Running a CloudMan created instance on Amazon.
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