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/abyss_
>>>>>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/uti
>>>>>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
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> ___________________________________________________________
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>>>> http://lists.bx.psu.edu/
>>> 
>> 
>


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