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qiime / qiime-deploy

Tool to easily install QIIME's dependencies on Linux systems
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installation failures due to lack of python-dev #10

Closed wdwvt1 closed 11 years ago

wdwvt1 commented 11 years ago

installing via the qiime-deploy on 12.04 LTS failed for me. 2012-12-06 00:27:56,970 - lib.application - ERROR - python download failed. 2012-12-06 00:27:56,970 - lib.deploy - ERROR - Deploy of python failed. 2012-12-06 00:27:59,927 - main - ERROR - Dependencies failed for cython. 2012-12-06 00:27:59,927 - main - ERROR - Dependencies failed for numpy. 2012-12-06 00:27:59,928 - main - ERROR - Dependencies failed for pyzmq. 2012-12-06 00:27:59,928 - main - ERROR - Dependencies failed for SQLAlchemy. 2012-12-06 00:27:59,928 - main - ERROR - Dependencies failed for tornado. 2012-12-06 00:27:59,928 - main - ERROR - Dependencies failed for matplotlib. 2012-12-06 00:27:59,928 - main - ERROR - Dependencies failed for ipython. 2012-12-06 00:27:59,928 - main - ERROR - Dependencies failed for setuptools. 2012-12-06 00:27:59,928 - main - ERROR - Dependencies failed for mpi4py.

when i installed python-dev via apt-get the errors where resolved and python, numpy, etc were installed without error. i think this is a 2 second fix -- add python-dev to the following command in the tutorial: $ sudo apt-get --force-yes -y install libssl-dev libzmq-dev libgsl0-dev openjdk-6-jdk libxml2 libxslt1.1 libxslt1-dev ant git subversion build-essential zlib1g-dev libpng12-dev libfreetype6-dev mpich2 libreadline-dev gfortran unzip libmysqlclient18 libmysqlclient-dev ghc

wdwvt1 commented 11 years ago

an additional required dependency for mothur 1.25.0 to compile was libncurses5-dev. sudo apt-get install sudo apt-get install libncurses5-dev completely resolved the issue. a check/call should be added for this as well

wdwvt1 commented 11 years ago

a final issue: python qiime-deploy.py $HOME/qiime_software/ -f $HOME/qiime-deploy-conf/qiime-1.5.0/qiime.conf --force-remove-failed-dirs

failed ŵhen absolute paths were not supplied. not sure how to fix this one other than a documentation change

pdmars commented 11 years ago

For the dependencies, let's update the documentation to list them, but we haven't implemented checks for ALL underlying packages/software due to the wide-variety of different linux distros, packaging mechanisms, possible configurations, etc.

The absolute path issue should be a relatively easy fix, I think, we just need to expand the path (via os.path), etc. Right now in config.py it doesn't look like it does anything special.

gregcaporaso commented 11 years ago

We need someone to assign this issue to themselves - it's critical for the upcoming QIIME release. Can someone commit to having it done by Thursday 12/13?

pdmars commented 11 years ago

Assigned it to me, should have it done today or tomorrow.

gregcaporaso commented 11 years ago

Thank you!

pdmars commented 11 years ago

Sent pull requests for adding the required packages in the README.

But what error are you seeing when running qiime-deploy.py for "absolute paths were not supplied"? And what are you running it on?

This command seems to work for me on ubuntu and debian.

jairideout commented 11 years ago

Hard to describe: Will and I were installing on two Ubuntu 12.04 64-bit systems with seemingly identical configuration. Will used absolute paths and I used relative paths, and his deploy ended up succeeding while mine would continually fail (I tried a few times). The issue was with installing numpy and any other python packages, as qiime-deploy would throw an error when trying to set the PYTHONPATH because the PYTHONPATH variable was None.

I think I ran the commands from one directory up from the qiime-deploy and qiime-deploy-conf directories, e.g.:

python qiime-deploy/qiime-deploy.py qiime_software/ -f qiime-deploy-conf/qiime-1.5.0-dev/qiime.conf --force-remove-failed-dirs --force-remove-previous-repos

Sorry for the lack of information; we had a very limited amount of time to install QIIME at a lab in Brazil and didn't have time to do further debugging as we ran into this issue.

pdmars commented 11 years ago

I've run this with various debian and ubuntu versions (both in the qiime-deploy directory and outside of it) and I can't seem to reproduce it so unless someone can provide more information to reproduce this, I'd say we close this issue.

wdwvt1 commented 11 years ago

I guess it could have been an artifact of something very system specific, or (more likely imo) it was an error with empty directories getting created that Jai and I didn't catch. I think its okay to close this issue, though something we should be wary of.

On Mon, Dec 10, 2012 at 9:36 AM, Paul notifications@github.com wrote:

I've run this with various debian and ubuntu versions (both in the qiime-deploy directory and outside of it) and I can't seem to reproduce it so unless someone can provide more information to reproduce this, I'd say we close this issue.

— Reply to this email directly or view it on GitHubhttps://github.com/qiime/qiime-deploy/issues/10#issuecomment-11204667.

jairideout commented 11 years ago

I agree- let's just close this but keep this issue in mind in case someone else runs into it in the future.

DrBeanie commented 11 years ago

I am having an issue whereby Python fails to unzip from the tmp folder and thus deploy; as a result many dependencies fail. I have the python-dev package but still the same problem. Thoughts?

Installing via qiime-deploy on Ubuntu 12.04 LTS

jairideout commented 11 years ago

Can you please post the exact command you're using? It'd also be helpful if you can post the output you receive from running qiime-deploy.

DrBeanie commented 11 years ago

Apologies,

boonyeoh@ubuntu:~/qiime-deploy$ python qiime-deploy.py $HOME/qiime_software/ -f $HOME/qiime-deploy-conf/qiime-1.6.0/qiime.conf --force-remove-failed-dirs

The very last error about the qiime_config 'operation not permitted' didn't used to happen for the first few times; not sure why it is doing that now. It used to show me which packages were successful, which were skipped and which were not deployed.

The most consistent error I have gotten is: 2013-03-23 08:07:46,417 - lib.application - ERROR - Unzip failed: /tmp/tmpWFPNGN/Python-2.7.3.tgz 2013-03-23 08:07:46,456 - lib.deploy - ERROR - Deploy of python failed.

2013-03-23 08:06:51,594 - main - INFO - Dependencies look good. 2013-03-23 08:06:51,594 - main - INFO - Starting status thread. 2013-03-23 08:06:51,594 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 08:06:51,595 - main - INFO - Starting 6 deploy threads. 2013-03-23 08:06:51,596 - main - INFO - Running deploy for data and apps without dependencies. 2013-03-23 08:06:51,596 - main - INFO - Searching for python... 2013-03-23 08:06:51,596 - main - INFO - python-exe is not specified. 2013-03-23 08:06:51,596 - main - INFO - Looks like python target is being deployed, using that version 2013-03-23 08:06:51,596 - main - INFO - Setting python: /home/boonyeoh/qiime_software/python-2.7.3-release/bin/python 2013-03-23 08:06:51,597 - main - INFO - Searching for R... 2013-03-23 08:06:51,597 - main - INFO - r-exe is not specified. 2013-03-23 08:06:51,597 - main - INFO - Looks like r target is being deployed, using that version 2013-03-23 08:06:51,597 - main - INFO - Setting R: /home/boonyeoh/qiime_software/r-2.12.0-release/bin/R 2013-03-23 08:06:56,126 - main - INFO - Launched initial deploy, remaining apps: ['pynast', 'pprospector', 'MySQL-python', 'biom-format', 'tax2tree', 'ape', 'cython', 'pycogent', 'r-color-brewer', 'numpy', 'pyzmq', 'SQLAlchemy', 'klar', 'qiime', 'gdata', 'tornado', 'matplotlib', 'ipython', 'sphinx', 'vegan', 'random-forest', 'gtools', 'setuptools', 'optparse', 'mpi4py'] 2013-03-23 08:06:56,127 - main - INFO - Deploying remaining apps. 2013-03-23 08:06:56,129 - lib.data - INFO - Deploying data: data-lanemask 2013-03-23 08:06:56,129 - lib.data - INFO - Deploying data: data-core 2013-03-23 08:06:56,132 - lib.application - INFO - Deploying app: clearcut 2013-03-23 08:06:56,132 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/clearcut-1.0.9-release 2013-03-23 08:06:56,132 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,133 - lib.deploy - INFO - Deploy of clearcut skipped. 2013-03-23 08:06:56,132 - lib.application - INFO - Deploying app: raxml 2013-03-23 08:06:56,132 - lib.application - INFO - Deploying app: blat 2013-03-23 08:06:56,133 - lib.application - INFO - Deploying app: cdbtools 2013-03-23 08:06:56,132 - lib.application - INFO - Deploying app: ampliconnoise 2013-03-23 08:06:56,133 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/ampliconnoise-1.27-release 2013-03-23 08:06:56,133 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,133 - lib.deploy - INFO - Deploy of ampliconnoise skipped. 2013-03-23 08:06:56,134 - lib.application - INFO - Deploying app: sourcetracker 2013-03-23 08:06:56,134 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/sourcetracker-0.9.4-release 2013-03-23 08:06:56,134 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,134 - lib.deploy - INFO - Deploy of sourcetracker skipped. 2013-03-23 08:06:56,134 - lib.application - INFO - Deploying app: rtax 2013-03-23 08:06:56,134 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/rtax-0.983-release 2013-03-23 08:06:56,134 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,134 - lib.deploy - INFO - Deploy of rtax skipped. 2013-03-23 08:06:56,134 - lib.application - INFO - Deploying app: cytoscape 2013-03-23 08:06:56,134 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/cytoscape-2.7.0-release 2013-03-23 08:06:56,135 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,135 - lib.deploy - INFO - Deploy of cytoscape skipped. 2013-03-23 08:06:56,135 - lib.application - INFO - Deploying app: chimeraslayer 2013-03-23 08:06:56,135 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/chimeraslayer-4.29.2010-release 2013-03-23 08:06:56,135 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,135 - lib.deploy - INFO - Deploy of chimeraslayer skipped. 2013-03-23 08:06:56,135 - lib.application - INFO - Deploying app: python 2013-03-23 08:06:56,133 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/cdbtools-10.11.2010-release 2013-03-23 08:06:56,135 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,135 - lib.deploy - INFO - Deploy of cdbtools skipped. 2013-03-23 08:06:56,136 - lib.application - INFO - Deploying app: drisee 2013-03-23 08:06:56,136 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/drisee-1.2-release 2013-03-23 08:06:56,136 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,136 - lib.deploy - INFO - Deploy of drisee skipped. 2013-03-23 08:06:56,136 - lib.application - INFO - Deploying app: gg_otus 2013-03-23 08:06:56,133 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/raxml-7.3.0-release 2013-03-23 08:06:56,133 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/blat-34-release 2013-03-23 08:06:56,136 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,136 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,137 - lib.deploy - INFO - Deploy of raxml skipped. 2013-03-23 08:06:56,137 - lib.deploy - INFO - Deploy of blat skipped. 2013-03-23 08:06:56,137 - lib.application - INFO - Deploying app: infernal 2013-03-23 08:06:56,137 - lib.application - INFO - Deploying app: vienna 2013-03-23 08:06:56,137 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/infernal-1.0.2-release 2013-03-23 08:06:56,137 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,137 - lib.deploy - INFO - Deploy of infernal skipped. 2013-03-23 08:06:56,137 - lib.application - INFO - Deploying app: mothur 2013-03-23 08:06:56,137 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/mothur-1.25.0-release 2013-03-23 08:06:56,138 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,138 - lib.deploy - INFO - Deploy of mothur skipped. 2013-03-23 08:06:56,138 - lib.application - INFO - Deploying app: fasttree 2013-03-23 08:06:56,137 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/vienna-1.8.4-release 2013-03-23 08:06:56,138 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,138 - lib.deploy - INFO - Deploy of vienna skipped. 2013-03-23 08:06:56,138 - lib.application - INFO - Deploying app: bwa 2013-03-23 08:06:56,138 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/bwa-0.6.2-release 2013-03-23 08:06:56,138 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,139 - lib.deploy - INFO - Deploy of bwa skipped. 2013-03-23 08:06:56,139 - lib.application - INFO - Deploying app: pplacer 2013-03-23 08:06:56,139 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/pplacer-1.1-release 2013-03-23 08:06:56,139 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,139 - lib.deploy - INFO - Deploy of pplacer skipped. 2013-03-23 08:06:56,139 - lib.application - INFO - Deploying app: blast 2013-03-23 08:06:56,139 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/blast-2.2.22-release 2013-03-23 08:06:56,139 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,139 - lib.deploy - INFO - Deploy of blast skipped. 2013-03-23 08:06:56,140 - lib.application - INFO - Deploying app: qiime_test_data 2013-03-23 08:06:56,140 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/fasttree-2.1.3-release 2013-03-23 08:06:56,140 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,140 - lib.deploy - INFO - Deploy of fasttree skipped. 2013-03-23 08:06:56,140 - lib.application - INFO - Deploying app: parsinsert 2013-03-23 08:06:56,140 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/parsinsert-1.0.4-release 2013-03-23 08:06:56,140 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,140 - lib.deploy - INFO - Deploy of parsinsert skipped. 2013-03-23 08:06:56,140 - lib.application - INFO - Deploying app: rdpclassifier 2013-03-23 08:06:56,141 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/rdpclassifier-2.2-release 2013-03-23 08:06:56,141 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,141 - lib.deploy - INFO - Deploy of rdpclassifier skipped. 2013-03-23 08:06:56,141 - lib.application - INFO - Deploying app: r 2013-03-23 08:06:56,141 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/r-2.12.0-release 2013-03-23 08:06:56,141 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,141 - lib.deploy - INFO - Deploy of r skipped. 2013-03-23 08:06:56,141 - lib.application - INFO - Deploying app: muscle 2013-03-23 08:06:56,141 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/muscle-3.8.31-release 2013-03-23 08:06:56,142 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,142 - lib.deploy - INFO - Deploy of muscle skipped. 2013-03-23 08:06:56,142 - lib.application - INFO - Deploying app: cdhit 2013-03-23 08:06:56,142 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/cdhit-3.1-release 2013-03-23 08:06:56,142 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,142 - lib.deploy - INFO - Deploy of cdhit skipped. 2013-03-23 08:06:56,142 - lib.application - INFO - Deploying app: uclust 2013-03-23 08:06:56,142 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/uclust-1.2.22-release 2013-03-23 08:06:56,142 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,143 - lib.deploy - INFO - Deploy of uclust skipped. 2013-03-23 08:06:56,199 - lib.data - INFO - data-lanemask exists, skipping download. 2013-03-23 08:06:56,199 - lib.deploy - INFO - Deploy of data-lanemask skipped. 2013-03-23 08:06:56,209 - lib.data - INFO - data-core exists, skipping download. 2013-03-23 08:06:56,210 - lib.deploy - INFO - Deploy of data-core skipped. 2013-03-23 08:06:56,210 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/python-2.7.3-release 2013-03-23 08:06:56,210 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/qiime_test_data-1.6.0-repository-101a2b9b 2013-03-23 08:06:56,210 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/gg_otus-12_10-release 2013-03-23 08:06:56,210 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,210 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:06:56,210 - lib.deploy - INFO - Deploy of gg_otus skipped. 2013-03-23 08:06:56,210 - lib.deploy - INFO - Deploy of qiime_test_data skipped. 2013-03-23 08:06:56,224 - lib.application - INFO - Downloading python 2013-03-23 08:06:56,224 - lib.util - INFO - Downloading http://www.python.org/ftp/python/2.7.3/Python-2.7.3.tgz 2013-03-23 08:07:01,135 - lib.application - INFO - Deploying app: ape 2013-03-23 08:07:01,136 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/ape-latest-r-package 2013-03-23 08:07:01,136 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:07:01,138 - lib.deploy - INFO - Deploy of ape skipped. 2013-03-23 08:07:01,138 - lib.application - INFO - Deploying app: r-color-brewer 2013-03-23 08:07:01,139 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/r-color-brewer-latest-r-package 2013-03-23 08:07:01,139 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:07:01,140 - lib.deploy - INFO - Deploy of r-color-brewer skipped. 2013-03-23 08:07:01,140 - lib.application - INFO - Deploying app: klar 2013-03-23 08:07:01,140 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/klar-latest-r-package 2013-03-23 08:07:01,141 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:07:01,141 - lib.deploy - INFO - Deploy of klar skipped. 2013-03-23 08:07:01,141 - lib.application - INFO - Deploying app: vegan 2013-03-23 08:07:01,142 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/vegan-latest-r-package 2013-03-23 08:07:01,142 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:07:01,143 - lib.deploy - INFO - Deploy of vegan skipped. 2013-03-23 08:07:01,143 - lib.application - INFO - Deploying app: random-forest 2013-03-23 08:07:01,143 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/random-forest-latest-r-package 2013-03-23 08:07:01,143 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:07:01,144 - lib.deploy - INFO - Deploy of random-forest skipped. 2013-03-23 08:07:01,144 - lib.application - INFO - Deploying app: gtools 2013-03-23 08:07:01,144 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/gtools-latest-r-package 2013-03-23 08:07:01,145 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:07:01,145 - lib.deploy - INFO - Deploy of gtools skipped. 2013-03-23 08:07:01,149 - lib.application - INFO - Deploying app: optparse 2013-03-23 08:07:01,149 - lib.application - INFO - Deploy directory exists: /home/boonyeoh/qiime_software/optparse-latest-r-package 2013-03-23 08:07:01,149 - lib.application - INFO - Skipping deployment, assuming successful. 2013-03-23 08:07:01,150 - lib.deploy - INFO - Deploy of optparse skipped. 2013-03-23 08:07:21,619 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 08:07:46,417 - lib.application - ERROR - Unzip failed: /tmp/tmpWFPNGN/Python-2.7.3.tgz 2013-03-23 08:07:46,456 - lib.deploy - ERROR - Deploy of python failed. 2013-03-23 08:07:51,200 - main - ERROR - Dependencies failed for cython. 2013-03-23 08:07:51,201 - main - ERROR - Dependencies failed for numpy. 2013-03-23 08:07:51,201 - main - ERROR - Dependencies failed for pyzmq. 2013-03-23 08:07:51,201 - main - ERROR - Dependencies failed for SQLAlchemy. 2013-03-23 08:07:51,202 - main - ERROR - Dependencies failed for gdata. 2013-03-23 08:07:51,202 - main - ERROR - Dependencies failed for tornado. 2013-03-23 08:07:51,203 - main - ERROR - Dependencies failed for matplotlib. 2013-03-23 08:07:51,203 - main - ERROR - Dependencies failed for ipython. 2013-03-23 08:07:51,203 - main - ERROR - Dependencies failed for setuptools. 2013-03-23 08:07:51,204 - main - ERROR - Dependencies failed for mpi4py. 2013-03-23 08:07:51,645 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 08:07:56,210 - main - ERROR - Dependencies failed for MySQL-python. 2013-03-23 08:07:56,210 - main - ERROR - Dependencies failed for biom-format. 2013-03-23 08:07:56,211 - main - ERROR - Dependencies failed for pycogent. 2013-03-23 08:07:56,211 - main - ERROR - Dependencies failed for qiime. 2013-03-23 08:07:56,212 - main - ERROR - Dependencies failed for sphinx. 2013-03-23 08:08:01,215 - main - ERROR - Dependencies failed for pynast. 2013-03-23 08:08:01,216 - main - ERROR - Dependencies failed for pprospector. 2013-03-23 08:08:01,216 - main - ERROR - Dependencies failed for tax2tree. 2013-03-23 08:08:31,152 - lib.util - INFO - Removing directory: /home/boonyeoh/qiime_software/python-2.7.3-release 2013-03-23 08:08:31,153 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/cython-0.17-release 2013-03-23 08:08:31,153 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/numpy-1.5.1-release 2013-03-23 08:08:31,154 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/pyzmq-2.1.9-release 2013-03-23 08:08:31,154 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/SQLAlchemy-0.7.1-release 2013-03-23 08:08:31,154 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/gdata-2.0.17-release 2013-03-23 08:08:31,154 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/tornado-2.2.1-release 2013-03-23 08:08:31,155 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/matplotlib-1.1.0-release 2013-03-23 08:08:31,155 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/ipython-latest-repository-d2354694 2013-03-23 08:08:31,155 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/setuptools-0.6c11-release 2013-03-23 08:08:31,156 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/mpi4py-1.2.2-release 2013-03-23 08:08:31,156 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/MySQL-python-1.2.3-release 2013-03-23 08:08:31,156 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/biom-format-1.1.1-release 2013-03-23 08:08:31,156 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/pycogent-1.5.3-release 2013-03-23 08:08:31,157 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/qiime-1.6.0-release 2013-03-23 08:08:31,157 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/sphinx-1.0.4-release 2013-03-23 08:08:31,157 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/pynast-1.2-release 2013-03-23 08:08:31,158 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/pprospector-1.0.1-release 2013-03-23 08:08:31,158 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/tax2tree-1.0-release 2013-03-23 08:08:31,158 - main - INFO - Generating activate.sh file 2013-03-23 08:08:31,231 - lib.util - INFO - Backing up /home/boonyeoh/qiime_software/activate.sh to /home/boonyeoh/qiime_software/activate.sh.bak.6 Traceback (most recent call last): File "qiime-deploy.py", line 431, in sys.exit(main()) File "qiime-deploy.py", line 426, in main opts.removePreviousRepos) File "qiime-deploy.py", line 363, in deploy_apps rc = custom.custom_finalize(custom_py_exe, deploy_dir, all_apps_to_deploy, log) File "/home/boonyeoh/qiime-deploy/lib/custom.py", line 329, in custom_finalize set_permissions_all_files(deploy_dir) File "/home/boonyeoh/qiime-deploy/lib/custom.py", line 318, in set_permissions_all_files os.chmod(full_name, int("644", 8)) OSError: [Errno 1] Operation not permitted: '/home/boonyeoh/qiime_software/qiime_config'

jairideout commented 11 years ago

Thanks for providing the output. I'm not sure what's going on, but you might check to make sure that you're not running out of disk space in /tmp (this is just a guess as to why unzipping is failing). You may want to clear out your /tmp area if you have lots of files left over from previous failed runs.

I also recommend completely removing your $HOME/qiime_software/ directory and then trying the command again. In the past this has usually worked out for me.

DrBeanie commented 11 years ago

Thanks for the suggestions. Deleted qiime_software, cleared out the TMP (by restarting my computer) but unfortunately still no joy. Still the same error with unable to unzip and then deploy python.

Frustrating because I have installed qiime successful before but my Unbuntu crashed about a month ago so I had to clean install (via Wubi)!

Any other suggestions?

boonyeoh@ubuntu:~/qiime-deploy$ python qiime-deploy.py $HOME/qiime_software/ -f $HOME/qiime-deploy-conf/qiime-1.6.0/qiime.conf --force-remove-failed-dirs2013-03-23 09:01:50,808 - main - INFO - Dependencies look good. 2013-03-23 09:01:50,808 - main - INFO - Starting status thread. 2013-03-23 09:01:50,809 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:01:50,809 - main - INFO - Starting 6 deploy threads. 2013-03-23 09:01:50,828 - main - INFO - Running deploy for data and apps without dependencies. 2013-03-23 09:01:50,828 - main - INFO - Searching for python... 2013-03-23 09:01:50,828 - main - INFO - python-exe is not specified. 2013-03-23 09:01:50,828 - main - INFO - Looks like python target is being deployed, using that version 2013-03-23 09:01:50,828 - main - INFO - Setting python: /home/boonyeoh/qiime_software/python-2.7.3-release/bin/python 2013-03-23 09:01:50,829 - main - INFO - Searching for R... 2013-03-23 09:01:50,829 - main - INFO - r-exe is not specified. 2013-03-23 09:01:50,829 - main - INFO - Looks like r target is being deployed, using that version 2013-03-23 09:01:50,829 - main - INFO - Setting R: /home/boonyeoh/qiime_software/r-2.12.0-release/bin/R 2013-03-23 09:01:54,680 - main - INFO - Launched initial deploy, remaining apps: ['pynast', 'pprospector', 'MySQL-python', 'biom-format', 'tax2tree', 'ape', 'cython', 'pycogent', 'r-color-brewer', 'numpy', 'pyzmq', 'SQLAlchemy', 'klar', 'qiime', 'gdata', 'tornado', 'matplotlib', 'ipython', 'sphinx', 'vegan', 'random-forest', 'gtools', 'setuptools', 'optparse', 'mpi4py'] 2013-03-23 09:01:54,680 - main - INFO - Deploying remaining apps. 2013-03-23 09:01:54,694 - lib.data - INFO - Deploying data: data-lanemask 2013-03-23 09:01:54,695 - lib.data - INFO - Deploying data: data-core 2013-03-23 09:01:54,695 - lib.application - INFO - Deploying app: clearcut 2013-03-23 09:01:54,695 - lib.application - INFO - Deploying app: raxml 2013-03-23 09:01:54,695 - lib.application - INFO - Deploying app: ampliconnoise 2013-03-23 09:01:54,696 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/ampliconnoise-1.27-release 2013-03-23 09:01:54,695 - lib.data - INFO - Downloading data-lanemask 2013-03-23 09:01:54,696 - lib.util - INFO - Downloading http://greengenes.lbl.gov/Download/Sequence_Data/lanemask_in_1s_and_0s 2013-03-23 09:01:54,695 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/clearcut-1.0.9-release 2013-03-23 09:01:54,696 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/raxml-7.3.0-release 2013-03-23 09:01:54,695 - lib.application - INFO - Deploying app: blat 2013-03-23 09:01:54,695 - lib.data - INFO - Downloading data-core 2013-03-23 09:01:54,956 - lib.util - INFO - Downloading http://greengenes.lbl.gov/Download/Sequence_Data/Fasta_data_files/core_set_aligned.fasta.imputed 2013-03-23 09:01:54,955 - lib.application - INFO - Downloading ampliconnoise 2013-03-23 09:01:54,956 - lib.util - INFO - Downloading http://ampliconnoise.googlecode.com/files/AmpliconNoiseV1.27.tar.gz 2013-03-23 09:01:54,962 - lib.application - INFO - Downloading clearcut 2013-03-23 09:01:54,962 - lib.application - INFO - Downloading raxml 2013-03-23 09:01:54,962 - lib.util - INFO - Downloading ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/stamatak-standard-RAxML-5_7_2012.tgz 2013-03-23 09:01:54,962 - lib.util - INFO - Downloading http://bioinformatics.hungry.com/clearcut/clearcut-1.0.9.tar.gz 2013-03-23 09:01:54,962 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/blat-34-release 2013-03-23 09:01:54,997 - lib.application - INFO - Downloading blat 2013-03-23 09:01:54,997 - lib.util - INFO - Downloading http://hgwdev.cse.ucsc.edu/~kent/exe/linux/blatSuite.34.zip 2013-03-23 09:01:55,920 - lib.deploy - INFO - Deploy of data-lanemask succeeded. 2013-03-23 09:01:55,921 - lib.application - INFO - Deploying app: cdbtools 2013-03-23 09:01:55,921 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/cdbtools-10.11.2010-release 2013-03-23 09:01:55,921 - lib.application - INFO - Downloading cdbtools 2013-03-23 09:01:55,921 - lib.util - INFO - Downloading ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta/cdbfasta.tar.gz 2013-03-23 09:01:57,853 - lib.application - INFO - Unzip succeeded: /tmp/tmpQVUv7G/clearcut-1.0.9.tar.gz 2013-03-23 09:01:57,853 - lib.util - INFO - Compiling clearcut 2013-03-23 09:01:58,257 - lib.application - INFO - Unzip succeeded: /tmp/tmp3UXI24/blatSuite.34.zip 2013-03-23 09:01:58,307 - lib.application - INFO - Successfully copied blat directory. 2013-03-23 09:01:58,309 - lib.deploy - INFO - Deploy of blat succeeded. 2013-03-23 09:01:58,309 - lib.application - INFO - Deploying app: sourcetracker 2013-03-23 09:01:58,310 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/sourcetracker-0.9.4-release 2013-03-23 09:01:58,331 - lib.application - INFO - Downloading sourcetracker 2013-03-23 09:01:58,331 - lib.util - INFO - Downloading http://sourceforge.net/projects/sourcetracker/files/sourcetracker-0.9.4.tar.gz 2013-03-23 09:01:59,584 - lib.application - INFO - Unzip succeeded: /tmp/tmpy5os6e/stamatak-standard-RAxML-5_7_2012.tgz 2013-03-23 09:01:59,584 - lib.util - INFO - Compiling raxml 2013-03-23 09:02:03,258 - lib.application - INFO - Unzip succeeded: /tmp/tmp21fZsG/cdbfasta.tar.gz 2013-03-23 09:02:03,258 - lib.util - INFO - Compiling cdbtools 2013-03-23 09:02:05,077 - lib.application - INFO - Unzip succeeded: /tmp/tmpXf5E13/AmpliconNoiseV1.27.tar.gz 2013-03-23 09:02:05,078 - lib.util - INFO - Compiling ampliconnoise 2013-03-23 09:02:05,272 - lib.application - INFO - Unzip succeeded: /tmp/tmp9gkPc5/sourcetracker-0.9.4.tar.gz 2013-03-23 09:02:05,395 - lib.application - INFO - Successfully copied sourcetracker directory. 2013-03-23 09:02:05,804 - lib.deploy - INFO - Deploy of sourcetracker succeeded. 2013-03-23 09:02:05,805 - lib.application - INFO - Deploying app: rtax 2013-03-23 09:02:05,805 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/rtax-0.983-release 2013-03-23 09:02:06,553 - lib.application - INFO - Downloading rtax 2013-03-23 09:02:06,553 - lib.util - INFO - Downloading http://static.davidsoergel.com/rtax-0.983.tgz 2013-03-23 09:02:08,555 - lib.application - INFO - Unzip succeeded: /tmp/tmpT9T4NJ/rtax-0.983.tgz 2013-03-23 09:02:08,598 - lib.application - INFO - Successfully copied rtax directory. 2013-03-23 09:02:08,599 - lib.deploy - INFO - Deploy of rtax succeeded. 2013-03-23 09:02:08,599 - lib.application - INFO - Deploying app: cytoscape 2013-03-23 09:02:08,600 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/cytoscape-2.7.0-release 2013-03-23 09:02:08,600 - lib.application - INFO - Downloading cytoscape 2013-03-23 09:02:08,600 - lib.util - INFO - Downloading http://chianti.ucsd.edu/Cyto-2_7_0/cytoscapeSource-v2.7.0.tar.gz 2013-03-23 09:02:08,613 - lib.application - INFO - Successfully made clearcut. 2013-03-23 09:02:08,660 - lib.application - INFO - Successfully copied clearcut directory. 2013-03-23 09:02:08,674 - lib.deploy - INFO - Deploy of clearcut succeeded. 2013-03-23 09:02:08,677 - lib.application - INFO - Deploying app: chimeraslayer 2013-03-23 09:02:08,679 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/chimeraslayer-4.29.2010-release 2013-03-23 09:02:08,684 - lib.application - INFO - Downloading chimeraslayer 2013-03-23 09:02:08,684 - lib.util - INFO - Downloading http://sourceforge.net/projects/microbiomeutil/files/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz 2013-03-23 09:02:14,912 - lib.application - INFO - Successfully made cdbtools. 2013-03-23 09:02:14,949 - lib.application - INFO - Successfully copied cdbtools directory. 2013-03-23 09:02:15,680 - lib.deploy - INFO - Deploy of cdbtools succeeded. 2013-03-23 09:02:15,681 - lib.application - INFO - Deploying app: python 2013-03-23 09:02:15,681 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/python-2.7.3-release 2013-03-23 09:02:15,682 - lib.application - INFO - Downloading python 2013-03-23 09:02:15,682 - lib.util - INFO - Downloading http://www.python.org/ftp/python/2.7.3/Python-2.7.3.tgz 2013-03-23 09:02:20,841 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:02:27,702 - lib.application - INFO - Successfully made raxml. 2013-03-23 09:02:27,729 - lib.application - INFO - Successfully copied raxml directory. 2013-03-23 09:02:27,734 - lib.deploy - INFO - Deploy of raxml succeeded. 2013-03-23 09:02:27,735 - lib.application - INFO - Deploying app: drisee 2013-03-23 09:02:27,735 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/drisee-1.2-release 2013-03-23 09:02:27,735 - lib.application - INFO - Downloading drisee 2013-03-23 09:02:27,735 - lib.util - INFO - Downloading https://github.com/MG-RAST/DRISEE/zipball/v1.2 2013-03-23 09:02:34,640 - lib.deploy - INFO - Deploy of ampliconnoise succeeded. 2013-03-23 09:02:34,640 - lib.application - INFO - Deploying app: gg_otus 2013-03-23 09:02:34,640 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/gg_otus-12_10-release 2013-03-23 09:02:34,640 - lib.application - INFO - Downloading gg_otus 2013-03-23 09:02:34,640 - lib.util - INFO - Downloading ftp://greengenes.microbio.me/greengenes_release/gg_12_10/gg_12_10_otus.tar.gz 2013-03-23 09:02:50,872 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:03:14,116 - lib.deploy - INFO - Deploy of data-core succeeded. 2013-03-23 09:03:14,117 - lib.application - INFO - Deploying app: infernal 2013-03-23 09:03:14,117 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/infernal-1.0.2-release 2013-03-23 09:03:14,118 - lib.application - INFO - Downloading infernal 2013-03-23 09:03:14,118 - lib.util - INFO - Downloading ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz 2013-03-23 09:03:20,903 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:03:50,933 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:04:20,963 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:04:50,993 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:05:08,918 - lib.application - ERROR - Unzip failed: /tmp/tmp_lENJB/Python-2.7.3.tgz 2013-03-23 09:05:08,960 - lib.deploy - ERROR - Deploy of python failed. 2013-03-23 09:05:08,960 - lib.application - INFO - Deploying app: vienna 2013-03-23 09:05:08,960 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/vienna-1.8.4-release 2013-03-23 09:05:08,960 - lib.application - INFO - Downloading vienna 2013-03-23 09:05:08,960 - lib.util - INFO - Downloading http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.8.4.tar.gz 2013-03-23 09:05:09,907 - main - ERROR - Dependencies failed for cython. 2013-03-23 09:05:09,907 - main - ERROR - Dependencies failed for numpy. 2013-03-23 09:05:09,907 - main - ERROR - Dependencies failed for pyzmq. 2013-03-23 09:05:09,908 - main - ERROR - Dependencies failed for SQLAlchemy. 2013-03-23 09:05:09,908 - main - ERROR - Dependencies failed for gdata. 2013-03-23 09:05:09,908 - main - ERROR - Dependencies failed for tornado. 2013-03-23 09:05:09,908 - main - ERROR - Dependencies failed for matplotlib. 2013-03-23 09:05:09,908 - main - ERROR - Dependencies failed for ipython. 2013-03-23 09:05:09,908 - main - ERROR - Dependencies failed for setuptools. 2013-03-23 09:05:09,909 - main - ERROR - Dependencies failed for mpi4py. 2013-03-23 09:05:14,731 - lib.application - INFO - Unzip succeeded: /tmp/tmpnWKpXs/ViennaRNA-1.8.4.tar.gz 2013-03-23 09:05:14,733 - lib.util - INFO - Configuring vienna 2013-03-23 09:05:14,914 - main - ERROR - Dependencies failed for MySQL-python. 2013-03-23 09:05:14,914 - main - ERROR - Dependencies failed for biom-format. 2013-03-23 09:05:14,915 - main - ERROR - Dependencies failed for pycogent. 2013-03-23 09:05:14,915 - main - ERROR - Dependencies failed for qiime. 2013-03-23 09:05:14,915 - main - ERROR - Dependencies failed for sphinx. 2013-03-23 09:05:19,920 - main - ERROR - Dependencies failed for pynast. 2013-03-23 09:05:19,921 - main - ERROR - Dependencies failed for pprospector. 2013-03-23 09:05:19,921 - main - ERROR - Dependencies failed for tax2tree. 2013-03-23 09:05:21,024 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:05:24,043 - lib.application - INFO - Unzip succeeded: /tmp/tmpr_7YWe/MG-RAST-DRISEE-v1.2-0-g-195855.zip 2013-03-23 09:05:24,113 - lib.application - INFO - Successfully copied drisee directory. 2013-03-23 09:05:24,127 - lib.deploy - INFO - Deploy of drisee succeeded. 2013-03-23 09:05:24,127 - lib.application - INFO - Deploying app: mothur 2013-03-23 09:05:24,127 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/mothur-1.25.0-release 2013-03-23 09:05:24,127 - lib.application - INFO - Downloading mothur 2013-03-23 09:05:24,128 - lib.util - INFO - Downloading ftp://thebeast.colorado.edu/pub/QIIME-v1.6.0-dependencies/mothur-1.25.0.tar.gz 2013-03-23 09:05:36,823 - lib.util - INFO - Compiling vienna 2013-03-23 09:05:51,054 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:06:21,084 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:06:51,095 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:07:13,374 - lib.application - INFO - Unzip succeeded: /tmp/tmpsf7fq3/infernal-1.0.2.tar.gz 2013-03-23 09:07:13,375 - lib.util - INFO - Configuring infernal 2013-03-23 09:07:21,101 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:07:51,131 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:08:16,859 - lib.application - INFO - Unzip succeeded: /tmp/tmpcdVnCI/mothur-1.25.0.tar.gz 2013-03-23 09:08:21,161 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:08:51,191 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:09:02,300 - lib.application - INFO - Successfully copied mothur directory. 2013-03-23 09:09:02,369 - lib.deploy - INFO - Deploy of mothur succeeded. 2013-03-23 09:09:02,369 - lib.application - INFO - Deploying app: fasttree 2013-03-23 09:09:02,369 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/fasttree-2.1.3-release 2013-03-23 09:09:02,369 - lib.application - INFO - Downloading fasttree 2013-03-23 09:09:02,369 - lib.util - INFO - Downloading http://www.microbesonline.org/fasttree/FastTree-2.1.3.c 2013-03-23 09:09:04,001 - lib.application - INFO - Unzip succeeded: /tmp/tmpEwz4AF/FastTree-2.1.3.c 2013-03-23 09:09:04,001 - lib.util - INFO - Compiling fasttree 2013-03-23 09:09:21,219 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:09:36,166 - lib.application - INFO - Successfully compiled fasttree. 2013-03-23 09:09:36,172 - lib.application - INFO - Successfully copied fasttree directory. 2013-03-23 09:09:36,173 - lib.deploy - INFO - Deploy of fasttree succeeded. 2013-03-23 09:09:36,173 - lib.application - INFO - Deploying app: bwa 2013-03-23 09:09:36,173 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/bwa-0.6.2-release 2013-03-23 09:09:41,772 - lib.application - INFO - Downloading bwa 2013-03-23 09:09:41,772 - lib.util - INFO - Downloading http://downloads.sourceforge.net/project/bio-bwa/bwa-0.6.2.tar.bz2 2013-03-23 09:09:46,262 - lib.application - INFO - Unzip succeeded: /tmp/tmp7Mt3Ae/bwa-0.6.2.tar.bz2 2013-03-23 09:09:46,263 - lib.util - INFO - Compiling bwa 2013-03-23 09:09:51,249 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:10:15,316 - lib.util - INFO - Compiling infernal 2013-03-23 09:10:21,279 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:10:51,309 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:11:21,340 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:11:51,362 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:12:21,382 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:12:51,413 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:13:01,425 - lib.application - INFO - Successfully made bwa. 2013-03-23 09:13:01,461 - lib.application - INFO - Successfully copied bwa directory. 2013-03-23 09:13:01,468 - lib.deploy - INFO - Deploy of bwa succeeded. 2013-03-23 09:13:01,469 - lib.application - INFO - Deploying app: pplacer 2013-03-23 09:13:01,469 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/pplacer-1.1-release 2013-03-23 09:13:02,436 - lib.application - INFO - Downloading pplacer 2013-03-23 09:13:02,436 - lib.util - INFO - Downloading http://matsen.fhcrc.org/pplacer/builds/pplacer-v1.1-Linux.tar.gz 2013-03-23 09:13:21,423 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:13:51,453 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:14:18,466 - lib.application - INFO - Unzip succeeded: /tmp/tmpwoaSLX/pplacer-v1.1-Linux.tar.gz 2013-03-23 09:14:18,888 - lib.application - INFO - Successfully copied pplacer directory. 2013-03-23 09:14:18,912 - lib.deploy - INFO - Deploy of pplacer succeeded. 2013-03-23 09:14:18,912 - lib.application - INFO - Deploying app: blast 2013-03-23 09:14:18,912 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/blast-2.2.22-release 2013-03-23 09:14:18,913 - lib.application - INFO - Downloading blast 2013-03-23 09:14:18,913 - lib.util - INFO - Downloading ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.22/blast-2.2.22-x64-linux.tar.gz 2013-03-23 09:14:21,484 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:14:51,511 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:14:51,861 - lib.application - INFO - Unzip succeeded: /tmp/tmpY6Sjoe/cytoscapeSource-v2.7.0.tar.gz 2013-03-23 09:15:21,541 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:15:45,464 - lib.application - INFO - Unzip succeeded: /tmp/tmpJN6lbM/blast-2.2.22-x64-linux.tar.gz 2013-03-23 09:15:51,557 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:16:18,550 - lib.application - INFO - Successfully copied blast directory. 2013-03-23 09:16:19,097 - lib.deploy - INFO - Deploy of blast succeeded. 2013-03-23 09:16:19,099 - lib.application - INFO - Deploying app: qiime_test_data 2013-03-23 09:16:19,100 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/qiime_test_data-1.6.0-repository-101a2b9b 2013-03-23 09:16:19,364 - lib.application - INFO - Downloading qiime_test_data 2013-03-23 09:16:19,364 - lib.util - INFO - Cloning git://github.com/qiime/qiime_test_data.git to /tmp/tmpVsJZFm 2013-03-23 09:16:21,568 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:16:51,591 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:17:21,621 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:17:51,651 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:18:21,657 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:18:51,688 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:18:57,167 - lib.application - INFO - Unzip succeeded: /tmp/tmpKciTpL/microbiomeutil_2010-04-29.tar.gz 2013-03-23 09:18:57,167 - lib.util - INFO - Compiling chimeraslayer 2013-03-23 09:19:21,718 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:19:51,747 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:20:03,913 - lib.application - INFO - Successfully made chimeraslayer. 2013-03-23 09:20:21,759 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:20:51,783 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:21:21,808 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:21:51,832 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:22:21,855 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:22:51,883 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:23:21,907 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:23:51,936 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:24:21,963 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:24:51,991 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:25:22,019 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:25:52,023 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:26:22,051 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:26:52,079 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:27:22,101 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:27:52,131 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:28:19,126 - lib.application - INFO - Unzip succeeded: /tmp/tmpZuzRDL/gg_12_10_otus.tar.gz 2013-03-23 09:28:22,159 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:28:52,189 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:29:22,219 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:29:52,250 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:30:22,280 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:30:52,311 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:31:22,339 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:31:52,369 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:32:07,340 - lib.util - INFO - Installing infernal 2013-03-23 09:32:22,372 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:32:41,835 - lib.application - INFO - Successfully built infernal. 2013-03-23 09:32:52,403 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:33:22,433 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:33:52,464 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:34:22,494 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:34:52,524 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:35:22,555 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:35:45,959 - lib.deploy - INFO - Deploy of infernal succeeded. 2013-03-23 09:35:45,960 - lib.application - INFO - Deploying app: parsinsert 2013-03-23 09:35:45,960 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/parsinsert-1.0.4-release 2013-03-23 09:35:46,108 - lib.application - INFO - Downloading parsinsert 2013-03-23 09:35:46,108 - lib.util - INFO - Downloading http://downloads.sourceforge.net/project/parsinsert/ParsInsert.1.04.tgz 2013-03-23 09:35:52,583 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:36:20,752 - lib.application - INFO - Unzip succeeded: /tmp/tmp8lxarI/ParsInsert.1.04.tgz 2013-03-23 09:36:20,752 - lib.util - INFO - Compiling parsinsert 2013-03-23 09:36:22,614 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:36:52,644 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:37:22,671 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:37:51,902 - lib.application - INFO - Successfully copied chimeraslayer directory. 2013-03-23 09:37:52,701 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:37:52,731 - lib.application - INFO - Successfully made parsinsert. 2013-03-23 09:37:52,987 - lib.application - INFO - Successfully copied parsinsert directory. 2013-03-23 09:37:52,993 - lib.deploy - INFO - Deploy of parsinsert succeeded. 2013-03-23 09:37:52,993 - lib.application - INFO - Deploying app: rdpclassifier 2013-03-23 09:37:52,993 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/rdpclassifier-2.2-release 2013-03-23 09:37:53,094 - lib.application - INFO - Downloading rdpclassifier 2013-03-23 09:37:53,095 - lib.util - INFO - Downloading http://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.2.zip 2013-03-23 09:37:53,636 - lib.deploy - INFO - Deploy of chimeraslayer succeeded. 2013-03-23 09:37:53,636 - lib.application - INFO - Deploying app: r 2013-03-23 09:37:53,636 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/r-2.12.0-release 2013-03-23 09:37:53,637 - lib.application - INFO - Downloading r 2013-03-23 09:37:53,637 - lib.util - INFO - Downloading http://cran.case.edu/src/base/R-2/R-2.12.0.tar.gz 2013-03-23 09:38:22,732 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:38:52,762 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:39:19,934 - lib.application - INFO - Unzip succeeded: /tmp/tmpH4fQsG/rdp_classifier_2.2.zip 2013-03-23 09:39:22,791 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:39:37,007 - lib.application - INFO - Successfully copied rdpclassifier directory. 2013-03-23 09:39:41,122 - lib.deploy - INFO - Deploy of rdpclassifier succeeded. 2013-03-23 09:39:41,123 - lib.application - INFO - Deploying app: muscle 2013-03-23 09:39:41,123 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/muscle-3.8.31-release 2013-03-23 09:39:41,123 - lib.application - INFO - Downloading muscle 2013-03-23 09:39:41,124 - lib.util - INFO - Downloading http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz 2013-03-23 09:39:52,821 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:39:53,106 - lib.application - INFO - Unzip succeeded: /tmp/tmpbCElpn/muscle3.8.31_i86linux64.tar.gz 2013-03-23 09:39:53,114 - lib.application - INFO - Successfully copied muscle directory. 2013-03-23 09:39:53,114 - lib.application - INFO - Executing post bash commands for muscle 2013-03-23 09:39:53,608 - lib.application - INFO - muscle post bash commands succeeded 2013-03-23 09:39:53,610 - lib.deploy - INFO - Deploy of muscle succeeded. 2013-03-23 09:39:53,611 - lib.application - INFO - Deploying app: cdhit 2013-03-23 09:39:53,612 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/cdhit-3.1-release 2013-03-23 09:39:53,612 - lib.application - INFO - Downloading cdhit 2013-03-23 09:39:53,613 - lib.util - INFO - Downloading ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/cd-hit-2007-0131.tgz 2013-03-23 09:40:02,210 - lib.application - INFO - Unzip succeeded: /tmp/tmp4AAGn4/R-2.12.0.tar.gz 2013-03-23 09:40:02,210 - lib.util - INFO - Configuring r 2013-03-23 09:40:03,665 - lib.application - INFO - Unzip succeeded: /tmp/tmpkYogyf/cd-hit-2007-0131.tar.gz 2013-03-23 09:40:03,665 - lib.util - INFO - Compiling cdhit 2013-03-23 09:40:22,852 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:40:48,537 - lib.application - INFO - Successfully made cdhit. 2013-03-23 09:40:48,641 - lib.application - INFO - Successfully copied cdhit directory. 2013-03-23 09:40:48,644 - lib.deploy - INFO - Deploy of cdhit succeeded. 2013-03-23 09:40:48,644 - lib.application - INFO - Deploying app: uclust 2013-03-23 09:40:48,644 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/uclust-1.2.22-release 2013-03-23 09:40:48,644 - lib.application - INFO - Downloading uclust 2013-03-23 09:40:48,644 - lib.util - INFO - Downloading http://drive5.com/uclust/uclustq1.2.22_i86linux64 2013-03-23 09:40:52,882 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:41:02,288 - lib.application - INFO - Unzip succeeded: /tmp/tmpFMp6Yq/uclustq1.2.22_i86linux64 2013-03-23 09:41:05,467 - lib.deploy - INFO - Deploy of uclust succeeded. 2013-03-23 09:41:22,912 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:41:35,840 - lib.util - INFO - Installing vienna 2013-03-23 09:41:52,943 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:42:22,971 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:42:53,001 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:43:23,026 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:43:27,659 - lib.application - INFO - Successfully built vienna. 2013-03-23 09:43:53,046 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:44:04,940 - lib.deploy - INFO - Deploy of vienna succeeded. 2013-03-23 09:44:23,067 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:44:53,097 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:45:23,127 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:45:53,139 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:46:03,898 - lib.application - INFO - Successfully copied cytoscape directory. 2013-03-23 09:46:23,170 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:46:53,199 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:47:23,218 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:47:53,238 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:48:23,267 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:48:26,591 - lib.application - INFO - Successfully copied gg_otus directory. 2013-03-23 09:48:53,298 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:49:02,508 - lib.deploy - INFO - Deploy of gg_otus succeeded. 2013-03-23 09:49:17,696 - lib.util - INFO - Compiling r 2013-03-23 09:49:23,328 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:49:53,354 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:50:23,383 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:50:38,400 - lib.application - INFO - Successfully copied qiime_test_data directory. 2013-03-23 09:50:53,413 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:51:00,565 - lib.deploy - INFO - Deploy of qiime_test_data succeeded. 2013-03-23 09:51:23,443 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:51:53,471 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:52:23,499 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:52:32,235 - lib.deploy - INFO - Deploy of cytoscape succeeded. 2013-03-23 09:52:53,527 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:53:23,555 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:53:53,583 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:54:23,606 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:54:53,635 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:55:23,663 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:55:53,691 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:56:23,719 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:56:53,747 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:57:19,183 - lib.util - INFO - Installing r 2013-03-23 09:57:23,762 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:57:25,385 - lib.application - INFO - Successfully built r. 2013-03-23 09:57:48,153 - lib.deploy - INFO - Deploy of r succeeded. 2013-03-23 09:57:52,905 - lib.application - INFO - Deploying app: ape 2013-03-23 09:57:52,905 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/ape-latest-r-package sh: 0: getcwd() failed: No such file or directory 2013-03-23 09:57:52,908 - lib.application - INFO - Deploying app: r-color-brewer 2013-03-23 09:57:52,908 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/r-color-brewer-latest-r-package sh: 0: getcwd() failed: No such file or directory 2013-03-23 09:57:52,927 - lib.application - INFO - Deploying app: klar 2013-03-23 09:57:52,928 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/klar-latest-r-package sh: 0: getcwd() failed: No such file or directory 2013-03-23 09:57:52,937 - lib.application - INFO - Deploying app: vegan 2013-03-23 09:57:52,937 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/vegan-latest-r-package 2013-03-23 09:57:52,938 - lib.application - INFO - Deploying app: random-forest 2013-03-23 09:57:52,939 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/random-forest-latest-r-package 2013-03-23 09:57:52,939 - lib.application - INFO - Deploying app: gtools 2013-03-23 09:57:52,941 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/gtools-latest-r-package sh: 0: getcwd() failed: No such file or directory sh: 0: getcwd() failed: No such file or directory sh: 0: getcwd() failed: No such file or directory 2013-03-23 09:57:53,791 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:58:01,231 - lib.deploy - INFO - Deploy of r-color-brewer succeeded. 2013-03-23 09:58:01,232 - lib.application - INFO - Deploying app: optparse 2013-03-23 09:58:01,232 - lib.application - INFO - Making deploy directory: /home/boonyeoh/qiime_software/optparse-latest-r-package sh: 0: getcwd() failed: No such file or directory 2013-03-23 09:58:04,245 - lib.deploy - INFO - Deploy of gtools succeeded. 2013-03-23 09:58:07,203 - lib.deploy - INFO - Deploy of klar succeeded. 2013-03-23 09:58:08,929 - lib.deploy - INFO - Deploy of random-forest succeeded. 2013-03-23 09:58:10,085 - lib.deploy - INFO - Deploy of optparse succeeded. 2013-03-23 09:58:23,384 - lib.deploy - INFO - Deploy of vegan succeeded. 2013-03-23 09:58:23,819 - lib.deploy - INFO - Still deploying applications and data... 2013-03-23 09:58:28,076 - lib.deploy - INFO - Deploy of ape succeeded. 2013-03-23 09:58:58,110 - lib.util - INFO - Removing directory: /home/boonyeoh/qiime_software/python-2.7.3-release 2013-03-23 09:58:58,143 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/cython-0.17-release 2013-03-23 09:58:58,143 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/numpy-1.5.1-release 2013-03-23 09:58:58,143 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/pyzmq-2.1.9-release 2013-03-23 09:58:58,143 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/SQLAlchemy-0.7.1-release 2013-03-23 09:58:58,143 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/gdata-2.0.17-release 2013-03-23 09:58:58,143 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/tornado-2.2.1-release 2013-03-23 09:58:58,143 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/matplotlib-1.1.0-release 2013-03-23 09:58:58,143 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/ipython-latest-repository-d2354694 2013-03-23 09:58:58,144 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/setuptools-0.6c11-release 2013-03-23 09:58:58,144 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/mpi4py-1.2.2-release 2013-03-23 09:58:58,144 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/MySQL-python-1.2.3-release 2013-03-23 09:58:58,144 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/biom-format-1.1.1-release 2013-03-23 09:58:58,144 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/pycogent-1.5.3-release 2013-03-23 09:58:58,144 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/qiime-1.6.0-release 2013-03-23 09:58:58,144 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/sphinx-1.0.4-release 2013-03-23 09:58:58,144 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/pynast-1.2-release 2013-03-23 09:58:58,144 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/pprospector-1.0.1-release 2013-03-23 09:58:58,144 - lib.util - ERROR - Unable to remove directory: /home/boonyeoh/qiime_software/tax2tree-1.0-release 2013-03-23 09:58:58,145 - main - INFO - Generating activate.sh file 2013-03-23 09:59:02,944 - main - INFO - Generating new /home/boonyeoh/qiime_software/qiime_config file 2013-03-23 09:59:03,306 - main - INFO - Generated new /home/boonyeoh/qiime_software/qiime_config file

DEPLOYMENT SUMMARY

Packages deployed successfully: data-lanemask, blat, sourcetracker, rtax, clearcut, cdbtools, raxml, ampliconnoise, data-core, drisee, mothur, fasttree, bwa, pplacer, blast, infernal, parsinsert, chimeraslayer, rdpclassifier, muscle, cdhit, uclust, vienna, gg_otus, qiime_test_data, cytoscape, r, r-color-brewer, gtools, klar, random-forest, optparse, vegan, ape

Packages skipped (assumed successful):

Packages failed to deploy: python, cython, numpy, pyzmq, SQLAlchemy, gdata, tornado, matplotlib, ipython, setuptools, mpi4py, MySQL-python, biom-format, pycogent, qiime, sphinx, pynast, pprospector, tax2tree

jairideout commented 11 years ago

Are you running out of disk space in /tmp? Try monitoring your disk usage while qiime-deploy is running.

Also, are you using the latest version of the qiime-deploy and qiime-deploy-conf repositories? If not, try updating them first.

DrBeanie commented 11 years ago

Disk space appears to be fine. Using the latest qiime-deploy and qiime-deploy-conf. I am out of ideas

Is there a way to manually unpack, ./configure make make install python 2.7.3 and then take that step out of the qiime-deploy-conf script?

pdmars commented 11 years ago

Can you try setting the log level to DEBUG in your conf file and see if that provides any other information about the error?

On Mar 22, 2013, at 5:16 PM, DrBeanie notifications@github.com wrote:

Disk space appears to be fine. Using the latest qiime-deploy and qiime-deploy-conf. I am out of ideas

— Reply to this email directly or view it on GitHub.