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/shar
>>>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/shar
>>>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/shar
>>>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/shar
>>>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/shar
>>>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/shar
>>>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_wrap
>>>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/util$
>>> 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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