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Downloading reference data using `data_fabfile.py` with the following command:
``` bash
fab -f data_fabfile.py -H localhost -c fabricrc.txt install_data_s3:biodata.yaml
```
fails at mm10 download:
…
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This is not an issue per se, but just an entry to provide context for the following commit:
https://github.com/citation-style-language/styles/commit/36eb37bb43c22879613f1312d8041dac42d72607.
Here is …
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Hello,
We have just installed bcbio-nextgen (0.7.8) and tried the RNAseq pipeline. Everything seems to have gone well, with two exceptions:
1) The STAR alignment step failed on the first try because…
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install runs fine if I manually create /mnt/biodata/genomes, and chown it to ubuntu before restarting it. My quick grep of the code didn't reveal unto me the source of the issue, but the log follows …
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python bcbio_nextgen_install.py ... --aligners star failed.
I suspect there is issues somewhere in cloudbiolinux with variable: genome_indexes : 'genome_indexes': ['bwa', 'star', 'seq', 'bowtie', 'b…
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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-inst…
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Hi Brad,
Brandon from UCSF again. Pulled your development code again today and ran into an IndexError in bcbio/pipeline/genome.py in the parts list that broke the run. Looking into this, both the v…
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I followed the steps on
https://bcbio-nextgen.readthedocs.org/en/latest/contents/installation.html#on-a-virtual-machine
to install bcbio-nextgen on a virtual machine. I downloaded virtualbox and vag…
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First!
Anyways, I tried the install as discussed. As I don't have root access I tried using Anaconda and followed Rory's instructions here https://github.com/chapmanb/bcbio-nextgen/issues/147 to set …
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Hello,
I am trying out the pipeline for my own data but I am not sure what is the best way to do it. We did two sequencing batches, where some samples failed to be sequenced twice. We want to find ho…