Accessing CRAMs on UKBiobank for testing

Note : Do not use the code in the zip with the v1.0 release it is broken. The docker image provided can still be used if when running the docker image a git pull and make command are run to make the most recent version of the tool. See the example below.

• The -t option is for number of threads (put 0 to let it choose).
• The --cram-path option is to specify a directory where there are CRAM files, the software will do random accesses in those files.
• Replace the path in -iimage_file to where your docker image is (you can download it here).
• Note : the repo is pulled and the cram accessor is built in the command below, to make sure the most recent version of the code is used

dx run swiss-army-knife -icmd="echo \"$(date)\"; cd /usr/src/cram_accessor/; git pull; make; time ./cram_accessor -t 12 --cram-path \"/mnt/project/Bulk/Whole genome sequences/Whole genome CRAM files/20\"" \
    --name CRAM_Accessor \
    -iimage_file=docker/cram_accessor_v1.0.tar.gz \
    --instance-type mem2_ssd1_v2_x4 -y

cd Docker
docker build -t cram_accessor:v1.0 .
# Takes some time !
time docker save cram_accessor:v1.0 | gzip > cram_accessor_v1.0.tar.gz

If you don't have HTSLIB

git submodule update --init --recursive htslib
cd htslib
autoreconf -i
./configure
make
make install
ldconfig
cd ..
make

If you have it installed, either :

git submodule update --init --recursive htslib
cd htslib
autoreconf -i
./configure
make
cd ..
make

or :

# Edit the Makefile and set the correct paths
make