>> 
>> Do you have any suggestions for fixing the error that are still
>>occurring
>> after running Bowtie?
>> 
>> 
>> Sequence file aligned.
>> ERROR: Unable to read builds file: [Errno 2] No such file or directory:
>> 
>>'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-data/share
>>d/
>> ucsc/publicbuilds.txt'
>> ERROR: Unable to read builds file: [Errno 2] No such file or directory:
>> 
>>'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-data/share
>>d/
>> ensembl/builds.txt'
>> ERROR: Unable to read builds file: [Errno 2] No such file or directory:
>> 
>>'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-data/share
>>d/
>> ncbi/builds.txt'
>> 
>> 
>> 
>> On 11/8/12 12:44 PM, "Dannon Baker" <dannonba...@me.com> wrote:
>> 
>>> You do not need to restart or add/remove worker nodes, the master's
>>>tool
>>> and data volumes are shared via NFS.
>>> 
>>> The easiest way to make this work for you in the cloud is probably
>>>going
>>> to be installing the version of the Abyss binaries you'd like to use
>>> manually in /mnt/galaxyTools/abyss/<version>/ using galaxy's dependency
>>> management 
>>> (http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies) and
>>> then, after it has been installed, modify the abyss wrapper to include
>>>a
>>> <requirement type="package">abyss</requirement> tag, and finally
>>>persist
>>> changes to galaxyTools (which will also restart Galaxy, reloading the
>>> tools).
>>> 
>>> -Dannon
>>> 
>>> 
>>> On Nov 8, 2012, at 12:09 PM, Scooter Willis <hwil...@scripps.edu>
>>>wrote:
>>> 
>>>> Dannon
>>>> 
>>>> If I install abyss to the galaxy tools volume and use cloud admin to
>>>>do
>>>> a
>>>> snapshot I assume I then need to remove and then add compute nodes?
>>>>From
>>>> the EC2 management console I see two 15GiB EBS volumes from the same
>>>> snapshot and I have a master and one compute node running. The other
>>>> approach is that the compute nodes have a NFS mount back into the
>>>> galaxy_tools volume. Trying to make sure I understand the need to
>>>> restart
>>>> the compute nodes after an install of third party tools.
>>>> 
>>>> From looking at the abyss wrapper it is expecting ABYSS to be found on
>>>> the
>>>> path via a .sh file that gets called. Where would I update the path
>>>>to a
>>>> particular installed tool such that it will be picked up for each
>>>> compute
>>>> node that gets started? I couldn't find any examples of doing a third
>>>> party install with discussion about how that install would persist to
>>>> future compute nodes. The missing element for me at the moment is
>>>>where
>>>> to
>>>> make path related changes that will be picked up by compute nodes. I
>>>> could
>>>> hard code the path in the .sh file used by the wrapper. Just trying to
>>>> figure out how to use the software as designed.
>>>> 
>>>> Thanks
>>>> 
>>>> Scooter
>>>> 
>>>> 
>>>> On 11/8/12 11:49 AM, "Dannon Baker" <dannonba...@me.com> wrote:
>>>> 
>>>>> Neither abyss wrapper in the toolshed installs binaries (you'd see a
>>>>> tool_dependencies.xml in the repository), that's left up to the end
>>>>> user.
>>>>> You might contact the authors of the wrappers via the toolshed to see
>>>>> if
>>>>> they were going to add dependency management and had a newer version,
>>>>> but
>>>>> otherwise you'll have to install binaries on your own.  The cloud
>>>>> volumes
>>>>> do have a version of the Abyss binaries preinstalled, but it's
>>>>> certainly
>>>>> possible to add a newer version to your particular instance and
>>>>>persist
>>>>> the changes to the tool volume (see the cloud admin panel).
>>>>> 
>>>>> 
>>>>> On Nov 8, 2012, at 11:20 AM, Scooter Willis <hwil...@scripps.edu>
>>>>> wrote:
>>>>> 
>>>>>> Ok that fixed Bowtie.
>>>>>> 
>>>>>> Any thoughts on expected state of installing Abyss from toolshed. It
>>>>>> indicates no requirements so my expectation is that installing from
>>>>>> toolshed should install the appropriate abyss package in a location
>>>>>> the
>>>>>> tool is expecting to find it.
>>>>>> 
>>>>>> In looking at the toolshed looks like two wrappers have been
>>>>>> configured.
>>>>>> One by msjeon and the other edward-kirton. I did the install for
>>>>>> msjeon.
>>>>>> Will try the other.
>>>>>> 
>>>>>> Is the abyss install located at
>>>>>>/mnt/galaxyTools/tools/abyss/1.2.5/bin
>>>>>> from prior testing and should be deleted. Current release version of
>>>>>> abyss
>>>>>> as of May 30 2012 is Abyss 1.3.4
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On 11/8/12 11:00 AM, "Dannon Baker" <dannonba...@me.com> wrote:
>>>>>> 
>>>>>>> Unfortunately the cloud instance upgrade path requires some manual
>>>>>>> intervention here due to tool migrations.  SSH in to your instance,
>>>>>>> edit
>>>>>>> /mnt/galaxyTools/galaxy-central/datatypes_conf.xml removing any
>>>>>>> references to BlastXML.  Save the file, restart galaxy, and you
>>>>>>> should
>>>>>>> be
>>>>>>> good to go.
>>>>>>> 
>>>>>>> -Dannon
>>>>>>> 
>>>>>>> On Nov 8, 2012, at 10:40 AM, Scooter Willis <hwil...@scripps.edu>
>>>>>>> wrote:
>>>>>>> 
>>>>>>>> Running a CloudMan created instance on Amazon.
>>>>>>>> 
>>>>>>>> Updated using cloudman from
>>>>>>>> http://bitbucket.org/galaxy/galaxy-central
>>>>>>>> to version 8167:b0c916349070
>>>>>>>> 
>>>>>>>> Tried to run bowtie and get the following error. Searched the
>>>>>>>> message
>>>>>>>> archives an someone else reported the same problem but thought it
>>>>>>>> was
>>>>>>>> related to a new version of cufflinks. Same problem also exists
>>>>>>>>when
>>>>>>>> running abyss. Given the nature of the error message not even sure
>>>>>>>> what
>>>>>>>> the actual path should be. Also for the abyss install from
>>>>>>>>toolshed
>>>>>>>> the
>>>>>>>> toolshed.g2.bx.psu.edu directory doesn't exist or the six
>>>>>>>> directories
>>>>>>>> underneath. However Abyss was/is installed at the following
>>>>>>>>location
>>>>>>>>> galaxy@ip-10-110-143-10:/mnt/galaxyTools/tools/abyss/1.2.5/bin$
>>>>>>>>>ls
>>>>>>>>> ABYSS      abyss-adjtodot  abyss-joindist  abyss-tofastq
>>>>>>>>> DistanceEst
>>>>>>>>> MergePaths   PathConsensus  SimpleGraph
>>>>>>>>> abyss2ace  abyss-fac       ABYSS-P         AdjList
>>>>>>>>>KAligner
>>>>>>>>> Overlap      PathOverlap
>>>>>>>>> abyss2afg  abyss-fixmate   abyss-pe        Consensus
>>>>>>>>> MergeContigs
>>>>>>>>> ParseAligns  PopBubbles
>>>>>>>> 
>>>>>>>> Would be great if someone could give some guidance on how to
>>>>>>>>resolve
>>>>>>>> the problems. I understand if I need to do something under the
>>>>>>>> covers
>>>>>>>> but the expectation is that the one click install/updates should
>>>>>>>>not
>>>>>>>> then require major command line work that isn't documented.
>>>>>>>> 
>>>>>>>> Thanks
>>>>>>>> 
>>>>>>>> Scooter
>>>>>>>> 
>>>>>>>> 
>>>>>>>> Bowtie
>>>>>>>> 
>>>>>>>> Stdout
>>>>>>>> 
>>>>>>>>> Sequence file aligned.
>>>>>>>>> ERROR: Unable to read builds file: [Errno 2] No such file or
>>>>>>>>> directory:
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>>'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-dat
>>>>>>>>>a/
>>>>>>>>> sh
>>>>>>>>> ar
>>>>>>>>> ed/ucsc/publicbuilds.txt'
>>>>>>>>> ERROR: Unable to read builds file: [Errno 2] No such file or
>>>>>>>>> directory:
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>>'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-dat
>>>>>>>>>a/
>>>>>>>>> sh
>>>>>>>>> ar
>>>>>>>>> ed/ensembl/builds.txt'
>>>>>>>>> ERROR: Unable to read builds file: [Errno 2] No such file or
>>>>>>>>> directory:
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>>'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-dat
>>>>>>>>>a/
>>>>>>>>> sh
>>>>>>>>> ar
>>>>>>>>> ed/ncbi/builds.txt'
>>>>>>>> 
>>>>>>>> Stderr
>>>>>>>>> WARNING:galaxy.datatypes.registry:Error loading datatype with
>>>>>>>>> extension 'blastxml': 'module' object has no attribute 'BlastXml'
>>>>>>>>> WARNING:galaxy.datatypes.registry:Error appending sniffer for
>>>>>>>>> datatype
>>>>>>>>> 'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object
>>>>>>>>>has
>>>>>>>>> no
>>>>>>>>> attribute 'BlastXml'
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> Using toolshed installed Abyss and get the same error in Stdout.
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> Stdout
>>>>>>>> 
>>>>>>>>> ERROR: Unable to read builds file: [Errno 2] No such file or
>>>>>>>>> directory:
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>>'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-dat
>>>>>>>>>a/
>>>>>>>>> sh
>>>>>>>>> ar
>>>>>>>>> ed/ucsc/publicbuilds.txt'
>>>>>>>>> ERROR: Unable to read builds file: [Errno 2] No such file or
>>>>>>>>> directory:
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>>'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-dat
>>>>>>>>>a/
>>>>>>>>> sh
>>>>>>>>> ar
>>>>>>>>> ed/ensembl/builds.txt'
>>>>>>>>> ERROR: Unable to read builds file: [Errno 2] No such file or
>>>>>>>>> directory:
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>>'/mnt/galaxyTools/galaxy-central/lib/galaxy/util/../../../tool-dat
>>>>>>>>>a/
>>>>>>>>> sh
>>>>>>>>> ar
>>>>>>>>> ed/ncbi/builds.txt'
>>>>>>>> 
>>>>>>>> Stderr
>>>>>>>>> COMMAND FAILURE:
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>>/mnt/galaxyTools/shed_tools/toolshed.g2.bx.psu.edu/repos/msjeon/ab
>>>>>>>>>ys
>>>>>>>>> s_
>>>>>>>>> to
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>>ol/ce99b6666d1f/abyss_tool/abyss_toolsuite-92636934a189/abyss/abys
>>>>>>>>>s_
>>>>>>>>> wr
>>>>>>>>> ap
>>>>>>>>> per.sh: line 9: ABYSS: command not found
>>>>>>>>> WARNING:galaxy.datatypes.registry:Error loading datatype with
>>>>>>>>> extension 'blastxml': 'module' object has no attribute 'BlastXml'
>>>>>>>>> WARNING:galaxy.datatypes.registry:Error appending sniffer for
>>>>>>>>> datatype
>>>>>>>>> 'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object
>>>>>>>>>has
>>>>>>>>> no
>>>>>>>>> attribute 'BlastXml'
>>>>>>>> 
>>>>>>>> Looking at the util directory based on the expected path of the
>>>>>>>>read
>>>>>>>> build file
>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>>galaxy@ip-10-110-143-10:/mnt/galaxyTools/galaxy-central/lib/galaxy
>>>>>>>>>/u
>>>>>>>>> ti
>>>>>>>>> l$
>>>>>>>>> ls
>>>>>>>>> aliaspickler.py   docutils_ext           heartbeat.py    json.pyc
>>>>>>>>> odict.py           streamball.py
>>>>>>>>> aliaspickler.pyc  docutils_template.txt  inflection.py
>>>>>>>>> lrucache.py
>>>>>>>>> odict.pyc          streamball.pyc
>>>>>>>>> backports         expressions.py         inflection.pyc
>>>>>>>>> lrucache.pyc
>>>>>>>>> sanitize_html.py   template.py
>>>>>>>>> bunch.py          expressions.pyc        __init__.py
>>>>>>>>>memdump.py
>>>>>>>>> sanitize_html.pyc  template.pyc
>>>>>>>>> bunch.pyc         hash_util.py           __init__.pyc
>>>>>>>>> none_like.py
>>>>>>>>> shed_util.py       topsort.py
>>>>>>>>> debugging.py      hash_util.pyc          json.py
>>>>>>>>> none_like.pyc
>>>>>>>>> shed_util.pyc      topsort.pyc
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> ___________________________________________________________
>>>>>>>> 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/
>>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>> 
>> 
>

<<attachment: default.png>>

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