Add a note about where our S3 buckets live. Also, tweak docker docs.

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 <other docker args> biocurious/sra-tools:2.9.0 /usr/local/ncbi/sra-tools/bin/fastq-dump <fastq-dump args>
+docker run <other docker args> biocurious/sra-tools:2.9.0 fastq-dump <fastq-dump args>
 ```
 
 ## Building images yourself

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 <fastqc image id>\
+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

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.