diff --git a/cloud/docker/README.md b/cloud/docker/README.md index 85dfa1e..ea96f9a 100644 --- a/cloud/docker/README.md +++ b/cloud/docker/README.md @@ -52,7 +52,7 @@ If there's an image that you want to run, like one of the ones from [BioCurious' Because the organization is `biocurious`, the repo is `sra-tools`, and the tag is `2.9.0`, the image would be named `biocurious/sra-tools:2.9.0` and you would use it like so: ``` -docker run biocurious/sra-tools:2.9.0 /usr/local/ncbi/sra-tools/bin/fastq-dump +docker run biocurious/sra-tools:2.9.0 fastq-dump ``` ## Building images yourself diff --git a/docs/bioinformatics/pichia_pipeline.md b/docs/bioinformatics/pichia_pipeline.md index 795c041..39f0a00 100644 --- a/docs/bioinformatics/pichia_pipeline.md +++ b/docs/bioinformatics/pichia_pipeline.md @@ -58,7 +58,7 @@ default location, your home directory, to a partition were there is ample space. the quality of raw NGS sequencing data. ``` -docker run -i --rm -t -v $BIO_DATA:/data \ +docker run -i --rm -t -v $BIO_DATA:/data biocurious/fastqc:0.11.7 \ /data/pichia/ERR1294016_1.fastq.gz \ /data/pichia/ERR1294016_2.fastq.gz \ -o /data/pichia/fastqc diff --git a/docs/data-management.md b/docs/data-management.md new file mode 100644 index 0000000..41fd453 --- /dev/null +++ b/docs/data-management.md @@ -0,0 +1,13 @@ +# S3 buckets + +The S3 buckets use the prefix `bioc-cf` for "BioCurious Cuttlefish". If you need access to them, ask at the meetups or in Slack and someone will help you out. + +- `bioc-cf-reference`: Reference data used in the cuttlefish project (e.g. sequences for comparable organisms). +- `bioc-cf-supplemental`: Stuff that would be in the supplemental section of a paper. Our eventual cuttlefish sequences, etc. +- `bioc-temp`: Temporary data. Contents are deleted automatically after 60 days. +- More can be created if further organization is helpful. + +There are different IAM roles you can be in, depending on your needs. + +- `researcher`: If you just need somewhere to store files temporarily that's not your hard drive. This will let you write to `bioc-temp` and read other buckets. +- `curator`: Everything in `researcher`, plus write access to other buckets.