Error in app-deploy-qiime-1.5.0
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Antonio González Peña
May 10, 2012, 3:15:07 PM5/10/12
to Qiime Forum
Dear users,
We notice that we have a small bug in app-deploy-qiime-1.5.0.tgz and
the new installations will not be able to run the scripts provided by
the biom-format package. This is important to be able to convert from
the regular OTU tables to the new biom files and viceversa.
The app-deploy-qiime-1.5.0.tgz has been fixed and posted in the same
location than the previous version. If you ran the installation script
and you want to patch your installation, the easiest thing to do is to
run this command:
echo "export PATH=[your_install_folder]/biom-format-0.9.3-release/scripts/:$PATH"
>> [your_install_folder]/activate.sh
replacing [your_install_folder] with the path of the original
installation. This also resulted in the creation of a new EC2 Amazon
image, the new id is ami-e4bf1b8d, the documentation has been also
updated.
We want to stress that this issue has nothing to do with qiime-1.5.0
and any analysis perform within this release is fine; this change is
only for convenience.
Sorry for any problems generated by this issue.
Happy QIIME-ing.
--
Antonio González Peña
Research Assistant, Knight Lab
University of Colorado at Boulder
https://chem.colorado.edu/knightgroup/
We notice that we have a small bug in app-deploy-qiime-1.5.0.tgz and
the new installations will not be able to run the scripts provided by
the biom-format package. This is important to be able to convert from
the regular OTU tables to the new biom files and viceversa.
The app-deploy-qiime-1.5.0.tgz has been fixed and posted in the same
location than the previous version. If you ran the installation script
and you want to patch your installation, the easiest thing to do is to
run this command:
echo "export PATH=[your_install_folder]/biom-format-0.9.3-release/scripts/:$PATH"
>> [your_install_folder]/activate.sh
replacing [your_install_folder] with the path of the original
installation. This also resulted in the creation of a new EC2 Amazon
image, the new id is ami-e4bf1b8d, the documentation has been also
updated.
We want to stress that this issue has nothing to do with qiime-1.5.0
and any analysis perform within this release is fine; this change is
only for convenience.
Sorry for any problems generated by this issue.
Happy QIIME-ing.
--
Antonio González Peña
Research Assistant, Knight Lab
University of Colorado at Boulder
https://chem.colorado.edu/knightgroup/
Manoj
Jun 11, 2012, 9:44:54 AM6/11/12
to Qiime Forum
Hi,
I am try to install QIIME 1.5 using following commands on RHEL
cluster
wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz
tar zxvf app-deploy-qiime-1.5.0.tgz
cd app-deploy-qiime-1.5.0
/usr/bin/python app-deploy.py $HOME/qiime_software/ -f etc/
qiime_1.5.0_repository.conf --force-remove-failed-dirs
I get error in building the QIIME and many other packages
DEPLOYMENT SUMMARY
Packages deployed successfully:
Packages skipped (assumed successful):
data-lanemask, data-core, clearcut, raxml, cdbtools, rtax,
chimeraslayer, drisee, gg_otus, infernal, vienna, mothur, python,
fasttree, blast, parsinsert, r, muscle, rdpclassifier, uclust, cdhit
Packages failed to deploy:
ampliconnoise, pplacer, tornado, numpy, setuptools, ipython, mpi4py,
pyzmq, SQLAlchemy, MySQL-python, biom-format, pycogent, matplotlib,
sphinx, pynast, pprospector, qiime, cytoscape
Is any one faced similar problem. If yes , please let me know any
solutions.
Manoj
I am try to install QIIME 1.5 using following commands on RHEL
cluster
wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz
tar zxvf app-deploy-qiime-1.5.0.tgz
cd app-deploy-qiime-1.5.0
/usr/bin/python app-deploy.py $HOME/qiime_software/ -f etc/
qiime_1.5.0_repository.conf --force-remove-failed-dirs
I get error in building the QIIME and many other packages
DEPLOYMENT SUMMARY
Packages deployed successfully:
Packages skipped (assumed successful):
data-lanemask, data-core, clearcut, raxml, cdbtools, rtax,
chimeraslayer, drisee, gg_otus, infernal, vienna, mothur, python,
fasttree, blast, parsinsert, r, muscle, rdpclassifier, uclust, cdhit
Packages failed to deploy:
ampliconnoise, pplacer, tornado, numpy, setuptools, ipython, mpi4py,
pyzmq, SQLAlchemy, MySQL-python, biom-format, pycogent, matplotlib,
sphinx, pynast, pprospector, qiime, cytoscape
Is any one faced similar problem. If yes , please let me know any
solutions.
Manoj
Manoj Bhasin
Jun 11, 2012, 11:50:55 AM6/11/12
to Qiime Forum
Hi all ,
I am still facing issues with installation of QIIME 1.5 on RHEL server. I got failure in deploying some packages along with QIIME
2012-06-11 11:40:21,600 - __main__ - INFO - Dependencies look good.
2012-06-11 11:40:21,600 - __main__ - INFO - Starting status thread.
2012-06-11 11:40:21,601 - lib.deploy - INFO - Still deploying applications and data...
2012-06-11 11:40:21,601 - __main__ - INFO - Starting 6 deploy threads.
2012-06-11 11:40:21,604 - __main__ - INFO - Running deploy for data and apps without dependencies.
2012-06-11 11:40:21,604 - __main__ - INFO - Searching for python...
2012-06-11 11:40:21,604 - __main__ - INFO - python-exe is not specified.
2012-06-11 11:40:21,605 - __main__ - INFO - Looks like python is being deployed, using that version
2012-06-11 11:40:21,605 - __main__ - INFO - Setting python: /home/mbhasin/qiime_software/python-2.7.1-release/bin/python
2012-06-11 11:40:23,915 - __main__ - INFO - Launched initial deploy, remaining apps: ['pynast', 'pprospector', 'MySQL-python', 'biom-format', 'qiime', 'pycogent', 'numpy', 'pyzmq', 'SQLAlchemy', 'tornado', 'matplotlib', 'ipython', 'sphinx', 'setuptools', 'mpi4py']
2012-06-11 11:40:23,915 - __main__ - INFO - Deploying remaining apps.
2012-06-11 11:40:23,924 - lib.data - INFO - Deploying data: data-lanemask
2012-06-11 11:40:23,924 - lib.data - INFO - data-lanemask exists, skipping download.
2012-06-11 11:40:23,925 - lib.deploy - INFO - Deploy of data-lanemask skipped.
2012-06-11 11:40:23,925 - lib.data - INFO - Deploying data: data-core
2012-06-11 11:40:23,925 - lib.application - INFO - Deploying app: clearcut
2012-06-11 11:40:23,925 - lib.application - INFO - Deploying app: raxml
2012-06-11 11:40:23,926 - lib.data - INFO - data-core exists, skipping download.
2012-06-11 11:40:23,926 - lib.deploy - INFO - Deploy of data-core skipped.
2012-06-11 11:40:23,926 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/clearcut-1.0.9-release
2012-06-11 11:40:23,926 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/raxml-7.3.0-release
2012-06-11 11:40:23,926 - lib.application - INFO - Deploying app: cdbtools
2012-06-11 11:40:23,926 - lib.application - INFO - Deploying app: ampliconnoise
2012-06-11 11:40:23,927 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,927 - lib.application - INFO - Deploying app: rtax
2012-06-11 11:40:23,927 - lib.application - INFO - Deploying app: cytoscape
2012-06-11 11:40:23,927 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,927 - lib.application - INFO - Making deploy directory: /home/mbhasin/qiime_software/ampliconnoise-1.25-release
2012-06-11 11:40:23,927 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/cdbtools-10.11.2010-release
2012-06-11 11:40:23,928 - lib.deploy - INFO - Deploy of clearcut skipped.
2012-06-11 11:40:23,928 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/rtax-0.981-release
2012-06-11 11:40:23,928 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/cytoscape-2.7.0-release
2012-06-11 11:40:23,929 - lib.deploy - INFO - Deploy of raxml skipped.
2012-06-11 11:40:23,929 - lib.application - INFO - Downloading ampliconnoise
2012-06-11 11:40:23,929 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,929 - lib.application - INFO - Deploying app: chimeraslayer
2012-06-11 11:40:23,929 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,929 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,929 - lib.application - INFO - Deploying app: drisee
2012-06-11 11:40:23,930 - lib.util - INFO - Downloading http://ampliconnoise.googlecode.com/files/AmpliconNoiseV1.25.tar.gz
2012-06-11 11:40:23,930 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/chimeraslayer-4.29.2010-release
2012-06-11 11:40:23,931 - lib.deploy - INFO - Deploy of cdbtools skipped.
2012-06-11 11:40:23,931 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/drisee-1.2-release
2012-06-11 11:40:23,936 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,937 - lib.deploy - INFO - Deploy of cytoscape skipped.
2012-06-11 11:40:23,937 - lib.application - INFO - Deploying app: gg_otus
2012-06-11 11:40:23,937 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,937 - lib.application - INFO - Deploying app: infernal
2012-06-11 11:40:23,938 - lib.deploy - INFO - Deploy of rtax skipped.
2012-06-11 11:40:23,938 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/gg_otus-4feb2011-release
2012-06-11 11:40:23,938 - lib.deploy - INFO - Deploy of chimeraslayer skipped.
2012-06-11 11:40:23,938 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,938 - lib.deploy - INFO - Deploy of drisee skipped.
2012-06-11 11:40:23,939 - lib.application - INFO - Deploying app: vienna
2012-06-11 11:40:23,939 - lib.application - INFO - Deploying app: mothur
2012-06-11 11:40:23,939 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/infernal-1.0.2-release
2012-06-11 11:40:23,939 - lib.deploy - INFO - Deploy of gg_otus skipped.
2012-06-11 11:40:23,939 - lib.application - INFO - Deploying app: python
2012-06-11 11:40:23,940 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/vienna-1.8.4-release
2012-06-11 11:40:23,940 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/mothur-1.25.0-release
2012-06-11 11:40:23,940 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,940 - lib.application - INFO - Deploying app: fasttree
2012-06-11 11:40:23,940 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,940 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,941 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/python-2.7.1-release
2012-06-11 11:40:23,941 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/fasttree-2.1.3-release
2012-06-11 11:40:23,941 - lib.deploy - INFO - Deploy of vienna skipped.
2012-06-11 11:40:23,941 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,942 - lib.deploy - INFO - Deploy of infernal skipped.
2012-06-11 11:40:23,942 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,942 - lib.deploy - INFO - Deploy of mothur skipped.
2012-06-11 11:40:23,942 - lib.application - INFO - Deploying app: pplacer
2012-06-11 11:40:23,942 - lib.application - INFO - Deploying app: blast
2012-06-11 11:40:23,943 - lib.deploy - INFO - Deploy of python skipped.
2012-06-11 11:40:23,943 - lib.application - INFO - Deploying app: parsinsert
2012-06-11 11:40:23,943 - lib.application - INFO - Making deploy directory: /home/mbhasin/qiime_software/pplacer-1.1-release
2012-06-11 11:40:23,943 - lib.deploy - INFO - Deploy of fasttree skipped.
2012-06-11 11:40:23,943 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/blast-2.2.22-release
2012-06-11 11:40:23,943 - lib.application - INFO - Deploying app: r
2012-06-11 11:40:23,944 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/parsinsert-1.0.4-release
2012-06-11 11:40:23,944 - lib.application - INFO - Deploying app: muscle
2012-06-11 11:40:23,944 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,944 - lib.application - INFO - Downloading pplacer
2012-06-11 11:40:23,944 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/r-2.12.0-release
2012-06-11 11:40:23,944 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,945 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/muscle-3.8.31-release
2012-06-11 11:40:23,945 - lib.util - INFO - Downloading http://matsen.fhcrc.org/pplacer/builds/pplacer-v1.1-Linux.tar.gz
2012-06-11 11:40:23,945 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,945 - lib.deploy - INFO - Deploy of blast skipped.
2012-06-11 11:40:23,946 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,946 - lib.application - INFO - Deploying app: rdpclassifier
2012-06-11 11:40:23,946 - lib.deploy - INFO - Deploy of parsinsert skipped.
2012-06-11 11:40:23,947 - lib.deploy - INFO - Deploy of r skipped.
2012-06-11 11:40:23,947 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/rdpclassifier-2.2-release
2012-06-11 11:40:23,947 - lib.application - INFO - Deploying app: cdhit
2012-06-11 11:40:23,947 - lib.deploy - INFO - Deploy of muscle skipped.
2012-06-11 11:40:23,947 - lib.application - INFO - Deploying app: uclust
2012-06-11 11:40:23,947 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,947 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/cdhit-3.1-release
2012-06-11 11:40:23,948 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/uclust-1.2.22-release
2012-06-11 11:40:23,948 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,948 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:23,948 - lib.deploy - INFO - Deploy of rdpclassifier skipped.
2012-06-11 11:40:23,949 - lib.deploy - INFO - Deploy of cdhit skipped.
2012-06-11 11:40:23,949 - lib.deploy - INFO - Deploy of uclust skipped.
2012-06-11 11:40:24,371 - lib.application - INFO - Unzip succeeded: /tmp/tmpSoY1cz/AmpliconNoiseV1.25.tar.gz
2012-06-11 11:40:24,371 - lib.util - INFO - Compiling ampliconnoise
2012-06-11 11:40:25,224 - lib.util - ERROR - Failed to compile ampliconnoise
2012-06-11 11:40:25,231 - lib.deploy - ERROR - Deploy of ampliconnoise failed.
2012-06-11 11:40:28,925 - lib.application - INFO - Deploying app: numpy
2012-06-11 11:40:28,925 - lib.application - INFO - Deploying app: pyzmq
2012-06-11 11:40:28,925 - lib.application - INFO - Making deploy directory: /home/mbhasin/qiime_software/pyzmq-2.1.9-release
2012-06-11 11:40:28,926 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/numpy-1.5.1-release
2012-06-11 11:40:28,926 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:28,926 - lib.application - INFO - Downloading pyzmq
2012-06-11 11:40:28,927 - lib.util - INFO - Downloading http://pypi.python.org/packages/source/p/pyzmq/pyzmq-2.1.9.tar.gz#md5=44efd9e7dd041b9f779e3026d189f870
2012-06-11 11:40:28,929 - lib.application - INFO - Deploying app: SQLAlchemy
2012-06-11 11:40:28,929 - lib.application - INFO - Deploying app: tornado
2012-06-11 11:40:28,929 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/SQLAlchemy-0.7.1-release
2012-06-11 11:40:28,930 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:28,931 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/tornado-2.2.1-release
2012-06-11 11:40:28,931 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:28,956 - lib.application - INFO - Deploying app: ipython
2012-06-11 11:40:28,956 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/ipython-0.12-release
2012-06-11 11:40:28,956 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:28,969 - lib.deploy - INFO - Deploy of numpy skipped.
2012-06-11 11:40:28,969 - lib.application - INFO - Deploying app: setuptools
2012-06-11 11:40:28,969 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/setuptools-0.6c11-release
2012-06-11 11:40:28,969 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:28,970 - lib.deploy - INFO - Deploy of SQLAlchemy skipped.
2012-06-11 11:40:28,971 - lib.application - INFO - Deploying app: mpi4py
2012-06-11 11:40:28,971 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/mpi4py-1.2.2-release
2012-06-11 11:40:28,971 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:28,972 - lib.deploy - INFO - Deploy of tornado skipped.
2012-06-11 11:40:28,998 - lib.deploy - INFO - Deploy of ipython skipped.
2012-06-11 11:40:29,006 - lib.deploy - INFO - Deploy of setuptools skipped.
2012-06-11 11:40:29,015 - lib.deploy - INFO - Deploy of mpi4py skipped.
2012-06-11 11:40:30,813 - lib.application - INFO - Unzip succeeded: /tmp/tmpWd9nI7/pyzmq-2.1.9.tar.gz
2012-06-11 11:40:30,860 - lib.util - INFO - Building pyzmq
2012-06-11 11:40:30,995 - lib.util - ERROR - Failed to build pyzmq
2012-06-11 11:40:30,995 - lib.application - ERROR - Problem building pyzmq.
2012-06-11 11:40:31,002 - lib.deploy - ERROR - Deploy of pyzmq failed.
2012-06-11 11:40:33,550 - lib.application - INFO - Unzip succeeded: /tmp/tmp51d9AZ/pplacer-v1.1-Linux.tar.gz
2012-06-11 11:40:33,551 - lib.application - ERROR - Unzipped directory does not exist: /tmp/tmp51d9AZ/pplacer-v1.1.alpha12-Linux-2.6.32
2012-06-11 11:40:33,560 - lib.deploy - ERROR - Deploy of pplacer failed.
2012-06-11 11:40:33,924 - lib.application - INFO - Deploying app: MySQL-python
2012-06-11 11:40:33,924 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/MySQL-python-1.2.3-release
2012-06-11 11:40:33,924 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:33,926 - lib.application - INFO - Deploying app: biom-format
2012-06-11 11:40:33,926 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/biom-format-0.9.3-release
2012-06-11 11:40:33,926 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:33,927 - lib.deploy - INFO - Deploy of biom-format skipped.
2012-06-11 11:40:33,927 - lib.application - INFO - Deploying app: pycogent
2012-06-11 11:40:33,927 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/pycogent-1.5.1-release
2012-06-11 11:40:33,927 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:33,934 - lib.application - INFO - Deploying app: matplotlib
2012-06-11 11:40:33,934 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/matplotlib-1.1.0-release
2012-06-11 11:40:33,934 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:33,942 - lib.application - INFO - Deploying app: sphinx
2012-06-11 11:40:33,942 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/sphinx-1.0.4-release
2012-06-11 11:40:33,942 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:33,986 - lib.deploy - INFO - Deploy of MySQL-python skipped.
2012-06-11 11:40:33,992 - lib.deploy - INFO - Deploy of pycogent skipped.
2012-06-11 11:40:33,996 - lib.deploy - INFO - Deploy of matplotlib skipped.
2012-06-11 11:40:34,001 - lib.deploy - INFO - Deploy of sphinx skipped.
2012-06-11 11:40:38,939 - lib.application - INFO - Deploying app: pynast
2012-06-11 11:40:38,939 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/pynast-1.1-release
2012-06-11 11:40:38,939 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:38,964 - lib.application - INFO - Deploying app: pprospector
2012-06-11 11:40:38,964 - lib.application - INFO - Deploy directory exists: /home/mbhasin/qiime_software/pprospector-1.0.1-release
2012-06-11 11:40:38,964 - lib.application - INFO - Skipping deployment, assuming successful.
2012-06-11 11:40:38,976 - lib.application - INFO - Deploying app: qiime
2012-06-11 11:40:38,976 - lib.application - INFO - Making deploy directory: /home/mbhasin/qiime_software/qiime-1.5.0-repository-3072
2012-06-11 11:40:38,976 - lib.application - INFO - Downloading qiime
2012-06-11 11:40:38,976 - lib.util - INFO - Checking out https://qiime.svn.sourceforge.net/svnroot/qiime/trunk
2012-06-11 11:40:39,025 - lib.deploy - INFO - Deploy of pynast skipped.
2012-06-11 11:40:39,053 - lib.deploy - INFO - Deploy of pprospector skipped.
2012-06-11 11:40:51,612 - lib.deploy - INFO - Still deploying applications and data...
2012-06-11 11:40:52,468 - lib.util - INFO - Building qiime
2012-06-11 11:40:52,754 - lib.util - INFO - Installing qiime
2012-06-11 11:40:53,285 - lib.util - ERROR - Failed to install qiime
2012-06-11 11:40:53,285 - lib.application - ERROR - Problem building qiime.
2012-06-11 11:40:53,355 - lib.deploy - ERROR - Deploy of qiime failed.
2012-06-11 11:41:23,356 - lib.util - INFO - Removing directory: /home/mbhasin/qiime_software/ampliconnoise-1.25-release
2012-06-11 11:41:23,357 - lib.util - INFO - Removing directory: /home/mbhasin/qiime_software/pyzmq-2.1.9-release
2012-06-11 11:41:23,357 - lib.util - INFO - Removing directory: /home/mbhasin/qiime_software/pplacer-1.1-release
2012-06-11 11:41:23,358 - lib.util - INFO - Removing directory: /home/mbhasin/qiime_software/qiime-1.5.0-repository-3072
2012-06-11 11:41:23,372 - __main__ - INFO - Generating activate.sh file
2012-06-11 11:41:23,372 - lib.util - INFO - Backing up /home/mbhasin/qiime_software/activate.sh to /home/mbhasin/qiime_software/activate.sh.bak.6
2012-06-11 11:41:23,373 - __main__ - INFO - Generating new ~/.qiime_config_default file
2012-06-11 11:41:23,373 - lib.util - INFO - Backing up /home/mbhasin/.qiime_config_default to /home/mbhasin/.qiime_config_default.bak.6
2012-06-11 11:41:23,373 - __main__ - INFO - Generated new ~/.qiime_config_default file
DEPLOYMENT SUMMARY
Packages deployed successfully:
Packages skipped (assumed successful):
data-lanemask, data-core, clearcut, raxml, cdbtools, cytoscape, rtax, chimeraslayer, drisee, gg_otus, vienna, infernal, mothur, python, fasttree, blast, parsinsert, r, muscle, rdpclassifier, cdhit, uclust, numpy, SQLAlchemy, tornado, ipython, setuptools, mpi4py, biom-format, MySQL-python, pycogent, matplotlib, sphinx, pynast, pprospector
Packages failed to deploy:
ampliconnoise, pyzmq, pplacer, qiime
Any help or suggestions to finish successful installation is highly appreciated.
Manoj
--
---------------------------------------------------------
Dr.Manoj K Bhasin
Director Bioinformatics Core
Beth Isreal Deaconess Medical Center, Harvard Medical School
CLS Building, Room 442
3 Blackfan Circle
Boston, MA 02115, USA
TL: 617 582 7951
FX: 617 632 3351
EM:bha...@research.dfci.harvard.edu
mbh...@bidmc.harvard.edu W3:http://bio.dfci.harvard.edu/~bhasin/
---------------------------------------------------------
---------------------------------------------------------
Dr.Manoj K Bhasin
Director Bioinformatics Core
Beth Isreal Deaconess Medical Center, Harvard Medical School
CLS Building, Room 442
3 Blackfan Circle
Boston, MA 02115, USA
TL: 617 582 7951
FX: 617 632 3351
EM:bha...@research.dfci.harvard.edu
mbh...@bidmc.harvard.edu W3:http://bio.dfci.harvard.edu/~bhasin/
---------------------------------------------------------
Antonio González Peña
Jun 11, 2012, 3:38:11 PM6/11/12
to qiime...@googlegroups.com
Hi Manoj,
I think your errors fall into three categories, either missing some
dependencies: qiime, do you have ghc 7.0.3 or higher? ampliconoise, do
you have mpi installed and active?; not needed for the actual
pipeline: pyzmq; and the link is broken: pplacer. My suggestion is
that for your install you should worry about setting qiime and if you
are interested in ampliconnoise then this one too. The rest is fine if
they are missing.
Hope this helps.
I think your errors fall into three categories, either missing some
dependencies: qiime, do you have ghc 7.0.3 or higher? ampliconoise, do
you have mpi installed and active?; not needed for the actual
pipeline: pyzmq; and the link is broken: pplacer. My suggestion is
that for your install you should worry about setting qiime and if you
are interested in ampliconnoise then this one too. The rest is fine if
they are missing.
Hope this helps.
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