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![blake-mizerany](https://cloud.githubusercontent.com/assets/1052069/3406457/8ca4517e-fd8f-11e3-991d-2d7a9d8cd28b.png)
OR
Blake's Headshot:
https://avatars2.githubusercontent.com/u/46?s=460
Biodata…
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[root@banehallow cache]# nginx -V
nginx version: nginx/1.4.1
built by gcc 4.4.7 20120313 (Red Hat 4.4.7-3) (GCC)
TLS SNI support enabled
configure arguments: --prefix=/etc/nginx --sbin-path=/usr/sbi…
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As discussed with @roryk, I'm having problems with my Vagrant box when developing the `neuro` flavor:
```
$ pwd
/Users/roman/dev/cloudbiolinux
$ fab -f fabfile.py -H 127.0.0.1:2222 -c contrib/flavor/…
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Hi,
I finished the org-trello and trello.com authorization process which finishes with entering the token.
Then I created a new empty .org file and added the below to it
#+TODO: TODO DOING | DONE …
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Hi Brad/Rory/John,
I've been trying out bcbio_vm on AWS (tumor/normal calling on a couple BAMs from s3 bucket). I was able to set up and start a cluster, and ssh into the head-node to start the run. …
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Probably we have a link error ?
> bcbio_nextgen.py upgrade --aligners star --genomes GRCh37 --data
INFO: Downloading genome from s3: GRCh37 star
[localhost] local: pwd
[localhost] local: echo $HOME
…
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The Workbook Assistant is designed to deal with Excel workbooks, which consist of a flat list of sheets.
I suggest that the Workbook Assistant will only be used by WCA delegates from now on. The WCA …
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A similar problem to install but this is upgrade !!
> bcbio_nextgen.py upgrade -u stable --tools --data
> Error: Unsatisfiable package specifications
> Hint: numpy 1.7\* has a conflict with the remai…
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Seems that we have wrong url for snpEff database
> bcbio_vm.py --datadir=~/install/bcbio-vm/data install --data --tool
Sourceforce is temporary down
[2014-06-13 00:30] DEBUG: bcbio-nextgen-stdout…
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https://s3.amazonaws.com/biodata/genomes/GRCh37-star.tar.xz does not exists
and there may be some issues with the available genome_indexes: 'genome_indexes': ['bwa', 'star', 'seq', 'bowtie', 'bowtie,…