chapmanb
commented
11 years ago Hi; Thanks for reporting this. It looks like the issue is that numpy setup.py tries to use /dev/null and the easy_install machinery flags this as a sandbox violation (incorrectly, since it's just dumping output to /dev/null). The best fix for this is to use pip, with:
pip install .from the bcbio-nextgen directory. The underlying issue is that easy_install and pip use different installation infrastructure. The community is generally moving towards pip, but I wish the installation story with python were cleaner.
A couple other approaches would also work. You can use the supplied installer with:
python bcbio_nextgen_install.py tooldir datadir --notools --nodata --nosudoto install this into a clean virtualenv without any of the other tools or data files. This lets you upgrade in place with:
bcbio_nextgen.py -u release
bcbio_nextgen.py -u developmentto get the latest release or GitHub version, respectively and avoids all these issues.
Finally, I'm hoping to remove the hard numpy dependency since it's a large package and I use it only for some simple stats calculations.
Hope one of those helps. Let me know if not. Thanks again, Brad
billyziege
I've installed previous versions (last version was about 3 weeks ago) of the pipeline using the following commands in the bcbio-nextgen directory:
python setup.py build python setup.py install
However, there is now a
error: SandboxViolation: open('/dev/null', 'w') {}
during the install, and the error further suggests EasyInstall is trying to access regions outside the build area and that I flag it as an issue. Incidentally, I can run
pip install numpy
so I am assuming that the problem may lie in the setup.py. I apologize in advance if this is an issue with my version of easy_install or some other python package.
Thanks!
The full output is below:
running install running bdist_egg running egg_info writing requirements to bcbio_nextgen.egg-info/requires.txt writing bcbio_nextgen.egg-info/PKG-INFO writing namespace_packages to bcbio_nextgen.egg-info/namespace_packages.txt writing top-level names to bcbio_nextgen.egg-info/top_level.txt writing dependency_links to bcbio_nextgen.egg-info/dependency_links.txt reading manifest file 'bcbio_nextgen.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.md' writing manifest file 'bcbio_nextgen.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/bcbio copying build/lib/bcbio/utils.py -> build/bdist.linux-x86_64/egg/bcbio copying build/lib/bcbio/init.py -> build/bdist.linux-x86_64/egg/bcbio creating build/bdist.linux-x86_64/egg/bcbio/upload copying build/lib/bcbio/upload/s3.py -> build/bdist.linux-x86_64/egg/bcbio/upload copying build/lib/bcbio/upload/shared.py -> build/bdist.linux-x86_64/egg/bcbio/upload copying build/lib/bcbio/upload/filesystem.py -> build/bdist.linux-x86_64/egg/bcbio/upload copying build/lib/bcbio/upload/galaxy.py -> build/bdist.linux-x86_64/egg/bcbio/upload copying build/lib/bcbio/upload/init.py -> build/bdist.linux-x86_64/egg/bcbio/upload creating build/bdist.linux-x86_64/egg/bcbio/distributed copying build/lib/bcbio/distributed/ipythontasks.py -> build/bdist.linux-x86_64/egg/bcbio/distributed copying build/lib/bcbio/distributed/split.py -> build/bdist.linux-x86_64/egg/bcbio/distributed copying build/lib/bcbio/distributed/ipython.py -> build/bdist.linux-x86_64/egg/bcbio/distributed copying build/lib/bcbio/distributed/manage.py -> build/bdist.linux-x86_64/egg/bcbio/distributed copying build/lib/bcbio/distributed/transaction.py -> build/bdist.linux-x86_64/egg/bcbio/distributed copying build/lib/bcbio/distributed/lsf.py -> build/bdist.linux-x86_64/egg/bcbio/distributed copying build/lib/bcbio/distributed/multitasks.py -> build/bdist.linux-x86_64/egg/bcbio/distributed copying build/lib/bcbio/distributed/messaging.py -> build/bdist.linux-x86_64/egg/bcbio/distributed copying build/lib/bcbio/distributed/sge.py -> build/bdist.linux-x86_64/egg/bcbio/distributed copying build/lib/bcbio/distributed/init.py -> build/bdist.linux-x86_64/egg/bcbio/distributed copying build/lib/bcbio/distributed/tasks.py -> build/bdist.linux-x86_64/egg/bcbio/distributed creating build/bdist.linux-x86_64/egg/bcbio/broad copying build/lib/bcbio/broad/metrics.py -> build/bdist.linux-x86_64/egg/bcbio/broad copying build/lib/bcbio/broad/picardrun.py -> build/bdist.linux-x86_64/egg/bcbio/broad copying build/lib/bcbio/broad/init.py -> build/bdist.linux-x86_64/egg/bcbio/broad creating build/bdist.linux-x86_64/egg/bcbio/structural copying build/lib/bcbio/structural/hydra.py -> build/bdist.linux-x86_64/egg/bcbio/structural copying build/lib/bcbio/structural/init.py -> build/bdist.linux-x86_64/egg/bcbio/structural creating build/bdist.linux-x86_64/egg/bcbio/hmmer copying build/lib/bcbio/hmmer/search.py -> build/bdist.linux-x86_64/egg/bcbio/hmmer copying build/lib/bcbio/hmmer/init.py -> build/bdist.linux-x86_64/egg/bcbio/hmmer creating build/bdist.linux-x86_64/egg/bcbio/log copying build/lib/bcbio/log/init.py -> build/bdist.linux-x86_64/egg/bcbio/log creating build/bdist.linux-x86_64/egg/bcbio/galaxy copying build/lib/bcbio/galaxy/api.py -> build/bdist.linux-x86_64/egg/bcbio/galaxy copying build/lib/bcbio/galaxy/init.py -> build/bdist.linux-x86_64/egg/bcbio/galaxy creating build/bdist.linux-x86_64/egg/bcbio/ngsalign copying build/lib/bcbio/ngsalign/tophat.py -> build/bdist.linux-x86_64/egg/bcbio/ngsalign copying build/lib/bcbio/ngsalign/novoalign.py -> build/bdist.linux-x86_64/egg/bcbio/ngsalign copying build/lib/bcbio/ngsalign/split.py -> build/bdist.linux-x86_64/egg/bcbio/ngsalign copying build/lib/bcbio/ngsalign/bowtie.py -> build/bdist.linux-x86_64/egg/bcbio/ngsalign copying build/lib/bcbio/ngsalign/bwa.py -> build/bdist.linux-x86_64/egg/bcbio/ngsalign copying build/lib/bcbio/ngsalign/bowtie2.py -> build/bdist.linux-x86_64/egg/bcbio/ngsalign copying build/lib/bcbio/ngsalign/mosaik.py -> build/bdist.linux-x86_64/egg/bcbio/ngsalign copying build/lib/bcbio/ngsalign/init.py -> build/bdist.linux-x86_64/egg/bcbio/ngsalign creating build/bdist.linux-x86_64/egg/bcbio/bam copying build/lib/bcbio/bam/callable.py -> build/bdist.linux-x86_64/egg/bcbio/bam copying build/lib/bcbio/bam/trim.py -> build/bdist.linux-x86_64/egg/bcbio/bam copying build/lib/bcbio/bam/fastq.py -> build/bdist.linux-x86_64/egg/bcbio/bam copying build/lib/bcbio/bam/cram.py -> build/bdist.linux-x86_64/egg/bcbio/bam copying build/lib/bcbio/bam/init.py -> build/bdist.linux-x86_64/egg/bcbio/bam copying build/lib/bcbio/bam/counts.py -> build/bdist.linux-x86_64/egg/bcbio/bam creating build/bdist.linux-x86_64/egg/bcbio/solexa copying build/lib/bcbio/solexa/samplesheet.py -> build/bdist.linux-x86_64/egg/bcbio/solexa copying build/lib/bcbio/solexa/flowcell.py -> build/bdist.linux-x86_64/egg/bcbio/solexa copying build/lib/bcbio/solexa/init.py -> build/bdist.linux-x86_64/egg/bcbio/solexa creating build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/alignment.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/demultiplex.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/lane.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/sample.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/region.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/run_info.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/cleanbam.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/shared.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/fastq.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/variation.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/config_utils.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/qcsummary.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/init.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/main.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/storage.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/merge.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline copying build/lib/bcbio/pipeline/toplevel.py -> build/bdist.linux-x86_64/egg/bcbio/pipeline creating build/bdist.linux-x86_64/egg/bcbio/rnaseq copying build/lib/bcbio/rnaseq/cufflinks.py -> build/bdist.linux-x86_64/egg/bcbio/rnaseq copying build/lib/bcbio/rnaseq/init.py -> build/bdist.linux-x86_64/egg/bcbio/rnaseq copying build/lib/bcbio/rnaseq/count.py -> build/bdist.linux-x86_64/egg/bcbio/rnaseq creating build/bdist.linux-x86_64/egg/bcbio/variation copying build/lib/bcbio/variation/effects.py -> build/bdist.linux-x86_64/egg/bcbio/variation copying build/lib/bcbio/variation/phasing.py -> build/bdist.linux-x86_64/egg/bcbio/variation copying build/lib/bcbio/variation/split.py -> build/bdist.linux-x86_64/egg/bcbio/variation copying build/lib/bcbio/variation/freebayes.py -> build/bdist.linux-x86_64/egg/bcbio/variation copying build/lib/bcbio/variation/ensemble.py -> build/bdist.linux-x86_64/egg/bcbio/variation copying build/lib/bcbio/variation/varscan.py -> build/bdist.linux-x86_64/egg/bcbio/variation copying build/lib/bcbio/variation/samtools.py -> build/bdist.linux-x86_64/egg/bcbio/variation copying build/lib/bcbio/variation/cortex.py -> build/bdist.linux-x86_64/egg/bcbio/variation copying build/lib/bcbio/variation/annotation.py -> build/bdist.linux-x86_64/egg/bcbio/variation copying build/lib/bcbio/variation/bamprep.py -> build/bdist.linux-x86_64/egg/bcbio/variation copying build/lib/bcbio/variation/multi.py -> build/bdist.linux-x86_64/egg/bcbio/variation copying build/lib/bcbio/variation/recalibrate.py -> build/bdist.linux-x86_64/egg/bcbio/variation copying build/lib/bcbio/variation/init.py -> build/bdist.linux-x86_64/egg/bcbio/variation copying build/lib/bcbio/variation/genotype.py -> build/bdist.linux-x86_64/egg/bcbio/variation copying build/lib/bcbio/variation/realign.py -> build/bdist.linux-x86_64/egg/bcbio/variation creating build/bdist.linux-x86_64/egg/bcbio/picard copying build/lib/bcbio/picard/metrics.py -> build/bdist.linux-x86_64/egg/bcbio/picard copying build/lib/bcbio/picard/utils.py -> build/bdist.linux-x86_64/egg/bcbio/picard copying build/lib/bcbio/picard/init.py -> build/bdist.linux-x86_64/egg/bcbio/picard creating build/bdist.linux-x86_64/egg/bcbio/workflow copying build/lib/bcbio/workflow/xprize.py -> build/bdist.linux-x86_64/egg/bcbio/workflow copying build/lib/bcbio/workflow/stormseq.py -> build/bdist.linux-x86_64/egg/bcbio/workflow copying build/lib/bcbio/workflow/init.py -> build/bdist.linux-x86_64/egg/bcbio/workflow byte-compiling build/bdist.linux-x86_64/egg/bcbio/utils.py to utils.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/upload/s3.py to s3.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/upload/shared.py to shared.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/upload/filesystem.py to filesystem.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/upload/galaxy.py to galaxy.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/upload/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/distributed/ipythontasks.py to ipythontasks.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/distributed/split.py to split.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/distributed/ipython.py to ipython.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/distributed/manage.py to manage.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/distributed/transaction.py to transaction.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/distributed/lsf.py to lsf.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/distributed/multitasks.py to multitasks.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/distributed/messaging.py to messaging.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/distributed/sge.py to sge.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/distributed/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/distributed/tasks.py to tasks.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/broad/metrics.py to metrics.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/broad/picardrun.py to picardrun.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/broad/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/structural/hydra.py to hydra.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/structural/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/hmmer/search.py to search.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/hmmer/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/log/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/galaxy/api.py to api.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/galaxy/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/ngsalign/tophat.py to tophat.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/ngsalign/novoalign.py to novoalign.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/ngsalign/split.py to split.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/ngsalign/bowtie.py to bowtie.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/ngsalign/bwa.py to bwa.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/ngsalign/bowtie2.py to bowtie2.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/ngsalign/mosaik.py to mosaik.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/ngsalign/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/bam/callable.py to callable.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/bam/trim.py to trim.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/bam/fastq.py to fastq.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/bam/cram.py to cram.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/bam/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/bam/counts.py to counts.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/solexa/samplesheet.py to samplesheet.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/solexa/flowcell.py to flowcell.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/solexa/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/alignment.py to alignment.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/demultiplex.py to demultiplex.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/lane.py to lane.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/sample.py to sample.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/region.py to region.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/run_info.py to run_info.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/cleanbam.py to cleanbam.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/shared.py to shared.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/fastq.py to fastq.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/variation.py to variation.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/config_utils.py to config_utils.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/qcsummary.py to qcsummary.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/main.py to main.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/storage.py to storage.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/merge.py to merge.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/pipeline/toplevel.py to toplevel.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/rnaseq/cufflinks.py to cufflinks.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/rnaseq/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/rnaseq/count.py to count.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/variation/effects.py to effects.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/variation/phasing.py to phasing.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/variation/split.py to split.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/variation/freebayes.py to freebayes.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/variation/ensemble.py to ensemble.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/variation/varscan.py to varscan.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/variation/samtools.py to samtools.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/variation/cortex.py to cortex.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/variation/annotation.py to annotation.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/variation/bamprep.py to bamprep.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/variation/multi.py to multi.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/variation/recalibrate.py to recalibrate.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/variation/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/variation/genotype.py to genotype.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/variation/realign.py to realign.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/picard/metrics.py to metrics.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/picard/utils.py to utils.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/picard/init.py to init.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/workflow/xprize.py to xprize.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/workflow/stormseq.py to stormseq.pyc byte-compiling build/bdist.linux-x86_64/egg/bcbio/workflow/init.py to init.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts running install_scripts running build_scripts creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/bcbio_nextgen.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/bam_to_wiggle.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/barcode_sort_trim.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/illumina_finished_msg.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/nextgen_analysis_server.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/solexa_qseq_to_fastq.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/bcbio_nextgen.py to 775 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/bam_to_wiggle.py to 775 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/barcode_sort_trim.py to 775 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/illumina_finished_msg.py to 775 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/nextgen_analysis_server.py to 775 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/solexa_qseq_to_fastq.py to 775 copying bcbio_nextgen.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying bcbio_nextgen.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying bcbio_nextgen.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying bcbio_nextgen.egg-info/namespace_packages.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying bcbio_nextgen.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying bcbio_nextgen.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... creating 'dist/bcbio_nextgen-0.6.3a-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing bcbio_nextgen-0.6.3a-py2.7.egg Removing /mnt/iscsi_speed/devel/pipeline/all_nodes_pipeline_env/lib/python2.7/site-packages/bcbio_nextgen-0.6.3a-py2.7.egg Copying bcbio_nextgen-0.6.3a-py2.7.egg to /mnt/iscsi_speed/devel/pipeline/all_nodes_pipeline_env/lib/python2.7/site-packages bcbio-nextgen 0.6.3a is already the active version in easy-install.pth Installing solexa_qseq_to_fastq.py script to /mnt/iscsi_speed/devel/pipeline/all_nodes_pipeline_env/bin Installing bam_to_wiggle.py script to /mnt/iscsi_speed/devel/pipeline/all_nodes_pipeline_env/bin Installing barcode_sort_trim.py script to /mnt/iscsi_speed/devel/pipeline/all_nodes_pipeline_env/bin Installing illumina_finished_msg.py script to /mnt/iscsi_speed/devel/pipeline/all_nodes_pipeline_env/bin Installing bcbio_nextgen.py script to /mnt/iscsi_speed/devel/pipeline/all_nodes_pipeline_env/bin Installing nextgen_analysis_server.py script to /mnt/iscsi_speed/devel/pipeline/all_nodes_pipeline_env/bin
Installed /mnt/iscsi_speed/devel/pipeline/all_nodes_pipeline_env/lib/python2.7/site-packages/bcbio_nextgen-0.6.3a-py2.7.egg Processing dependencies for bcbio-nextgen==0.6.3a Searching for numpy>=1.7.0 Reading http://pypi.python.org/simple/numpy/ Reading http://numpy.scipy.org Reading http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=175103 Reading http://www.numpy.org Reading http://sourceforge.net/projects/numpy/files/NumPy/ Reading http://numeric.scipy.org Best match: numpy 1.7.0 Downloading http://pypi.python.org/packages/source/n/numpy/numpy-1.7.0.zip#md5=ca27913c59393940e880fab420f985b4 Processing numpy-1.7.0.zip Running numpy-1.7.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-83_HXo/numpy-1.7.0/egg-dist-tmp-XJTB6D Running from numpy source directory. error: SandboxViolation: open('/dev/null', 'w') {}
The package setup script has attempted to modify files on your system that are not within the EasyInstall build area, and has been aborted.
This package cannot be safely installed by EasyInstall, and may not support alternate installation locations even if you run its setup script by hand. Please inform the package's author and the EasyInstall maintainers to find out if a fix or workaround is available.