IMP db default path
The path to database is defaulted where IMP is launched.
For instance, when launching in my work directory, the database path is set to :/mnt/internal/work/users/snarayanasamy/Work/db
.
Isn't it better for the default setting to be in the IMP home directory? Below is the example.
E.g.:
$ pwd
/home/snarayanasamy/Work
$ python3.4 ~/Work/tools/IMP_new/IMP/IMP -m /mnt/md1200/snarayanasamy/IMP_data/TEST_DATA/MG.R1.5_percent.fq -m /mnt/md1200/snarayanasamy/IMP_data/TEST_DATA/MG.R1.5_percent.fq -t /mnt/md1200/snarayanasamy/IMP_data/TEST_DATA/MT.R1.5_percent.fq -t /mnt/md1200/snarayanasamy/IMP_data/TEST_DATA/MT.R2.5_percent.fq -o /home/snarayanasamy/Work/IMP_MGMT_TEST -c /home/snarayanasamy/Work/IMP_conf_files/userconfig.imp.json -a megahit --current
Executing " docker run -v /mnt/md1200/snarayanasamy/IMP_data/TEST_DATA:/home/imp/data -v /home/snarayanasamy/Work/IMP_MGMT_TEST:/home/imp/output -v /mnt/internal/work/users/snarayanasamy/Work/db:/home/imp/databases -v /home/snarayanasamy/Work/IMP_conf_files:/home/imp/conf -v /home/snarayanasamy/Work/tools/IMP_new/IMP:/home/imp/code -e MG="/home/imp/data/MG.R1.5_percent.fq /home/imp/data/MG.R1.5_percent.fq" -e MT="/home/imp/data/MT.R1.5_percent.fq /home/imp/data/MT.R2.5_percent.fq" -e CONFIGFILE=/home/imp/conf/userconfig.imp.json -e IMP_ASSEMBLER=megahit --rm -e "LOCAL_USER_ID=`id -u $USER`" -e "LOCAL_GROUP_ID=`id -g $USER`" --name home_snarayanasamy_Work_IMP_MGMT_TEST docker-r3lab.uni.lu/imp/imp:1.3 snakemake ALL -s /home/imp/code/Snakefile "
MissingInputException in line 1 of /home/imp/code/rules/Preprocessing/trimming.rules:
Missing input files for rule trimming:
/home/imp/databases/adapters/adapters.done