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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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biodata.yaml missing? #53

Closed davidhoover closed 11 years ago

davidhoover commented 11 years ago

I was trying to add other genome builds to my bcbio-nextgen installation, and I am getting this error:

IOError: [Errno 2] No such file or directory: '/usr/local/apps/bcbio-nextgen/0.6.5/tmpbcbio-install/cloudbiolinux/config/biodata.yaml'

The website that the documentation links to is broken:

https://github.com/chapmanb/cloudbiolinux/blob/master/config/biodata.yaml

What is happening?

chapmanb commented 11 years ago

David; Apologies, this was mistakenly removed from the cloudbiolinux repository while doing other work. If you do:

rm -rf /usr/local/apps/bcbio-nextgen/0.6.5/tmpbcbio-install/cloudbiolinux/

and then re-run the installer, it should work again. Thanks for the report and sorry again about the problem.

davidhoover commented 11 years ago

That did the trick.

However, now I have a slightly different problem. Once I got the data to start downloading, I got this error:

$ python bcbio_nextgen_install.py --genomes mm9 --nosudo --distribution centos --notools tooldir datadir ... INFO: Downloading genome mm9 to /usr/local/apps/bcbio-nextgen/0.6.5/datadir/genomes/Mmusculus/mm9 [localhost] run: wget --no-check-certificate https://s3.amazonaws.com/biodata/genomes/mm9-bowtie2.tar.xz [localhost] out: --2013-07-16 13:47:32-- https://s3.amazonaws.com/biodata/genomes/mm9-bowtie2.tar.xz [localhost] out: Resolving s3.amazonaws.com... 207.171.163.131 [localhost] out: Connecting to s3.amazonaws.com|207.171.163.131|:443... connected. [localhost] out: HTTP request sent, awaiting response... 404 Not Found [localhost] out: 2013-07-16 13:47:32 ERROR 404: Not Found. [localhost] out: [localhost] out:

Fatal error: run() received nonzero return code 1 while executing!

Requested: wget --no-check-certificate https://s3.amazonaws.com/biodata/genomes/mm9-bowtie2.tar.xz Executed: /bin/bash --noprofile -i -l -c "cd /usr/local/apps/bcbio-nextgen/0.6.5/datadir/genomes/Mmusculus/mm9 && wget --no-check-certificate https://s3.amazonaws.com/biodata/genomes/mm9-bowtie2.tar.xz"

Aborting.

It would be much better if there was a pipeline available for taking a genome reference fasta file and generate the indexes locally, instead of relying on Amazon to have it.

David

On Jul 16, 2013, at 12:43 PM, Brad Chapman wrote:

David; Apologies, this was mistakenly removed from the cloudbiolinux repository while doing other work. If you do:

rm -rf /usr/local/apps/bcbio-nextgen/0.6.5/tmpbcbio-install/cloudbiolinux/

and then re-run the installer, it should work again. Thanks for the report and sorry again about the problem.

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

chapmanb commented 11 years ago

David; Thanks for the heads up. Mouse support is still in progress right now, so not all of the indices are present. We do have code for generating indexes locally; I will work on adding that as a backup in case of missing S3 indices. I'll reopen this as a ticket since that will take some work.

chapmanb commented 11 years ago

David; The latest version of installer (0.7.0) provides local indexing if the S3 download fails or is unavailable for a particular organism/aligner combination. It works by first trying S3, then falling back to the local index command if it fails. Thanks for these suggestions, much appreciated.