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/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'

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/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'

Stderr
COMMAND FAILURE: 
/mnt/galaxyTools/shed_tools/toolshed.g2.bx.psu.edu/repos/msjeon/abyss_tool/ce99b6666d1f/abyss_tool/abyss_toolsuite-92636934a189/abyss/abyss_wrapper.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










___________________________________________________________
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/

Reply via email to