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 <HWillis@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" <dannonbaker@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 <HWillis@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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