Stand Alone version of SGN CRISPGET Tool
Developed on a Catalyst framework
unzip GCA_003287315.1.zip
in emacs, replace the string >lcl| with > , if present (otherwise, fastacmd will not work correctly)
Copy the dataset to the correct location, where the CRISPGET tool can see it. If using the docker, this target directory has to be mounted into the docker at /home/crispget_sequence_files/GCA_003287315.1/cds.
sudo cp ncbi_dataset/data/GCA_003287315.1/cds_from_genomic.fna /export/prod/blast/databases/current/crispget/Phytophthora_cactorum_GCA_003287315.1_cds.fa
Enter the docker and issue the following command to index the file for BLAST:
docker exec -it crispget_tool bash
cd /home/crispget_sequence_files/GCA_003287315.1/cds
sudo makeblastdb -in Phytophthora_cactorum_GCA_003287315.1_cds.fa -dbtype nucl -out Phytophthora_cactorum_GCA_003287315.1_cds -parse_seqids
Index the file for use with bowtie2:
sudo bowtie-build -f /export/prod/blast/databases/current/crispget/Phytophthora_cactorum_GCA_003287315.1_cds.fa /export/prod/blast/databases/current/crispget/Phytophthora_cactorum_GCA_003287315.1_cds
A docker build for the CRISPGET tool is available from docker hub and is the recommended installation method.
To install the CRISPGET tool, first install docker. Refer to the docker installation instructions on the Docker site.
In Debian, Ubuntu, PoP_OS, etc., install git using apt install git. On other platforms, use the respective packaging systems to install git.
To install the crispget_tool system, clone the git repository that contains the example docker-compose.yml file.
git clone https://github.com/solgenomics/CRISPGET
Run the crispget_tool from within the CRISPGET folder using:
docker build -t breedbase/crispget_tool_final:v0.01 .
docker-compose up --detach
By default, the CRISPGET interface will be available at localhost:8088.