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/shared/
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/shared/
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/shared/
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-data/
>>>>>>>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-data/
>>>>>>>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-data/
>>>>>>>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-data/
>>>>>>>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-data/
>>>>>>>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-data/
>>>>>>>sh
>>>>>>> ar
>>>>>>> ed/ncbi/builds.txt'
>>>>>> 
>>>>>> Stderr
>>>>>>> COMMAND FAILURE:
>>>>>>> 
>>>>>>> 
>>>>>>>/mnt/galaxyTools/shed_tools/toolshed.g2.bx.psu.edu/repos/msjeon/abys
>>>>>>>s_
>>>>>>> to
>>>>>>> 
>>>>>>> 
>>>>>>>ol/ce99b6666d1f/abyss_tool/abyss_toolsuite-92636934a189/abyss/abyss_
>>>>>>>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/
>>>>> 
>>>> 
>>> 
>> 
>


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