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First draft to set user:group file permissions #3

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17 changes: 16 additions & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -101,6 +101,7 @@ docker run --rm ncbi/blast efetch -db protein -format fasta \

## Step 2. Make BLAST database
docker run --rm \
--user $(id -u):$(id -g) \
-v $HOME/blastdb_custom:/blast/blastdb_custom:rw \
-v $HOME/fasta:/blast/fasta:ro \
-w /blast/blastdb_custom \
Expand All @@ -111,6 +112,7 @@ docker run --rm \

## Step 3. Run BLAST+
docker run --rm \
--user $(id -u):$(id -g) \
-v $HOME/blastdb:/blast/blastdb:ro \
-v $HOME/blastdb_custom:/blast/blastdb_custom:ro \
-v $HOME/queries:/blast/queries:ro \
Expand Down Expand Up @@ -138,13 +140,15 @@ ls queries/P01349.fsa

## Download Protein Data Bank Version 5 database (pdb_v5)
docker run --rm \
--user $(id -u):$(id -g) \
-v $HOME/blastdb:/blast/blastdb:rw \
-w /blast/blastdb \
ncbi/blast \
update_blastdb.pl --source gcp pdb_v5

## Run BLAST+
docker run --rm \
--user $(id -u):$(id -g) \
-v $HOME/blastdb:/blast/blastdb:ro \
-v $HOME/blastdb_custom:/blast/blastdb_custom:ro \
-v $HOME/queries:/blast/queries:ro \
Expand Down Expand Up @@ -265,6 +269,7 @@ Below is a list of `docker run` command line [options](https://docs.docker.com/e
|`--rm`|Automatically remove the container when it exits|
|`--volume` , `-v`|Bind mount a volume|
|`--workdir` , `-w`| Working directory inside the container|
|`--user $(id -u):$(id -g) `|Set the user and group for files written by the docker image|

### Docker run command structure
*This section is optional.*
Expand All @@ -275,6 +280,7 @@ For this tutorial, it would be useful to understand the structure of a Docker co
docker run --rm ncbi/blast \
```
```
--user $(id -u):$(id -g) \
-v $HOME/blastdb_custom:/blast/blastdb_custom:rw \
-v $HOME/fasta:/blast/fasta:ro \
-w /blast/blastdb_custom \
Expand All @@ -287,7 +293,7 @@ docker run --rm ncbi/blast \

The first part of the command `docker run --rm ncbi/blast` is an instruction to run the docker image `ncbi/blast` and remove the container when the run is completed.

The second part of the command makes the query sequence data accessible in the container. [Docker bind mounts]( https://docs.docker.com/storage/bind-mounts/) uses `-v` to mount the local directories to directories inside the container and provide access permission rw (read and write) or ro (read only). For instance, assuming your subject sequences are stored in the $HOME/fasta directory on the local host, you can use the following parameter to make that directory accessible inside the container in /blast/fasta as a read-only directory `-v $HOME/fasta:/blast/fasta:ro`. The `-w /blast/blastdb_custom` flag sets the working directory inside the container.
The second part of the command makes the query sequence data accessible in the container and provides non-root user and group file permissions to files written by the container. [Docker bind mounts]( https://docs.docker.com/storage/bind-mounts/) uses `-v` to mount the local directories to directories inside the container and provide access permission rw (read and write) or ro (read only). For instance, assuming your subject sequences are stored in the $HOME/fasta directory on the local host, you can use the following parameter to make that directory accessible inside the container in /blast/fasta as a read-only directory `-v $HOME/fasta:/blast/fasta:ro`. The `-w /blast/blastdb_custom` flag sets the working directory inside the container.

The third part of the command is the BLAST+ command. In this case, it is executing makeblastdb to create BLAST database files.

Expand Down Expand Up @@ -366,6 +372,7 @@ docker run --rm ncbi/blast efetch -db protein -format fasta \

## Make BLAST database
docker run --rm \
--user $(id -u):$(id -g) \
-v $HOME/blastdb_custom:/blast/blastdb_custom:rw \
-v $HOME/fasta:/blast/fasta:ro \
-w /blast/blastdb_custom \
Expand Down Expand Up @@ -408,6 +415,7 @@ databases at this location.
```
## Download Protein Data Bank Version 5 database (pdb_v5)
docker run --rm \
--user $(id -u):$(id -g) \
-v $HOME/blastdb:/blast/blastdb:rw \
-w /blast/blastdb \
ncbi/blast \
Expand Down Expand Up @@ -437,6 +445,7 @@ mount provides access to the query sequence(s), and the fourth mount provides a

```
docker run --rm \
--user $(id -u):$(id -g) \
-v $HOME/blastdb:/blast/blastdb:ro \
-v $HOME/blastdb_custom:/blast/blastdb_custom:ro \
-v $HOME/queries:/blast/queries:ro \
Expand Down Expand Up @@ -530,6 +539,7 @@ docker run --rm ncbi/blast update_blastdb.pl --showall pretty --source gcp
## Download nt_v5 (nucleotide collection version 5) database
## This step takes approximately 10 min. The following command runs in the background.
docker run --rm \
--user $(id -u):$(id -g) \
-v $HOME/blastdb:/blast/blastdb:rw \
-w /blast/blastdb \
ncbi/blast \
Expand All @@ -553,6 +563,7 @@ ls -al $HOME/queries
## This command will take approximately 9 minutes to complete.
## Expected output size: 3.1 GB
docker run --rm \
--user $(id -u):$(id -g) \
-v $HOME/blastdb:/blast/blastdb:ro -v $HOME/blastdb_custom:/blast/blastdb_custom:ro \
-v $HOME/queries:/blast/queries:ro \
-v $HOME/results:/blast/results:rw \
Expand All @@ -564,6 +575,7 @@ docker run --rm \
## This command will take approximately 30 minutes to complete.
## Expected output size: 10.4 GB
docker run --rm \
--user $(id -u):$(id -g) \
-v $HOME/blastdb:/blast/blastdb:ro -v $HOME/blastdb_custom:/blast/blastdb_custom:ro \
-v $HOME/queries:/blast/queries:ro \
-v $HOME/results:/blast/results:rw \
Expand All @@ -575,6 +587,7 @@ docker run --rm \
## This command will take approximately 147 minutes to complete.
## Expected output size: 47.8 GB
docker run --rm \
--user $(id -u):$(id -g) \
-v $HOME/blastdb:/blast/blastdb:ro -v $HOME/blastdb_custom:/blast/blastdb_custom:ro \
-v $HOME/queries:/blast/queries:ro \
-v $HOME/results:/blast/results:rw \
Expand Down Expand Up @@ -639,6 +652,7 @@ __When to use__: This is useful for running a few (e.g., fewer than 5-10) BLAST

```
docker run --rm -it \
--user $(id -u):$(id -g) \
-v $HOME/blastdb:/blast/blastdb:ro -v $HOME/blastdb_custom:/blast/blastdb_custom:ro \
-v $HOME/queries:/blast/queries:ro \
-v $HOME/results:/blast/results:rw \
Expand Down Expand Up @@ -670,6 +684,7 @@ specified when the container is started.
```
# Start a container named 'blast' in detached mode
docker run --rm -dit --name blast \
--user $(id -u):$(id -g) \
-v $HOME/blastdb:/blast/blastdb:ro -v $HOME/blastdb_custom:/blast/blastdb_custom:ro \
-v $HOME/queries:/blast/queries:ro \
-v $HOME/results:/blast/results:rw \
Expand Down