README.md


git clone https://github.com/bioinformatics-ufsc/FastProtein
cd FastProtein
docker build -t bioinfoufsc/fastprotein:latest .
cd FastProtein
docker build --build-arg INTERPRO_INSTALL=Y -t bioinfoufsc/fastprotein-interproscan:latest .
   #Light version 900Mb compressed
   docker pull bioinfoufsc/fastprotein
   #Full version with interpro installed (don't need to execute Step 4, just change the image name in the end of the command)
   docker pull bioinfoufsc/fastprotein-interpro
   docker run -it --name FastProtein -p 5000:5000 bioinfoufsc/fastprotein:latest
   Login: admin
   Password: admin
# Step 1 - Create a local directory that will be used to exchange files with Docker (example FastProtein/ inside user home)
#          ~/FastProtein is the work directory
#          ~/FastProtein/runs the directory that stores the FastProtein web server requests
#
mkdir -p <your_home>/FastProtein/runs

# Step 2 - File sharing - If you are using MacOS you have to share your folder before go to Step 3
# Step 3 - Create a container named FastProtein that will have the volume associated with the locally created directory.
#          Port 5000 is used to access the FastProtein web server.
#          PS 1: this command is executed only one time and it will create and start your container
docker run -it --name FastProtein -p 5000:5000 -v <your_directory_output>:/FastProtein/runs bioinfoufsc/fastprotein:latest
# Step 3.1 - If you have InterProScan on your host, you can direct it to the FastProtein Docker InterProScan directory as follows.
#          The supported version is interproscan-5.61-93.0 (http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.61-93.0/interproscan-5.61-93.0-64-bit.tar.gz)
docker run -it --name FastProtein -p 5000:5000 -v <your_directory_output>:/FastProtein/runs -v <your_interpro_home>:/bioinformatic/interproscan-5.61-93.0 bioinfoufsc/fastprotein:latest
#
# Step 4 - InterProScan installation
#          This step may take ~1 hour total
docker exec -it FastProtein interpro_install

# The 'docker run' command starts the container for the first time.
# If everything runs without errors, open a browser and go to 127.0.0.1:5000 to access the FastProtein web.

# The following commands are for you to learn how to control a Docker container.
# If you want to STOP the container, the command is:
docker stop FastProtein
# If you want to START the container, the command is:
docker start FastProtein
# To check if your container is running, the command is:
docker ps | grep FastProtein
# If you want to enter inside the container, the command is:
docker exec -it FastProtein /bin/bash
# To exchange files between the host and the container without using a volume, use the command:
# docker cp <local_file> <container_id>:<container_file>
# E.g: copy a fasta file test/human.fasta to /FastProtein (or other directory if you need)
docker cp test/human.fasta FastProtein:/FastProtein
# E.g: copy the folder runs from container to local runs folder
docker cp FastProtein:/FastProtein/runs ./runs
## To learn about the execution parameters, type:
docker exec -it FastProtein fastprotein -h
## Example of execution:
##        input.fasta - proteins to analyze
##        db.fasta - database for blast search (protein FASTA)
##        result_test - local inside the container with the results (/fastprotein/result_test is linked with the local folder ~/fastprotein/result_test)
docker exec -it FastProtein fastprotein -i /example/input.fasta -db /example/db.fasta -o result_test
## Enter into container
docker exec -it FastProtein /bin/bash
##
## Execute the command:
fastprotein -h
##
## Simplest execution (the default output is fastprotein_results)
fastprotein -i /example/input.fasta
##
## Example of a complete execution (with InterproScan and Diamond [default]) with output in folder result_test
fastprotein -i /example/input.fasta -db /example/db.fasta --interpro -o result_test
##
## Example of a complete execution (with InterproScan and BlastP) with output in folder result_test
fastprotein -i /example/input.fasta -db /example/db.fasta -am blastp --interpro -o result_test
##
## The same example but with output in zip mode
fastprotein -i /example/input.fasta -db /example/db.fasta --interpro -o result_test --zip
  ## WoLFPSORT (output = <local_execution_folder>/wolfsort.out)
  docker exec -it FastProtein wolfpsort animal /example/input.fasta > wolfpsort.out
  ## SignalP5 (output = <local_execution_folder>/signalp.out)
  docker exec -it FastProtein signalp -fasta /example/input.fasta -stdout > signalp.out
  ##Phobius (output = <local_execution_folder>/phobius.out)
  docker exec -it FastProtein phobius -short /example/input.fasta > phobius.out
  #TMHMM2 (output = <local_execution_folder>/tmhmm.out)
  docker exec -it FastProtein tmhmm2 /example/input.fasta > tmhmm2.out
  #PredGPI (output = <local_execution_folder>/predgpi.out)
  docker exec -it FastProtein predgpi /example/input.fasta > predgpi.out
  #InterProScan5 (output = <shared_folder>/interpro.out)
  docker exec -it FastProtein interproscan -i /example/input.fasta -f tsv -o interpro.out --goterms